Sun 23 Dec 22:22:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkd-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.4-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.4-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 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 ============================================================ Sun 23 Dec 22:23:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.4-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1692 and 0 Target number of residues in the AU: 1692 Target solvent content: 0.5928 Checking the provided sequence file Detected sequence length: 338 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 2028 Adjusted target solvent content: 0.51 Input MTZ file: 1vkd-3.4-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 16224 target number of atoms Had to go as low as 0.65 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 3 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 with 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 127.440 3.400 Wilson plot Bfac: 49.74 31768 reflections ( 99.74 % complete ) and 0 restraints for refining 18060 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.2838 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2372 (Rfree = 0.000) for 18060 atoms. Found 136 (136 requested) and removed 124 (68 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.00 Search for helices and strands: 0 residues in 0 chains, 18227 seeds are put forward NCS extension: 0 residues added, 18227 seeds are put forward Round 1: 1124 peptides, 187 chains. Longest chain 18 peptides. Score 0.452 Round 2: 1356 peptides, 176 chains. Longest chain 28 peptides. Score 0.616 Round 3: 1379 peptides, 161 chains. Longest chain 26 peptides. Score 0.660 Round 4: 1449 peptides, 154 chains. Longest chain 40 peptides. Score 0.704 Round 5: 1496 peptides, 143 chains. Longest chain 38 peptides. Score 0.742 Taking the results from Round 5 Chains 154, Residues 1353, Estimated correctness of the model 68.0 % 25 chains (430 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 243 A and 251 A Built loop between residues 272 A and 276 A Built loop between residues 292 A and 299 A Built loop between residues 258 B and 267 B Built loop between residues 303 F and 307 F 146 chains (1368 residues) following loop building 20 chains (457 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 31768 reflections ( 99.74 % complete ) and 25962 restraints for refining 14746 atoms. 18845 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2507 (Rfree = 0.000) for 14746 atoms. Found 111 (111 requested) and removed 152 (55 requested) atoms. Cycle 2: After refmac, R = 0.2345 (Rfree = 0.000) for 14485 atoms. Found 62 (109 requested) and removed 85 (55 requested) atoms. Cycle 3: After refmac, R = 0.2274 (Rfree = 0.000) for 14356 atoms. Found 43 (105 requested) and removed 75 (54 requested) atoms. Cycle 4: After refmac, R = 0.2209 (Rfree = 0.000) for 14293 atoms. Found 33 (102 requested) and removed 61 (54 requested) atoms. Cycle 5: After refmac, R = 0.2177 (Rfree = 0.000) for 14232 atoms. Found 33 (98 requested) and removed 63 (53 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.99 Search for helices and strands: 0 residues in 0 chains, 14506 seeds are put forward NCS extension: 54 residues added (44 deleted due to clashes), 14560 seeds are put forward Round 1: 1416 peptides, 173 chains. Longest chain 32 peptides. Score 0.651 Round 2: 1505 peptides, 148 chains. Longest chain 49 peptides. Score 0.736 Round 3: 1515 peptides, 136 chains. Longest chain 46 peptides. Score 0.760 Round 4: 1511 peptides, 134 chains. Longest chain 48 peptides. Score 0.762 Round 5: 1516 peptides, 147 chains. Longest chain 36 peptides. Score 0.742 Taking the results from Round 4 Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Chains 152, Residues 1377, Estimated correctness of the model 72.4 % 22 chains (390 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 265 A and 270 A Built loop between residues 246 B and 254 B Built loop between residues 273 B and 276 B 147 chains (1386 residues) following loop building 19 chains (403 residues) in sequence following loop building ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 27210 restraints for refining 14751 atoms. 