Thu Nov 5 10:21:33 GMT 2015 ############### You are running ARP/wARP 7.5, patch 2 ############### Working directory /home/adam/test_set/data_with_expdata/3O2E/AMPLE/AMPLE_6/MRBUMP/search_c1_t14_r2_allatom_mrbump/data/loc0_ALL_c1_t14_r2_allatom/unmod/mr/phaser/build/arpwarp Job ID is set to . X-ray data file /home/adam/test_set/data_with_expdata/3O2E/AMPLE/AMPLE_6/MRBUMP/search_c1_t14_r2_allatom_mrbump/data/loc0_ALL_c1_t14_r2_allatom/unmod/mr/phaser/refine/refmac_phaser_HKLOUT_loc0_ALL_c1_t14_r2_allatom_UNMOD.mtz Sequence file /home/adam/test_set/data_with_expdata/3O2E/AMPLE/AMPLE_6/MRBUMP/search_c1_t14_r2_allatom_mrbump/input/3o2e.pir Tracing mode WARPNTRACEPHASES Accepted label: fp=F Accepted label: sigfp=SIGF Accepted label: phibest=PHIC Accepted label: fom=FOM Accepted label: freelabin=FreeR_flag mtz labels taken: F SIGF PHIC FOM FreeR_flag Parameter file /home/adam/test_set/data_with_expdata/3O2E/AMPLE/AMPLE_6/MRBUMP/search_c1_t14_r2_allatom_mrbump/data/loc0_ALL_c1_t14_r2_allatom/unmod/mr/phaser/build/arpwarp/arp_warp_tracing.par Job launched in /home/adam/test_set/data_with_expdata/3O2E/AMPLE/AMPLE_6/MRBUMP/search_c1_t14_r2_allatom_mrbump/data/loc0_ALL_c1_t14_r2_allatom/unmod/mr/phaser/build/arpwarp ############### You are running ARP/wARP 7.5, patch 2 ############### ================================================================================== | Please cite at least one of the publications below for | | the ARP/wARP application you are using: | | | | Langer G, Cohen SX, Lamzin VS, Perrakis A. (2008) Automated macromolecular | | model building for x-ray crystallography using ARP/wARP version 7. | | Nat. Protoc. 3, 1171-1179 | | | | Perrakis A, Morris RM, Lamzin VS. (1999) Automated protein model building | | combined with iterative structure refinement. Nature Struct. Biol. 6, 458-463 | | | | Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual | | automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. | | 69, 635-641 | | | | Use of Refmac is an essential part of model building with ARP/wARP. | | Please acknowledge the use of Refmac by citing the following publication: | | | | Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, | | Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular | | crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 | ================================================================================== Thu Nov 5 10:21:43 GMT 2015 You are running ARP/wARP version 7.5 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /home/adam/test_set/data_with_expdata/3O2E/AMPLE/AMPLE_6/MRBUMP/search_c1_t14_r2_allatom_mrbump/data/loc0_ALL_c1_t14_r2_allatom/unmod/mr/phaser/build/arpwarp ARP/wARP software version: 7.5 The parameter file: /home/adam/test_set/data_with_expdata/3O2E/AMPLE/AMPLE_6/MRBUMP/search_c1_t14_r2_allatom_mrbump/data/loc0_ALL_c1_t14_r2_allatom/unmod/mr/phaser/build/arpwarp/arp_warp_tracing.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Target number of residues in the AU: 105 Target solvent content: 0.2673 Checking the provided sequence file Detected sequence length: 105 Number of NCS-related molecules: 1 Adjusted target number of residues: 105 Adjusted target solvent content: 0.27 Input MTZ file: refmac_phaser_HKLOUT_loc0_ALL_c1_t14_r2_allatom_UNMOD.mtz.cad Column labels for model refinement: F SIGF FreeR_flag Rfree value for free reflections: 0 Column labels to obtain initial map: F PHIC FOM FreeR_flag Space group number: 92 Cell parameters: 66.300 66.300 35.290 90.000 90.000 90.000 Input sequence file: 3o2e.pir_lf Building free atoms model in initial map for 840 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling, No bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 46.881 2.200 Wilson plot Bfac: 16.52 3107 reflections ( 76.26 % complete ) and 0 restraints for refining 945 atoms. Observations/parameters ratio is 0.82 ------------------------------------------------------ Starting model: R = 0.3726 (Rfree = 0.597). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3072 (Rfree = 0.584) for 945 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.03 2.84 Round 1: 24 peptides, 5 chains. Longest chain 8 peptides. Score 0.268 Round 2: 23 peptides, 4 chains. Longest chain 10 peptides. Score 0.345 Round 3: 31 peptides, 6 chains. Longest chain 9 peptides. Score 0.332 Round 4: 28 peptides, 5 chains. Longest chain 9 peptides. Score 0.360 Round 5: 35 peptides, 7 chains. Longest chain 10 peptides. Score 0.328 Taking the results from Round 4 Chains 5, Residues 23, Estimated correctness of the model 57.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 87 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2886 (Rfree = 0.566) for 819 atoms. Found 12 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 2: After refmac, R = 0.2544 (Rfree = 0.556) for 821 atoms. Found 11 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 3: After refmac, R = 0.2369 (Rfree = 0.572) for 822 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 4: After refmac, R = 0.2250 (Rfree = 0.563) for 817 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 5: After refmac, R = 0.2190 (Rfree = 0.558) for 809 atoms. Found 4 (21 requested) and removed 5 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.00 2.80 Round 1: 40 peptides, 9 chains. Longest chain 8 peptides. Score 0.257 Round 2: 46 peptides, 9 chains. Longest chain 13 peptides. Score 0.383 Round 3: 37 peptides, 7 chains. Longest chain 11 peptides. Score 0.370 Round 4: 38 peptides, 6 chains. Longest chain 13 peptides. Score 0.475 Round 5: 39 peptides, 6 chains. Longest chain 13 peptides. Score 0.494 Taking the results from Round 5 Chains 6, Residues 33, Estimated correctness of the model 72.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 126 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2446 (Rfree = 0.547) for 819 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 7: After refmac, R = 0.2255 (Rfree = 0.559) for 830 atoms. Found 10 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 8: After refmac, R = 0.2158 (Rfree = 0.551) for 830 atoms. Found 5 (21 requested) and removed 7 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 9: After refmac, R = 0.2114 (Rfree = 0.535) for 828 atoms. Found 8 (21 requested) and removed 7 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 10: After refmac, R = 0.2081 (Rfree = 0.537) for 829 atoms. Found 2 (21 requested) and removed 4 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.02 2.83 Round 1: 22 peptides, 3 chains. Longest chain 12 peptides. Score 0.423 Round 2: 23 peptides, 3 chains. Longest chain 13 peptides. Score 0.444 Round 3: 20 peptides, 2 chains. Longest chain 15 peptides. Score 0.481 Round 4: 25 peptides, 3 chains. Longest chain 15 peptides. Score 0.484 Round 5: 16 peptides, 2 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 4 Chains 3, Residues 22, Estimated correctness of the model 71.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 85 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2194 (Rfree = 0.563) for 819 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 12: After refmac, R = 0.2122 (Rfree = 0.564) for 830 atoms. Found 7 (21 requested) and removed 2 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 13: After refmac, R = 0.2083 (Rfree = 0.554) for 835 atoms. Found 2 (21 requested) and removed 4 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 14: After refmac, R = 0.2062 (Rfree = 0.559) for 833 atoms. Found 1 (21 requested) and removed 0 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 15: After refmac, R = 0.2056 (Rfree = 0.564) for 834 atoms. Found 0 (21 requested) and removed 1 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.03 2.84 Round 1: 26 peptides, 4 chains. Longest chain 12 peptides. Score 0.411 Round 2: 26 peptides, 4 chains. Longest chain 13 peptides. Score 0.411 Round 3: 27 peptides, 4 chains. Longest chain 14 peptides. Score 0.432 Round 4: 23 peptides, 3 chains. Longest chain 14 peptides. Score 0.444 Round 5: 23 peptides, 3 chains. Longest chain 14 peptides. Score 0.444 Taking the results from Round 5 Chains 3, Residues 20, Estimated correctness of the model 67.