Mon 24 Dec 07:31:26 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr0-2.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-2.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-2.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-2.5-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-2.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-2.5-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:31:31 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-2.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-2.5-parrot-noncs/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 613 and 0 Target number of residues in the AU: 613 Target solvent content: 0.5471 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-2.5-parrot-noncs.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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-2.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 5928 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 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: 226.759 2.490 Wilson plot Bfac: 34.68 22751 reflections ( 85.61 % complete ) and 0 restraints for refining 6561 atoms. Observations/parameters ratio is 0.87 ------------------------------------------------------ Starting model: R = 0.3203 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2505 (Rfree = 0.000) for 6561 atoms. Found 28 (120 requested) and removed 73 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.45 2.62 NCS extension: 0 residues added, 6516 seeds are put forward Round 1: 353 peptides, 61 chains. Longest chain 12 peptides. Score 0.425 Round 2: 443 peptides, 52 chains. Longest chain 39 peptides. Score 0.654 Round 3: 482 peptides, 50 chains. Longest chain 37 peptides. Score 0.717 Round 4: 492 peptides, 41 chains. Longest chain 52 peptides. Score 0.775 Round 5: 496 peptides, 41 chains. Longest chain 58 peptides. Score 0.779 Taking the results from Round 5 Chains 41, Residues 455, Estimated correctness of the model 91.0 % 7 chains (189 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 173 B and 180 B Built loop between residues 197 B and 206 B 37 chains (463 residues) following loop building 5 chains (203 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 9793 restraints for refining 5554 atoms. 7214 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2967 (Rfree = 0.000) for 5554 atoms. Found 66 (101 requested) and removed 64 (50 requested) atoms. Cycle 2: After refmac, R = 0.2996 (Rfree = 0.000) for 5500 atoms. Found 60 (99 requested) and removed 60 (50 requested) atoms. Cycle 3: After refmac, R = 0.2752 (Rfree = 0.000) for 5456 atoms. Found 33 (96 requested) and removed 57 (50 requested) atoms. Cycle 4: After refmac, R = 0.2553 (Rfree = 0.000) for 5404 atoms. Found 38 (93 requested) and removed 52 (49 requested) atoms. Cycle 5: After refmac, R = 0.2471 (Rfree = 0.000) for 5370 atoms. Found 31 (90 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.43 2.60 NCS extension: 162 residues added (194 deleted due to clashes), 5538 seeds are put forward Round 1: 529 peptides, 44 chains. Longest chain 64 peptides. Score 0.796 Round 2: 535 peptides, 39 chains. Longest chain 50 peptides. Score 0.821 Round 3: 555 peptides, 39 chains. Longest chain 60 peptides. Score 0.836 Round 4: 535 peptides, 38 chains. Longest chain 54 peptides. Score 0.825 Round 5: 534 peptides, 40 chains. Longest chain 54 peptides. Score 0.817 Taking the results from Round 3 Chains 45, Residues 516, Estimated correctness of the model 94.8 % 13 chains (333 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 142 C and 150 C Built loop between residues 196 C and 204 C Built loop between residues 73 B and 79 B Built loop between residues 140 B and 151 B Built loop between residues 176 B and 179 B Built loop between residues 220 B and 225 B 33 chains (533 residues) following loop building 7 chains (368 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 7967 restraints for refining 5558 atoms. 