20103 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2467 (Rfree = 0.000) for 14751 atoms. Found 98 (100 requested) and removed 135 (55 requested) atoms. Cycle 7: After refmac, R = 0.2281 (Rfree = 0.000) for 14631 atoms. Found 45 (98 requested) and removed 78 (55 requested) atoms. Cycle 8: After refmac, R = 0.2171 (Rfree = 0.000) for 14566 atoms. Found 34 (95 requested) and removed 65 (55 requested) atoms. Cycle 9: After refmac, R = 0.2084 (Rfree = 0.000) for 14507 atoms. Found 24 (92 requested) and removed 56 (54 requested) atoms. Cycle 10: After refmac, R = 0.2031 (Rfree = 0.000) for 14464 atoms. Found 21 (89 requested) and removed 57 (54 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 3.02 Search for helices and strands: 0 residues in 0 chains, 14671 seeds are put forward NCS extension: 70 residues added (6 deleted due to clashes), 14741 seeds are put forward Round 1: 1362 peptides, 164 chains. Longest chain 32 peptides. Score 0.645 Round 2: 1430 peptides, 138 chains. Longest chain 35 peptides. Score 0.726 Round 3: 1475 peptides, 141 chains. Longest chain 51 peptides. Score 0.737 Round 4: 1469 peptides, 135 chains. Longest chain 51 peptides. Score 0.746 Round 5: 1416 peptides, 142 chains. Longest chain 42 peptides. Score 0.713 Taking the results from Round 4 Chains 152, Residues 1334, Estimated correctness of the model 68.9 % 20 chains (357 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 282 B and 291 B 150 chains (1340 residues) following loop building 19 chains (365 residues) in sequence following loop building ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 27879 restraints for refining 14750 atoms. 21144 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2368 (Rfree = 0.000) for 14750 atoms. Found 89 (89 requested) and removed 129 (55 requested) atoms. Cycle 12: After refmac, R = 0.2193 (Rfree = 0.000) for 14642 atoms. Found 49 (87 requested) and removed 71 (55 requested) atoms. Cycle 13: After refmac, R = 0.2112 (Rfree = 0.000) for 14580 atoms. Found 28 (84 requested) and removed 61 (55 requested) atoms. Cycle 14: After refmac, R = 0.2060 (Rfree = 0.000) for 14533 atoms. Found 25 (81 requested) and removed 55 (54 requested) atoms. Cycle 15: After refmac, R = 0.2022 (Rfree = 0.000) for 14495 atoms. Found 23 (78 requested) and removed 55 (54 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 14667 seeds are put forward NCS extension: 22 residues added (7 deleted due to clashes), 14689 seeds are put forward Round 1: 1320 peptides, 165 chains. Longest chain 30 peptides. Score 0.622 Round 2: 1418 peptides, 149 chains. Longest chain 31 peptides. Score 0.701 Round 3: 1414 peptides, 150 chains. Longest chain 35 peptides. Score 0.697 Round 4: 1426 peptides, 151 chains. Longest chain 30 peptides. Score 0.700 Round 5: 1425 peptides, 152 chains. Longest chain 36 peptides. Score 0.698 Taking the results from Round 2 Chains 159, Residues 1269, Estimated correctness of the model 58.1 % 21 chains (315 residues) have been docked in sequence Building loops using Loopy2018 159 chains (1269 residues) following loop building 21 chains (315 residues) in sequence following loop building ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 28766 restraints for refining 14749 atoms. 22512 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2266 (Rfree = 0.000) for 14749 atoms. Found 78 (78 requested) and removed 115 (55 requested) atoms. Cycle 17: After refmac, R = 0.2109 (Rfree = 0.000) for 14672 atoms. Found 30 (75 requested) and removed 62 (55 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2026 (Rfree = 0.000) for 14619 atoms. Found 34 (73 requested) and removed 56 (55 requested) atoms. Cycle 19: After refmac, R = 0.1994 (Rfree = 0.000) for 14586 atoms. Found 28 (70 requested) and removed 55 (55 requested) atoms. Cycle 20: After refmac, R = 0.1970 (Rfree = 0.000) for 14538 atoms. Found 35 (68 requested) and removed 54 (54 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 14752 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 14777 seeds are put forward Round 1: 1216 peptides, 160 chains. Longest chain 20 peptides. Score 0.580 Round 2: 1339 peptides, 150 chains. Longest chain 34 peptides. Score 0.664 Round 3: 1342 peptides, 142 chains. Longest chain 30 peptides. Score 0.682 Round 4: 1359 peptides, 147 chains. Longest chain 28 peptides. Score 0.679 Round 5: 1357 peptides, 143 chains. Longest chain 34 peptides. Score 0.687 Taking the results from Round 5 Chains 155, Residues 1214, Estimated correctness of the model 54.5 % 14 chains (144 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 30826 restraints for refining 14751 atoms. 