Tue 25 Dec 19:27:57 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 2op5-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2op5-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2op5-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-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/2op5-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-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 19:28:07 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/2op5-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-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 637 and 0 Target number of residues in the AU: 637 Target solvent content: 0.5032 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-2.2-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: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 5616 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 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: 73.087 2.190 Wilson plot Bfac: 24.02 36536 reflections ( 99.76 % complete ) and 0 restraints for refining 6250 atoms. Observations/parameters ratio is 1.46 ------------------------------------------------------ Starting model: R = 0.3387 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2878 (Rfree = 0.000) for 6250 atoms. Found 128 (165 requested) and removed 103 (82 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.18 2.33 NCS extension: 0 residues added, 6275 seeds are put forward Round 1: 418 peptides, 56 chains. Longest chain 16 peptides. Score 0.603 Round 2: 502 peptides, 40 chains. Longest chain 32 peptides. Score 0.804 Round 3: 542 peptides, 35 chains. Longest chain 54 peptides. Score 0.855 Round 4: 558 peptides, 37 chains. Longest chain 54 peptides. Score 0.859 Round 5: 575 peptides, 30 chains. Longest chain 74 peptides. Score 0.890 Taking the results from Round 5 Chains 35, Residues 545, Estimated correctness of the model 98.3 % 14 chains (417 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 B and 62 B Built loop between residues 86 B and 95 B Built loop between residues 41 E and 47 E Built loop between residues 79 D and 83 D 29 chains (563 residues) following loop building 10 chains (438 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 7264 restraints for refining 5774 atoms. 3051 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3145 (Rfree = 0.000) for 5774 atoms. Found 120 (152 requested) and removed 89 (76 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2910 (Rfree = 0.000) for 5769 atoms. Found 96 (150 requested) and removed 78 (76 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2753 (Rfree = 0.000) for 5765 atoms. Found 72 (147 requested) and removed 76 (76 requested) atoms. Cycle 4: After refmac, R = 0.2639 (Rfree = 0.000) for 5748 atoms. Found 73 (143 requested) and removed 76 (76 requested) atoms. Cycle 5: After refmac, R = 0.2572 (Rfree = 0.000) for 5734 atoms. Found 51 (139 requested) and removed 56 (75 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.14 2.29 NCS extension: 42 residues added (43 deleted due to clashes), 5784 seeds are put forward Round 1: 564 peptides, 26 chains. Longest chain 54 peptides. Score 0.897 Round 2: 586 peptides, 20 chains. Longest chain 90 peptides. Score 0.922 Round 3: 578 peptides, 26 chains. Longest chain 55 peptides. Score 0.903 Round 4: 578 peptides, 26 chains. Longest chain 54 peptides. Score 0.903 Round 5: 580 peptides, 26 chains. Longest chain 51 peptides. Score 0.904 Taking the results from Round 2 Chains 22, Residues 566, Estimated correctness of the model 99.1 % 12 chains (457 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 A and 22 A Built loop between residues 56 A and 61 A Built loop between residues 87 A and 95 A 19 chains (579 residues) following loop building 9 chains (470 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 36536 reflections ( 99.76 % complete ) and 7008 restraints for refining 5850 atoms. 