4488 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2678 (Rfree = 0.000) for 5558 atoms. Found 71 (91 requested) and removed 57 (50 requested) atoms. Cycle 7: After refmac, R = 0.2526 (Rfree = 0.000) for 5540 atoms. Found 45 (90 requested) and removed 54 (51 requested) atoms. Cycle 8: After refmac, R = 0.2445 (Rfree = 0.000) for 5520 atoms. Found 49 (87 requested) and removed 51 (50 requested) atoms. Cycle 9: After refmac, R = 0.2410 (Rfree = 0.000) for 5504 atoms. Found 44 (85 requested) and removed 51 (50 requested) atoms. Cycle 10: After refmac, R = 0.2245 (Rfree = 0.000) for 5480 atoms. Found 37 (82 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.46 2.63 NCS extension: 243 residues added (350 deleted due to clashes), 5741 seeds are put forward Round 1: 538 peptides, 37 chains. Longest chain 89 peptides. Score 0.832 Round 2: 551 peptides, 31 chains. Longest chain 76 peptides. Score 0.862 Round 3: 553 peptides, 33 chains. Longest chain 67 peptides. Score 0.857 Round 4: 557 peptides, 34 chains. Longest chain 103 peptides. Score 0.856 Round 5: 551 peptides, 37 chains. Longest chain 55 peptides. Score 0.841 Taking the results from Round 2 Chains 33, Residues 520, Estimated correctness of the model 96.2 % 13 chains (385 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 A and 84 A Built loop between residues 99 A and 104 A Built loop between residues 143 A and 151 A Built loop between residues 223 A and 226 A Built loop between residues 109 B and 116 B Built loop between residues 145 B and 148 B Built loop between residues 222 B and 225 B 25 chains (547 residues) following loop building 6 chains (417 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 7512 restraints for refining 5558 atoms. 3753 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2465 (Rfree = 0.000) for 5558 atoms. Found 79 (81 requested) and removed 60 (50 requested) atoms. Cycle 12: After refmac, R = 0.2290 (Rfree = 0.000) for 5561 atoms. Found 55 (80 requested) and removed 53 (51 requested) atoms. Cycle 13: After refmac, R = 0.2110 (Rfree = 0.000) for 5549 atoms. Found 42 (78 requested) and removed 51 (51 requested) atoms. Cycle 14: After refmac, R = 0.2053 (Rfree = 0.000) for 5528 atoms. Found 41 (75 requested) and removed 50 (50 requested) atoms. Cycle 15: After refmac, R = 0.2025 (Rfree = 0.000) for 5513 atoms. Found 37 (73 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.44 2.61 NCS extension: 348 residues added (517 deleted due to clashes), 5866 seeds are put forward Round 1: 550 peptides, 36 chains. Longest chain 94 peptides. Score 0.844 Round 2: 577 peptides, 24 chains. Longest chain 100 peptides. Score 0.898 Round 3: 570 peptides, 30 chains. Longest chain 63 peptides. Score 0.876 Round 4: 585 peptides, 27 chains. Longest chain 63 peptides. Score 0.893 Round 5: 561 peptides, 33 chains. Longest chain 51 peptides. Score 0.861 Taking the results from Round 2 Chains 25, Residues 553, Estimated correctness of the model 97.8 % 12 chains (431 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 93 A Built loop between residues 125 A and 129 A Built loop between residues 144 A and 151 A Built loop between residues 203 B and 207 B Built loop between residues 231 B and 234 B 20 chains (569 residues) following loop building 7 chains (448 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 7005 restraints for refining 5557 atoms. 3078 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2274 (Rfree = 0.000) for 5557 atoms. Found 71 (71 requested) and removed 58 (50 requested) atoms. Cycle 17: After refmac, R = 0.2107 (Rfree = 0.000) for 5563 atoms. Found 55 (69 requested) and removed 52 (51 requested) atoms. Cycle 18: After refmac, R = 0.2047 (Rfree = 0.000) for 5557 atoms. Found 42 (67 requested) and removed 51 (51 requested) atoms. Cycle 19: After refmac, R = 0.2025 (Rfree = 0.000) for 5546 atoms. Found 38 (65 requested) and removed 51 (50 requested) atoms. Cycle 20: After refmac, R = 0.1979 (Rfree = 0.000) for 5531 atoms. Found 42 (63 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.44 2.61 NCS extension: 178 residues added (469 deleted due to clashes), 5713 seeds are put forward Round 1: 565 peptides, 34 chains. Longest chain 99 peptides. Score 0.861 Round 2: 577 peptides, 25 chains. Longest chain 56 peptides. Score 0.895 Round 3: 565 peptides, 30 chains. Longest chain 63 peptides. Score 0.874 Round 4: 562 peptides, 28 chains. Longest chain 58 peptides. Score 0.878 Round 5: 562 peptides, 26 chains. Longest chain 112 peptides. Score 0.884 Taking the results from Round 2 Chains 32, Residues 552, Estimated correctness of the model 97.7 % 13 chains (420 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 A and 130 A Built loop between residues 143 A and 152 A Built loop between residues 148 C and 151 C Built loop between residues 204 C and 206 C 27 chains (564 residues) following loop building 9 chains (433 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 7086 restraints for refining 5557 atoms. 