25549 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2250 (Rfree = 0.000) for 14751 atoms. Found 67 (67 requested) and removed 75 (55 requested) atoms. Cycle 22: After refmac, R = 0.2082 (Rfree = 0.000) for 14707 atoms. Found 30 (67 requested) and removed 59 (55 requested) atoms. Cycle 23: After refmac, R = 0.2015 (Rfree = 0.000) for 14657 atoms. Found 29 (66 requested) and removed 56 (55 requested) atoms. Cycle 24: After refmac, R = 0.2009 (Rfree = 0.000) for 14615 atoms. Found 23 (66 requested) and removed 56 (55 requested) atoms. Cycle 25: After refmac, R = 0.1970 (Rfree = 0.000) for 14572 atoms. Found 19 (66 requested) and removed 56 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 3.02 Search for helices and strands: 0 residues in 0 chains, 14747 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 14772 seeds are put forward Round 1: 1212 peptides, 178 chains. Longest chain 19 peptides. Score 0.532 Round 2: 1318 peptides, 157 chains. Longest chain 25 peptides. Score 0.639 Round 3: 1379 peptides, 165 chains. Longest chain 21 peptides. Score 0.651 Round 4: 1354 peptides, 164 chains. Longest chain 24 peptides. Score 0.641 Round 5: 1346 peptides, 152 chains. Longest chain 28 peptides. Score 0.663 Taking the results from Round 5 Chains 156, Residues 1194, Estimated correctness of the model 47.9 % 14 chains (170 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 30337 restraints for refining 14750 atoms. 25011 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2227 (Rfree = 0.000) for 14750 atoms. Found 67 (67 requested) and removed 92 (55 requested) atoms. Cycle 27: After refmac, R = 0.2047 (Rfree = 0.000) for 14663 atoms. Found 33 (67 requested) and removed 61 (55 requested) atoms. Cycle 28: After refmac, R = 0.2006 (Rfree = 0.000) for 14606 atoms. Found 32 (66 requested) and removed 59 (55 requested) atoms. Cycle 29: After refmac, R = 0.1988 (Rfree = 0.000) for 14565 atoms. Found 31 (66 requested) and removed 57 (55 requested) atoms. Cycle 30: After refmac, R = 0.1946 (Rfree = 0.000) for 14524 atoms. Found 30 (65 requested) and removed 60 (54 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 3.02 Search for helices and strands: 0 residues in 0 chains, 14688 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 14703 seeds are put forward Round 1: 1167 peptides, 168 chains. Longest chain 22 peptides. Score 0.531 Round 2: 1267 peptides, 155 chains. Longest chain 24 peptides. Score 0.619 Round 3: 1268 peptides, 152 chains. Longest chain 22 peptides. Score 0.626 Round 4: 1272 peptides, 155 chains. Longest chain 24 peptides. Score 0.621 Round 5: 1291 peptides, 158 chains. Longest chain 22 peptides. Score 0.624 Taking the results from Round 3 Chains 158, Residues 1116, Estimated correctness of the model 36.9 % 14 chains (149 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 31198 restraints for refining 14751 atoms. 26328 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2122 (Rfree = 0.000) for 14751 atoms. Found 67 (67 requested) and removed 75 (55 requested) atoms. Cycle 32: After refmac, R = 0.2006 (Rfree = 0.000) for 14705 atoms. Found 26 (67 requested) and removed 57 (55 requested) atoms. Cycle 33: After refmac, R = 0.1969 (Rfree = 0.000) for 14659 atoms. Found 19 (66 requested) and removed 55 (55 requested) atoms. Cycle 34: After refmac, R = 0.1955 (Rfree = 0.000) for 14608 atoms. Found 21 (66 requested) and removed 55 (55 requested) atoms. Cycle 35: After refmac, R = 0.1923 (Rfree = 0.000) for 14563 atoms. Found 17 (66 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 14686 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 14702 seeds are put forward Round 1: 1089 peptides, 165 chains. Longest chain 17 peptides. Score 0.491 Round 2: 1201 peptides, 157 chains. Longest chain 33 peptides. Score 0.579 Round 3: 1213 peptides, 149 chains. Longest chain 38 peptides. Score 0.605 Round 4: 1234 peptides, 149 chains. Longest chain 25 peptides. Score 0.616 Round 5: 1216 peptides, 149 chains. Longest chain 28 peptides. Score 0.606 Taking the results from Round 4 Chains 157, Residues 1085, Estimated correctness of the model 33.8 % 13 chains (127 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 31768 reflections ( 99.74 % complete ) and 31273 restraints for refining 14751 atoms. 