2577 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2746 (Rfree = 0.000) for 5850 atoms. Found 104 (139 requested) and removed 88 (77 requested) atoms. Cycle 7: After refmac, R = 0.2601 (Rfree = 0.000) for 5856 atoms. Found 78 (136 requested) and removed 77 (77 requested) atoms. Cycle 8: After refmac, R = 0.2502 (Rfree = 0.000) for 5846 atoms. Found 55 (132 requested) and removed 69 (77 requested) atoms. Cycle 9: After refmac, R = 0.2426 (Rfree = 0.000) for 5828 atoms. Found 65 (129 requested) and removed 31 (77 requested) atoms. Cycle 10: After refmac, R = 0.2367 (Rfree = 0.000) for 5859 atoms. Found 48 (130 requested) and removed 29 (77 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.11 2.26 NCS extension: 20 residues added (53 deleted due to clashes), 5903 seeds are put forward Round 1: 589 peptides, 21 chains. Longest chain 83 peptides. Score 0.920 Round 2: 593 peptides, 28 chains. Longest chain 64 peptides. Score 0.904 Round 3: 597 peptides, 26 chains. Longest chain 74 peptides. Score 0.911 Round 4: 603 peptides, 23 chains. Longest chain 59 peptides. Score 0.921 Round 5: 600 peptides, 23 chains. Longest chain 54 peptides. Score 0.920 Taking the results from Round 4 Chains 26, Residues 580, Estimated correctness of the model 99.1 % 14 chains (474 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 82 A and 92 A Built loop between residues 81 C and 86 C 22 chains (593 residues) following loop building 11 chains (489 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 7079 restraints for refining 5973 atoms. 2525 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2591 (Rfree = 0.000) for 5973 atoms. Found 107 (129 requested) and removed 83 (78 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2438 (Rfree = 0.000) for 5990 atoms. Found 67 (126 requested) and removed 79 (79 requested) atoms. Cycle 13: After refmac, R = 0.2327 (Rfree = 0.000) for 5973 atoms. Found 59 (123 requested) and removed 67 (79 requested) atoms. Cycle 14: After refmac, R = 0.2270 (Rfree = 0.000) for 5960 atoms. Found 53 (119 requested) and removed 37 (78 requested) atoms. Cycle 15: After refmac, R = 0.2222 (Rfree = 0.000) for 5970 atoms. Found 53 (117 requested) and removed 28 (79 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.11 2.26 NCS extension: 22 residues added (13 deleted due to clashes), 6022 seeds are put forward Round 1: 597 peptides, 25 chains. Longest chain 74 peptides. Score 0.914 Round 2: 606 peptides, 17 chains. Longest chain 79 peptides. Score 0.935 Round 3: 602 peptides, 24 chains. Longest chain 74 peptides. Score 0.918 Round 4: 603 peptides, 19 chains. Longest chain 68 peptides. Score 0.930 Round 5: 605 peptides, 21 chains. Longest chain 55 peptides. Score 0.926 Taking the results from Round 2 Chains 18, Residues 589, Estimated correctness of the model 99.4 % 14 chains (560 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 37 A Built loop between residues 56 C and 62 C Built loop between residues 57 B and 64 B Built loop between residues 82 E and 92 E Built loop between residues 36 D and 39 D Built loop between residues 56 D and 61 D 12 chains (618 residues) following loop building 8 chains (589 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6317 restraints for refining 6135 atoms. 1177 conditional restraints added. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2505 (Rfree = 0.000) for 6135 atoms. Found 112 (117 requested) and removed 100 (81 requested) atoms. Cycle 17: After refmac, R = 0.2353 (Rfree = 0.000) for 6144 atoms. Found 85 (113 requested) and removed 81 (81 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2266 (Rfree = 0.000) for 6144 atoms. Found 76 (110 requested) and removed 69 (81 requested) atoms. Cycle 19: After refmac, R = 0.2205 (Rfree = 0.000) for 6148 atoms. Found 66 (107 requested) and removed 61 (81 requested) atoms. Cycle 20: After refmac, R = 0.2167 (Rfree = 0.000) for 6148 atoms. Found 75 (104 requested) and removed 48 (81 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.10 2.25 NCS extension: 33 residues added (45 deleted due to clashes), 6215 seeds are put forward Round 1: 608 peptides, 20 chains. Longest chain 81 peptides. Score 0.929 Round 2: 605 peptides, 20 chains. Longest chain 107 peptides. Score 0.928 Round 3: 609 peptides, 22 chains. Longest chain 56 peptides. Score 0.925 Round 4: 608 peptides, 21 chains. Longest chain 66 peptides. Score 0.927 Round 5: 610 peptides, 26 chains. Longest chain 88 peptides. Score 0.916 Taking the results from Round 1 Chains 22, Residues 588, Estimated correctness of the model 99.3 % 13 chains (529 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 C and 62 C Built loop between residues 71 C and 74 C Built loop between residues 56 B and 61 B Built loop between residues 87 D and 95 D Built loop between residues 55 F and 60 F 14 chains (603 residues) following loop building 8 chains (550 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6607 restraints for refining 6116 atoms. 1695 conditional restraints added. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2383 (Rfree = 0.000) for 6116 atoms. Found 100 (100 requested) and removed 86 (80 requested) atoms. Cycle 22: After refmac, R = 0.2245 (Rfree = 0.000) for 6125 atoms. Found 86 (97 requested) and removed 81 (81 requested) atoms. Cycle 23: After refmac, R = 0.2166 (Rfree = 0.000) for 6125 atoms. Found 68 (94 requested) and removed 47 (81 requested) atoms. Cycle 24: After refmac, R = 0.2105 (Rfree = 0.000) for 6144 atoms. Found 62 (91 requested) and removed 36 (81 requested) atoms. Cycle 25: After refmac, R = 0.2055 (Rfree = 0.000) for 6165 atoms. Found 53 (88 requested) and removed 25 (81 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.10 2.25 NCS extension: 32 residues added (83 deleted due to clashes), 6234 seeds are put forward Round 1: 605 peptides, 19 chains. Longest chain 81 peptides. Score 0.931 Round 2: 609 peptides, 23 chains. Longest chain 55 peptides. Score 0.923 Round 3: 612 peptides, 21 chains. Longest chain 74 peptides. Score 0.929 Round 4: 617 peptides, 21 chains. Longest chain 75 peptides. Score 0.930 Round 5: 618 peptides, 18 chains. Longest chain 56 peptides. Score 0.937 Taking the results from Round 5 Chains 21, Residues 600, Estimated correctness of the model 99.4 % 15 chains (564 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 43 A Built loop between residues 57 A and 61 A Built loop between residues 56 C and 61 C Built loop between residues 57 B and 62 B Built loop between residues 42 E and 46 E Built loop between residues 82 D and 91 D 14 chains (623 residues) following loop building 9 chains (588 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6401 restraints for refining 6233 atoms. 1262 conditional restraints added. Observations/parameters ratio is 1.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2420 (Rfree = 0.000) for 6233 atoms. Found 89 (89 requested) and removed 102 (82 requested) atoms. Cycle 27: After refmac, R = 0.2271 (Rfree = 0.000) for 6213 atoms. Found 83 (85 requested) and removed 82 (82 requested) atoms. Cycle 28: After refmac, R = 0.2174 (Rfree = 0.000) for 6207 atoms. Found 63 (82 requested) and removed 69 (82 requested) atoms. Cycle 29: After refmac, R = 0.2111 (Rfree = 0.000) for 6195 atoms. Found 82 (82 requested) and removed 36 (82 requested) atoms. Cycle 30: After refmac, R = 0.2049 (Rfree = 0.000) for 6238 atoms. Found 74 (82 requested) and removed 43 (82 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.11 2.26 NCS extension: 49 residues added (75 deleted due to clashes), 6321 seeds are put forward Round 1: 615 peptides, 18 chains. Longest chain 81 peptides. Score 0.936 Round 2: 618 peptides, 23 chains. Longest chain 107 peptides. Score 0.926 Round 3: 618 peptides, 25 chains. Longest chain 56 peptides. Score 0.921 Round 4: 624 peptides, 22 chains. Longest chain 56 peptides. Score 0.930 Round 5: 620 peptides, 25 chains. Longest chain 55 peptides. Score 0.922 Taking the results from Round 1 Chains 19, Residues 597, Estimated correctness of the model 99.4 % 13 chains (560 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 C and 62 C Built loop between residues 58 B and 61 B Built loop between residues 82 B and 90 B Built loop between residues 57 E and 62 E Built loop between residues 87 D and 90 D 13 chains (617 residues) following loop building 8 chains (581 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6516 restraints for refining 6247 atoms. 1418 conditional restraints added. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2315 (Rfree = 0.000) for 6247 atoms. Found 82 (82 requested) and removed 90 (82 requested) atoms. Cycle 32: After refmac, R = 0.2182 (Rfree = 0.000) for 6224 atoms. Found 82 (82 requested) and removed 82 (82 requested) atoms. Cycle 33: After refmac, R = 0.2107 (Rfree = 0.000) for 6221 atoms. Found 60 (82 requested) and removed 51 (82 requested) atoms. Cycle 34: After refmac, R = 0.2079 (Rfree = 0.000) for 6222 atoms. Found 71 (82 requested) and removed 26 (82 requested) atoms. Cycle 35: After refmac, R = 0.2037 (Rfree = 0.000) for 6264 atoms. Found 57 (82 requested) and removed 35 (82 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.10 2.25 NCS extension: 48 residues added (120 deleted due to clashes), 6340 seeds are put forward Round 1: 620 peptides, 17 chains. Longest chain 81 peptides. Score 0.940 Round 2: 616 peptides, 20 chains. Longest chain 73 peptides. Score 0.932 Round 3: 624 peptides, 20 chains. Longest chain 75 peptides. Score 0.934 Round 4: 622 peptides, 24 chains. Longest chain 76 peptides. Score 0.925 Round 5: 620 peptides, 22 chains. Longest chain 68 peptides. Score 0.929 Taking the results from Round 1 Chains 17, Residues 603, Estimated correctness of the model 99.4 % 11 chains (547 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 C and 61 C Built loop between residues 57 B and 61 B Built loop between residues 87 D and 90 D 14 chains (612 residues) following loop building 8 chains (556 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6588 restraints for refining 6179 atoms. 