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 77 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2227 (Rfree = 0.552) for 819 atoms. Found 17 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 17: After refmac, R = 0.2147 (Rfree = 0.582) for 826 atoms. Found 9 (21 requested) and removed 9 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 18: After refmac, R = 0.2098 (Rfree = 0.581) for 826 atoms. Found 2 (21 requested) and removed 3 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 19: After refmac, R = 0.2109 (Rfree = 0.575) for 825 atoms. Found 2 (21 requested) and removed 1 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 20: After refmac, R = 0.2129 (Rfree = 0.581) for 826 atoms. Found 0 (21 requested) and removed 1 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.01 2.81 Round 1: 38 peptides, 7 chains. Longest chain 14 peptides. Score 0.391 Round 2: 38 peptides, 7 chains. Longest chain 10 peptides. Score 0.391 Round 3: 36 peptides, 6 chains. Longest chain 12 peptides. Score 0.437 Round 4: 31 peptides, 6 chains. Longest chain 10 peptides. Score 0.332 Round 5: 32 peptides, 6 chains. Longest chain 12 peptides. Score 0.354 Taking the results from Round 3 Chains 6, Residues 30, Estimated correctness of the model 66.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 114 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2271 (Rfree = 0.573) for 819 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 22: After refmac, R = 0.2130 (Rfree = 0.561) for 830 atoms. Found 10 (21 requested) and removed 7 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 23: After refmac, R = 0.2106 (Rfree = 0.565) for 833 atoms. Found 6 (21 requested) and removed 2 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 24: After refmac, R = 0.2093 (Rfree = 0.577) for 837 atoms. Found 0 (21 requested) and removed 3 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 25: After refmac, R = 0.2091 (Rfree = 0.571) for 834 atoms. Found 1 (21 requested) and removed 1 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.96 2.74 Round 1: 36 peptides, 7 chains. Longest chain 12 peptides. Score 0.349 Round 2: 43 peptides, 8 chains. Longest chain 12 peptides. Score 0.407 Round 3: 45 peptides, 8 chains. Longest chain 14 peptides. Score 0.446 Round 4: 38 peptides, 7 chains. Longest chain 11 peptides. Score 0.391 Round 5: 39 peptides, 7 chains. Longest chain 11 peptides. Score 0.411 Taking the results from Round 3 Chains 8, Residues 37, Estimated correctness of the model 67.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 140 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2307 (Rfree = 0.563) for 819 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 27: After refmac, R = 0.2210 (Rfree = 0.562) for 830 atoms. Found 7 (21 requested) and removed 8 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 28: After refmac, R = 0.2207 (Rfree = 0.574) for 829 atoms. Found 1 (21 requested) and removed 2 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 29: After refmac, R = 0.2208 (Rfree = 0.579) for 828 atoms. Found 3 (21 requested) and removed 3 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 30: After refmac, R = 0.2213 (Rfree = 0.578) for 828 atoms. Found 2 (21 requested) and removed 4 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.95 2.73 Round 1: 39 peptides, 7 chains. Longest chain 12 peptides. Score 0.411 Round 2: 38 peptides, 7 chains. Longest chain 12 peptides. Score 0.391 Round 3: 36 peptides, 7 chains. Longest chain 12 peptides. Score 0.349 Round 4: 39 peptides, 7 chains. Longest chain 12 peptides. Score 0.411 Round 5: 30 peptides, 5 chains. Longest chain 12 peptides. Score 0.403 Taking the results from Round 4 Chains 7, Residues 32, Estimated correctness of the model 63.