Tue 25 Dec 19:27:55 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 1z82-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z82-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z82-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-2.0-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/1z82-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-2.0-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 ============================================================ Tue 25 Dec 19:28:05 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/1z82-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-2.0-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 575 and 0 Target number of residues in the AU: 575 Target solvent content: 0.4891 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-2.0-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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.40 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 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: 29.850 2.000 Wilson plot Bfac: 21.30 40537 reflections ( 99.47 % complete ) and 0 restraints for refining 5947 atoms. Observations/parameters ratio is 1.70 ------------------------------------------------------ Starting model: R = 0.3042 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2530 (Rfree = 0.000) for 5947 atoms. Found 113 (203 requested) and removed 104 (101 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.08 2.38 NCS extension: 0 residues added, 5956 seeds are put forward Round 1: 451 peptides, 60 chains. Longest chain 35 peptides. Score 0.666 Round 2: 527 peptides, 38 chains. Longest chain 37 peptides. Score 0.864 Round 3: 564 peptides, 25 chains. Longest chain 97 peptides. Score 0.922 Round 4: 576 peptides, 22 chains. Longest chain 103 peptides. Score 0.933 Round 5: 583 peptides, 24 chains. Longest chain 72 peptides. Score 0.931 Taking the results from Round 4 Chains 27, Residues 554, Estimated correctness of the model 99.5 % 15 chains (500 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 50 A and 56 A Built loop between residues 118 A and 125 A Built loop between residues 93 B and 96 B Built loop between residues 114 B and 116 B Built loop between residues 182 B and 185 B Built loop between residues 239 B and 242 B Built loop between residues 290 B and 297 B 17 chains (574 residues) following loop building 8 chains (524 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 6153 restraints for refining 5341 atoms. 1827 conditional restraints added. Observations/parameters ratio is 1.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2868 (Rfree = 0.000) for 5341 atoms. Found 132 (183 requested) and removed 98 (91 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2568 (Rfree = 0.000) for 5349 atoms. Found 113 (180 requested) and removed 92 (92 requested) atoms. Cycle 3: After refmac, R = 0.2427 (Rfree = 0.000) for 5330 atoms. Found 109 (176 requested) and removed 55 (91 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2327 (Rfree = 0.000) for 5352 atoms. Found 76 (173 requested) and removed 33 (92 requested) atoms. Cycle 5: After refmac, R = 0.2255 (Rfree = 0.000) for 5381 atoms. Found 70 (173 requested) and removed 34 (92 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.04 2.33 NCS extension: 12 residues added (261 deleted due to clashes), 5435 seeds are put forward Round 1: 594 peptides, 16 chains. Longest chain 98 peptides. Score 0.951 Round 2: 604 peptides, 10 chains. Longest chain 152 peptides. Score 0.965 Round 3: 597 peptides, 14 chains. Longest chain 158 peptides. Score 0.956 Round 4: 600 peptides, 14 chains. Longest chain 123 peptides. Score 0.957 Round 5: 610 peptides, 8 chains. Longest chain 238 peptides. Score 0.969 Taking the results from Round 5 Chains 9, Residues 602, Estimated correctness of the model 99.9 % 7 chains (596 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 83 A Built loop between residues 168 A and 178 A Built loop between residues 235 A and 238 A Built loop between residues 253 B and 256 B Built loop between residues 286 B and 289 B 3 chains (617 residues) following loop building 2 chains (616 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 40537 reflections ( 99.47 % complete ) and 5555 restraints for refining 5497 atoms. 