1631 conditional restraints added. Observations/parameters ratio is 1.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2239 (Rfree = 0.000) for 6179 atoms. Found 81 (81 requested) and removed 88 (81 requested) atoms. Cycle 37: After refmac, R = 0.2144 (Rfree = 0.000) for 6165 atoms. Found 81 (81 requested) and removed 72 (81 requested) atoms. Cycle 38: After refmac, R = 0.2091 (Rfree = 0.000) for 6174 atoms. Found 60 (81 requested) and removed 35 (81 requested) atoms. Cycle 39: After refmac, R = 0.2053 (Rfree = 0.000) for 6198 atoms. Found 63 (81 requested) and removed 33 (81 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2027 (Rfree = 0.000) for 6223 atoms. Found 60 (82 requested) and removed 39 (82 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.10 2.25 NCS extension: 52 residues added (113 deleted due to clashes), 6300 seeds are put forward Round 1: 614 peptides, 19 chains. Longest chain 81 peptides. Score 0.934 Round 2: 621 peptides, 22 chains. Longest chain 74 peptides. Score 0.929 Round 3: 617 peptides, 25 chains. Longest chain 59 peptides. Score 0.921 Round 4: 611 peptides, 25 chains. Longest chain 74 peptides. Score 0.919 Round 5: 613 peptides, 25 chains. Longest chain 76 peptides. Score 0.920 Taking the results from Round 1 Chains 19, Residues 595, Estimated correctness of the model 99.3 % 12 chains (537 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 C and 62 C Built loop between residues 56 E and 61 E Built loop between residues 87 D and 90 D 16 chains (605 residues) following loop building 9 chains (547 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDBFailed to save intermediate PDB 36536 reflections ( 99.76 % complete ) and 6707 restraints for refining 6156 atoms. 1814 conditional restraints added. Observations/parameters ratio is 1.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2216 (Rfree = 0.000) for 6156 atoms. Found 81 (81 requested) and removed 91 (81 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2134 (Rfree = 0.000) for 6144 atoms. Found 81 (81 requested) and removed 58 (81 requested) atoms. Cycle 43: After refmac, R = 0.2072 (Rfree = 0.000) for 6164 atoms. Found 67 (81 requested) and removed 39 (81 requested) atoms. Cycle 44: After refmac, R = 0.2038 (Rfree = 0.000) for 6189 atoms. Found 64 (81 requested) and removed 25 (81 requested) atoms. Cycle 45: After refmac, R = 0.2001 (Rfree = 0.000) for 6227 atoms. Found 56 (82 requested) and removed 34 (82 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.11 2.26 NCS extension: 53 residues added (116 deleted due to clashes), 6305 seeds are put forward Round 1: 614 peptides, 18 chains. Longest chain 107 peptides. Score 0.936 Round 2: 615 peptides, 20 chains. Longest chain 73 peptides. Score 0.932 Round 3: 614 peptides, 22 chains. Longest chain 56 peptides. Score 0.927 Round 4: 613 peptides, 26 chains. Longest chain 55 peptides. Score 0.917 Round 5: 609 peptides, 23 chains. Longest chain 109 peptides. Score 0.923 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 596, Estimated correctness of the model 99.4 % 11 chains (531 residues) have been docked in sequence Sequence coverage is 88 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 58 C and 61 C Built loop between residues 55 E and 61 E 17 chains (602 residues) following loop building 9 chains (538 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. Update only waters. 36536 reflections ( 99.76 % complete ) and 4838 restraints for refining 4760 atoms. Observations/parameters ratio is 1.92 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3041 (Rfree = 0.000) for 4760 atoms. Found 36 (62 requested) and removed 0 (62 requested) atoms. Cycle 47: After refmac, R = 0.2951 (Rfree = 0.000) for 4760 atoms. Found 13 (63 requested) and removed 1 (63 requested) atoms. Cycle 48: After refmac, R = 0.2897 (Rfree = 0.000) for 4760 atoms. Found 3 (63 requested) and removed 1 (63 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2862 (Rfree = 0.000) for 4760 atoms. Found 5 (63 requested) and removed 2 (63 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:09:11 GMT 2018 Job finished. TimeTaking 101.23