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 121 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2353 (Rfree = 0.579) for 819 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 32: After refmac, R = 0.2273 (Rfree = 0.583) for 830 atoms. Found 12 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 33: After refmac, R = 0.2249 (Rfree = 0.582) for 832 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 34: After refmac, R = 0.2260 (Rfree = 0.595) for 826 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 35: After refmac, R = 0.2269 (Rfree = 0.607) for 824 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.93 2.70 Round 1: 36 peptides, 8 chains. Longest chain 7 peptides. Score 0.259 Round 2: 37 peptides, 8 chains. Longest chain 7 peptides. Score 0.281 Round 3: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.284 Round 4: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.306 Round 5: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.306 Taking the results from Round 5 Chains 7, Residues 27, Estimated correctness of the model 50.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 101 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2400 (Rfree = 0.589) for 819 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 37: After refmac, R = 0.2312 (Rfree = 0.613) for 830 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 38: After refmac, R = 0.2325 (Rfree = 0.621) for 826 atoms. Found 7 (21 requested) and removed 3 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 39: After refmac, R = 0.2317 (Rfree = 0.620) for 830 atoms. Found 1 (21 requested) and removed 2 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 40: After refmac, R = 0.2336 (Rfree = 0.627) for 829 atoms. Found 2 (21 requested) and removed 1 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.91 2.67 Round 1: 11 peptides, 2 chains. Longest chain 7 peptides. Score 0.268 Round 2: 12 peptides, 3 chains. Longest chain 4 peptides. Score 0.167 Round 3: 11 peptides, 2 chains. Longest chain 7 peptides. Score 0.268 Round 4: 14 peptides, 2 chains. Longest chain 10 peptides. Score 0.348 Round 5: 13 peptides, 3 chains. Longest chain 5 peptides. Score 0.198 Taking the results from Round 4 Chains 2, Residues 12, Estimated correctness of the model 56.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 46 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2348 (Rfree = 0.622) for 819 atoms. Found 11 (21 requested) and removed 6 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 42: After refmac, R = 0.2349 (Rfree = 0.609) for 824 atoms. Found 5 (21 requested) and removed 0 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 43: After refmac, R = 0.2319 (Rfree = 0.630) for 829 atoms. Found 3 (21 requested) and removed 0 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 44: After refmac, R = 0.2377 (Rfree = 0.657) for 832 atoms. Found 5 (21 requested) and removed 3 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 45: After refmac, R = 0.2389 (Rfree = 0.658) for 834 atoms. Found 6 (21 requested) and removed 3 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.89 2.64 Round 1: 18 peptides, 3 chains. Longest chain 10 peptides. Score 0.332 Round 2: 19 peptides, 4 chains. Longest chain 6 peptides. Score 0.248 Round 3: 20 peptides, 3 chains. Longest chain 10 peptides. Score 0.379 Round 4: 17 peptides, 3 chains. Longest chain 7 peptides. Score 0.308 Round 5: 20 peptides, 3 chains. Longest chain 10 peptides. Score 0.379 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 17, Estimated correctness of the model 59.8 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using refmac_phaser_HKLOUT_loc0_ALL_c1_t14_r2_allatom_UNMOD_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. *** WARNING *** Conditional restraints for refinement could not be generated 3107 reflections ( 76.26 % complete ) and 65 restraints for refining 819 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2461 (Rfree = 0.638) for 819 atoms. Found 0 (21 requested) and removed 0 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 47: After refmac, R = 0.2437 (Rfree = 0.646) for 819 atoms. Found 0 (21 requested) and removed 0 (10 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated grep: arp_49.pdb: No such file or directory Cycle 48: After refmac, R = (Rfree = 0.000) for 0 atoms.