666 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2371 (Rfree = 0.000) for 5497 atoms. Found 118 (177 requested) and removed 97 (94 requested) atoms. Cycle 7: After refmac, R = 0.2246 (Rfree = 0.000) for 5506 atoms. Found 97 (174 requested) and removed 94 (94 requested) atoms. Cycle 8: After refmac, R = 0.2181 (Rfree = 0.000) for 5494 atoms. Found 91 (169 requested) and removed 53 (94 requested) atoms. Cycle 9: After refmac, R = 0.2150 (Rfree = 0.000) for 5517 atoms. Found 87 (166 requested) and removed 51 (94 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2102 (Rfree = 0.000) for 5540 atoms. Found 86 (163 requested) and removed 49 (95 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.05 2.35 NCS extension: 34 residues added (275 deleted due to clashes), 5613 seeds are put forward Round 1: 616 peptides, 4 chains. Longest chain 262 peptides. Score 0.977 Round 2: 609 peptides, 11 chains. Longest chain 238 peptides. Score 0.964 Round 3: 605 peptides, 9 chains. Longest chain 190 peptides. Score 0.967 Round 4: 605 peptides, 12 chains. Longest chain 226 peptides. Score 0.961 Round 5: 605 peptides, 12 chains. Longest chain 135 peptides. Score 0.961 Taking the results from Round 1 Chains 4, Residues 612, Estimated correctness of the model 99.9 % 4 chains (612 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 83 A Built loop between residues 62 B and 65 B 2 chains (617 residues) following loop building 2 chains (617 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5533 restraints for refining 5532 atoms. 636 conditional restraints added. Observations/parameters ratio is 1.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2220 (Rfree = 0.000) for 5532 atoms. Found 141 (159 requested) and removed 94 (94 requested) atoms. Cycle 12: After refmac, R = 0.2113 (Rfree = 0.000) for 5570 atoms. Found 93 (157 requested) and removed 94 (95 requested) atoms. Cycle 13: After refmac, R = 0.2075 (Rfree = 0.000) for 5562 atoms. Found 92 (152 requested) and removed 37 (95 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2040 (Rfree = 0.000) for 5608 atoms. Found 84 (154 requested) and removed 45 (96 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2011 (Rfree = 0.000) for 5641 atoms. Found 84 (151 requested) and removed 40 (96 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.05 2.35 NCS extension: 4 residues added (305 deleted due to clashes), 5692 seeds are put forward Round 1: 613 peptides, 7 chains. Longest chain 156 peptides. Score 0.971 Round 2: 611 peptides, 8 chains. Longest chain 243 peptides. Score 0.969 Round 3: 605 peptides, 11 chains. Longest chain 119 peptides. Score 0.963 Round 4: 604 peptides, 13 chains. Longest chain 153 peptides. Score 0.959 Round 5: 606 peptides, 13 chains. Longest chain 114 peptides. Score 0.960 Taking the results from Round 1 Chains 7, Residues 606, Estimated correctness of the model 99.9 % 7 chains (606 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 66 A Built loop between residues 79 A and 83 A Built loop between residues 167 A and 170 A Built loop between residues 61 B and 64 B Built loop between residues 205 B and 208 B 2 chains (618 residues) following loop building 2 chains (618 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5541 restraints for refining 5588 atoms. 633 conditional restraints added. Observations/parameters ratio is 1.81 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2160 (Rfree = 0.000) for 5588 atoms. Found 146 (149 requested) and removed 97 (95 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2064 (Rfree = 0.000) for 5625 atoms. Found 100 (147 requested) and removed 79 (96 requested) atoms. Cycle 18: After refmac, R = 0.2010 (Rfree = 0.000) for 5637 atoms. Found 78 (143 requested) and removed 50 (96 requested) atoms. Cycle 19: After refmac, R = 0.1986 (Rfree = 0.000) for 5660 atoms. Found 78 (140 requested) and removed 39 (97 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1958 (Rfree = 0.000) for 5689 atoms. Found 83 (140 requested) and removed 48 (97 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.05 2.35 NCS extension: 4 residues added (306 deleted due to clashes), 5732 seeds are put forward Round 1: 608 peptides, 11 chains. Longest chain 123 peptides. Score 0.964 Round 2: 609 peptides, 13 chains. Longest chain 142 peptides. Score 0.960 Round 3: 608 peptides, 10 chains. Longest chain 234 peptides. Score 0.965 Round 4: 605 peptides, 10 chains. Longest chain 155 peptides. Score 0.965 Round 5: 608 peptides, 11 chains. Longest chain 150 peptides. Score 0.964 Taking the results from Round 4 Chains 11, Residues 595, Estimated correctness of the model 99.8 % 10 chains (592 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 86 A Built loop between residues 98 A and 101 A Built loop between residues 253 A and 256 A Built loop between residues 292 A and 296 A Built loop between residues 59 B and 65 B Built loop between residues 79 B and 84 B Built loop between residues 237 B and 243 B Built loop between residues 300 B and 303 B 2 chains (617 residues) following loop building 2 chains (617 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 40537 reflections ( 99.47 % complete ) and 5583 restraints for refining 5604 atoms. 