26551 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2134 (Rfree = 0.000) for 14751 atoms. Found 67 (67 requested) and removed 73 (55 requested) atoms. Cycle 37: After refmac, R = 0.1998 (Rfree = 0.000) for 14716 atoms. Found 27 (67 requested) and removed 60 (55 requested) atoms. Cycle 38: After refmac, R = 0.1958 (Rfree = 0.000) for 14669 atoms. Found 27 (66 requested) and removed 59 (55 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1899 (Rfree = 0.000) for 14623 atoms. Found 24 (66 requested) and removed 57 (55 requested) atoms. Cycle 40: After refmac, R = 0.1864 (Rfree = 0.000) for 14582 atoms. Found 24 (66 requested) and removed 57 (55 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 14738 seeds are put forward NCS extension: 16 residues added (12 deleted due to clashes), 14754 seeds are put forward Round 1: 1064 peptides, 161 chains. Longest chain 18 peptides. Score 0.487 Round 2: 1178 peptides, 152 chains. Longest chain 21 peptides. Score 0.578 Round 3: 1235 peptides, 155 chains. Longest chain 25 peptides. Score 0.602 Round 4: 1217 peptides, 153 chains. Longest chain 28 peptides. Score 0.597 Round 5: 1186 peptides, 151 chains. Longest chain 24 peptides. Score 0.585 Taking the results from Round 3 Chains 166, Residues 1080, Estimated correctness of the model 29.3 % 13 chains (153 residues) have been docked in sequence ------------------------------------------------------ 31768 reflections ( 99.74 % complete ) and 31079 restraints for refining 14750 atoms. 26296 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2069 (Rfree = 0.000) for 14750 atoms. Found 60 (67 requested) and removed 79 (55 requested) atoms. Cycle 42: After refmac, R = 0.1965 (Rfree = 0.000) for 14707 atoms. Found 28 (67 requested) and removed 58 (55 requested) atoms. Cycle 43: After refmac, R = 0.1931 (Rfree = 0.000) for 14662 atoms. Found 32 (66 requested) and removed 56 (55 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1871 (Rfree = 0.000) for 14626 atoms. Found 23 (66 requested) and removed 56 (55 requested) atoms. Cycle 45: After refmac, R = 0.1836 (Rfree = 0.000) for 14583 atoms. Found 24 (66 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.05 Search for helices and strands: 0 residues in 0 chains, 14702 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 14726 seeds are put forward Round 1: 1032 peptides, 168 chains. Longest chain 17 peptides. Score 0.446 Round 2: 1160 peptides, 151 chains. Longest chain 22 peptides. Score 0.571 Round 3: 1161 peptides, 151 chains. Longest chain 26 peptides. Score 0.572 Round 4: 1177 peptides, 149 chains. Longest chain 23 peptides. Score 0.585 Round 5: 1124 peptides, 144 chains. Longest chain 19 peptides. Score 0.568 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 152, Residues 1028, Estimated correctness of the model 23.7 % 6 chains (60 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 152 chains (1028 residues) following loop building 6 chains (60 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 31768 reflections ( 99.74 % complete ) and 32438 restraints for refining 14751 atoms. 28243 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2074 (Rfree = 0.000) for 14751 atoms. Found 0 (67 requested) and removed 55 (55 requested) atoms. Cycle 47: After refmac, R = 0.2013 (Rfree = 0.000) for 14667 atoms. Found 0 (66 requested) and removed 55 (55 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1990 (Rfree = 0.000) for 14600 atoms. Found 0 (66 requested) and removed 55 (55 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1935 (Rfree = 0.000) for 14533 atoms. Found 0 (65 requested) and removed 50 (54 requested) atoms. Writing output files ... TimeTaking 170.7