686 conditional restraints added. Observations/parameters ratio is 1.81 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2149 (Rfree = 0.000) for 5604 atoms. Found 134 (134 requested) and removed 97 (95 requested) atoms. Cycle 22: After refmac, R = 0.2071 (Rfree = 0.000) for 5630 atoms. Found 87 (131 requested) and removed 67 (96 requested) atoms. Cycle 23: After refmac, R = 0.2011 (Rfree = 0.000) for 5640 atoms. Found 99 (127 requested) and removed 47 (96 requested) atoms. Cycle 24: After refmac, R = 0.1991 (Rfree = 0.000) for 5678 atoms. Found 90 (128 requested) and removed 48 (97 requested) atoms. Cycle 25: After refmac, R = 0.1980 (Rfree = 0.000) for 5717 atoms. Found 87 (125 requested) and removed 53 (97 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.04 2.33 NCS extension: 0 residues added, 5752 seeds are put forward Round 1: 611 peptides, 6 chains. Longest chain 185 peptides. Score 0.973 Round 2: 609 peptides, 8 chains. Longest chain 236 peptides. Score 0.969 Round 3: 611 peptides, 7 chains. Longest chain 224 peptides. Score 0.971 Round 4: 608 peptides, 9 chains. Longest chain 106 peptides. Score 0.967 Round 5: 613 peptides, 7 chains. Longest chain 238 peptides. Score 0.971 Taking the results from Round 1 Chains 6, Residues 605, Estimated correctness of the model 99.9 % 6 chains (605 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 84 A Built loop between residues 205 A and 208 A Built loop between residues 240 A and 243 A Built loop between residues 138 B and 141 B 2 chains (615 residues) following loop building 2 chains (615 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5596 restraints for refining 5629 atoms. 722 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2123 (Rfree = 0.000) for 5629 atoms. Found 119 (119 requested) and removed 96 (96 requested) atoms. Cycle 27: After refmac, R = 0.2039 (Rfree = 0.000) for 5640 atoms. Found 112 (116 requested) and removed 58 (96 requested) atoms. Cycle 28: After refmac, R = 0.1996 (Rfree = 0.000) for 5687 atoms. Found 90 (113 requested) and removed 50 (97 requested) atoms. Cycle 29: After refmac, R = 0.1976 (Rfree = 0.000) for 5715 atoms. Found 92 (110 requested) and removed 46 (98 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1950 (Rfree = 0.000) for 5754 atoms. Found 87 (110 requested) and removed 48 (98 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.04 2.33 NCS extension: 0 residues added, 5793 seeds are put forward Round 1: 614 peptides, 6 chains. Longest chain 227 peptides. Score 0.973 Round 2: 609 peptides, 12 chains. Longest chain 119 peptides. Score 0.962 Round 3: 614 peptides, 6 chains. Longest chain 242 peptides. Score 0.973 Round 4: 608 peptides, 12 chains. Longest chain 114 peptides. Score 0.962 Round 5: 612 peptides, 7 chains. Longest chain 230 peptides. Score 0.971 Taking the results from Round 3 Chains 6, Residues 608, Estimated correctness of the model 99.9 % 5 chains (605 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 52 A Built loop between residues 74 A and 84 A Built loop between residues 112 B and 115 B 2 chains (618 residues) following loop building 2 chains (618 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5560 restraints for refining 5625 atoms. 655 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2134 (Rfree = 0.000) for 5625 atoms. Found 104 (104 requested) and removed 100 (96 requested) atoms. Cycle 32: After refmac, R = 0.2054 (Rfree = 0.000) for 5619 atoms. Found 100 (100 requested) and removed 52 (96 requested) atoms. Cycle 33: After refmac, R = 0.2009 (Rfree = 0.000) for 5657 atoms. Found 97 (97 requested) and removed 45 (97 requested) atoms. Cycle 34: After refmac, R = 0.1971 (Rfree = 0.000) for 5703 atoms. Found 89 (97 requested) and removed 40 (97 requested) atoms. Cycle 35: After refmac, R = 0.1943 (Rfree = 0.000) for 5743 atoms. Found 88 (98 requested) and removed 57 (98 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.05 2.35 NCS extension: 0 residues added, 5774 seeds are put forward Round 1: 612 peptides, 7 chains. Longest chain 145 peptides. Score 0.971 Round 2: 613 peptides, 8 chains. Longest chain 156 peptides. Score 0.970 Round 3: 613 peptides, 9 chains. Longest chain 145 peptides. Score 0.968 Round 4: 606 peptides, 11 chains. Longest chain 191 peptides. Score 0.963 Round 5: 605 peptides, 10 chains. Longest chain 145 peptides. Score 0.965 Taking the results from Round 1 Chains 7, Residues 605, Estimated correctness of the model 99.9 % 7 chains (605 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 138 A and 141 A Built loop between residues 240 A and 243 A Built loop between residues 74 B and 79 B Built loop between residues 178 B and 181 B 2 chains (617 residues) following loop building 2 chains (617 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5621 restraints for refining 5663 atoms. 724 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2086 (Rfree = 0.000) for 5663 atoms. Found 97 (97 requested) and removed 97 (97 requested) atoms. Cycle 37: After refmac, R = 0.2010 (Rfree = 0.000) for 5650 atoms. Found 97 (97 requested) and removed 51 (97 requested) atoms. Cycle 38: After refmac, R = 0.1972 (Rfree = 0.000) for 5692 atoms. Found 97 (97 requested) and removed 41 (97 requested) atoms. Cycle 39: After refmac, R = 0.1962 (Rfree = 0.000) for 5739 atoms. Found 96 (98 requested) and removed 55 (98 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1947 (Rfree = 0.000) for 5773 atoms. Found 99 (99 requested) and removed 56 (99 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.05 2.35 NCS extension: 40 residues added (270 deleted due to clashes), 5857 seeds are put forward Round 1: 609 peptides, 9 chains. Longest chain 156 peptides. Score 0.967 Round 2: 613 peptides, 5 chains. Longest chain 308 peptides. Score 0.975 Round 3: 610 peptides, 9 chains. Longest chain 242 peptides. Score 0.967 Round 4: 607 peptides, 9 chains. Longest chain 308 peptides. Score 0.967 Round 5: 604 peptides, 11 chains. Longest chain 150 peptides. Score 0.963 Taking the results from Round 2 Chains 5, Residues 608, Estimated correctness of the model 99.9 % 4 chains (604 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 A and 84 A Built loop between residues 167 A and 170 A 2 chains (615 residues) following loop building 2 chains (615 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5674 restraints for refining 5655 atoms. 800 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2113 (Rfree = 0.000) for 5655 atoms. Found 96 (96 requested) and removed 96 (96 requested) atoms. Cycle 42: After refmac, R = 0.2024 (Rfree = 0.000) for 5639 atoms. Found 96 (96 requested) and removed 43 (96 requested) atoms. Cycle 43: After refmac, R = 0.1977 (Rfree = 0.000) for 5687 atoms. Found 91 (97 requested) and removed 49 (97 requested) atoms. Cycle 44: After refmac, R = 0.1955 (Rfree = 0.000) for 5721 atoms. Found 97 (98 requested) and removed 48 (98 requested) atoms. Cycle 45: After refmac, R = 0.1938 (Rfree = 0.000) for 5763 atoms. Found 87 (98 requested) and removed 67 (98 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.04 2.33 NCS extension: 0 residues added, 5783 seeds are put forward Round 1: 612 peptides, 7 chains. Longest chain 262 peptides. Score 0.971 Round 2: 609 peptides, 5 chains. Longest chain 184 peptides. Score 0.974 Round 3: 611 peptides, 8 chains. Longest chain 227 peptides. Score 0.969 Round 4: 602 peptides, 10 chains. Longest chain 156 peptides. Score 0.964 Round 5: 606 peptides, 10 chains. Longest chain 273 peptides. Score 0.965 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 604, Estimated correctness of the model 99.9 % 5 chains (604 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 73 A and 77 A Built loop between residues 167 A and 170 A Built loop between residues 139 B and 142 B 2 chains (611 residues) following loop building 2 chains (611 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 40537 reflections ( 99.47 % complete ) and 4839 restraints for refining 4758 atoms. Observations/parameters ratio is 2.13 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2754 (Rfree = 0.000) for 4758 atoms. Found 67 (81 requested) and removed 0 (81 requested) atoms. Cycle 47: After refmac, R = 0.2524 (Rfree = 0.000) for 4758 atoms. Found 35 (82 requested) and removed 0 (82 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2404 (Rfree = 0.000) for 4758 atoms. Found 25 (83 requested) and removed 4 (83 requested) atoms. Cycle 49: After refmac, R = 0.2330 (Rfree = 0.000) for 4758 atoms. Found 14 (83 requested) and removed 8 (83 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:03:24 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 95.49