3192 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2221 (Rfree = 0.000) for 5557 atoms. Found 61 (61 requested) and removed 55 (50 requested) atoms. Cycle 22: After refmac, R = 0.2068 (Rfree = 0.000) for 5546 atoms. Found 59 (59 requested) and removed 51 (51 requested) atoms. Cycle 23: After refmac, R = 0.1984 (Rfree = 0.000) for 5549 atoms. Found 48 (57 requested) and removed 50 (50 requested) atoms. Cycle 24: After refmac, R = 0.1950 (Rfree = 0.000) for 5539 atoms. Found 42 (55 requested) and removed 50 (50 requested) atoms. Cycle 25: After refmac, R = 0.1949 (Rfree = 0.000) for 5523 atoms. Found 53 (53 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.43 2.60 NCS extension: 311 residues added (376 deleted due to clashes), 5847 seeds are put forward Round 1: 565 peptides, 28 chains. Longest chain 99 peptides. Score 0.880 Round 2: 576 peptides, 24 chains. Longest chain 140 peptides. Score 0.897 Round 3: 582 peptides, 26 chains. Longest chain 67 peptides. Score 0.894 Round 4: 579 peptides, 25 chains. Longest chain 145 peptides. Score 0.896 Round 5: 571 peptides, 25 chains. Longest chain 56 peptides. Score 0.892 Taking the results from Round 2 Chains 28, Residues 552, Estimated correctness of the model 97.8 % 15 chains (458 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 67 A Built loop between residues 145 A and 152 A Built loop between residues 73 C and 76 C Built loop between residues 89 C and 93 C Built loop between residues 105 C and 108 C 22 chains (564 residues) following loop building 10 chains (473 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6913 restraints for refining 5557 atoms. 2875 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2182 (Rfree = 0.000) for 5557 atoms. Found 50 (50 requested) and removed 58 (50 requested) atoms. Cycle 27: After refmac, R = 0.2039 (Rfree = 0.000) for 5544 atoms. Found 50 (50 requested) and removed 51 (50 requested) atoms. Cycle 28: After refmac, R = 0.1969 (Rfree = 0.000) for 5538 atoms. Found 50 (50 requested) and removed 50 (50 requested) atoms. Cycle 29: After refmac, R = 0.1910 (Rfree = 0.000) for 5534 atoms. Found 48 (50 requested) and removed 50 (50 requested) atoms. Cycle 30: After refmac, R = 0.1895 (Rfree = 0.000) for 5527 atoms. Found 50 (50 requested) and removed 51 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.44 2.61 NCS extension: 382 residues added (626 deleted due to clashes), 5917 seeds are put forward Round 1: 568 peptides, 27 chains. Longest chain 99 peptides. Score 0.885 Round 2: 572 peptides, 22 chains. Longest chain 156 peptides. Score 0.901 Round 3: 561 peptides, 28 chains. Longest chain 72 peptides. Score 0.878 Round 4: 576 peptides, 23 chains. Longest chain 109 peptides. Score 0.900 Round 5: 562 peptides, 27 chains. Longest chain 100 peptides. Score 0.881 Taking the results from Round 2 Chains 25, Residues 550, Estimated correctness of the model 97.9 % 12 chains (444 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 32 A Built loop between residues 73 A and 76 A Built loop between residues 88 A and 92 A 22 chains (557 residues) following loop building 9 chains (451 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 22751 reflections ( 85.61 % complete ) and 7185 restraints for refining 5558 atoms. 3269 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2065 (Rfree = 0.000) for 5558 atoms. Found 50 (50 requested) and removed 59 (50 requested) atoms. Cycle 32: After refmac, R = 0.1920 (Rfree = 0.000) for 5543 atoms. Found 50 (50 requested) and removed 50 (50 requested) atoms. Cycle 33: After refmac, R = 0.1850 (Rfree = 0.000) for 5540 atoms. Found 42 (50 requested) and removed 52 (50 requested) atoms. Cycle 34: After refmac, R = 0.1808 (Rfree = 0.000) for 5525 atoms. Found 38 (50 requested) and removed 52 (50 requested) atoms. Cycle 35: After refmac, R = 0.1774 (Rfree = 0.000) for 5510 atoms. Found 32 (50 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.43 2.60 NCS extension: 731 residues added (1547 deleted due to clashes), 6229 seeds are put forward Round 1: 565 peptides, 32 chains. Longest chain 99 peptides. Score 0.867 Round 2: 580 peptides, 21 chains. Longest chain 111 peptides. Score 0.907 Round 3: 572 peptides, 25 chains. Longest chain 99 peptides. Score 0.892 Round 4: 579 peptides, 23 chains. Longest chain 125 peptides. Score 0.901 Round 5: 565 peptides, 27 chains. Longest chain 104 peptides. Score 0.883 Taking the results from Round 2 Chains 24, Residues 559, Estimated correctness of the model 98.2 % 11 chains (447 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 42 A Built loop between residues 90 A and 97 A Built loop between residues 131 A and 137 A Built loop between residues 92 B and 95 B Built loop between residues 144 B and 151 B 17 chains (573 residues) following loop building 6 chains (469 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6862 restraints for refining 5558 atoms. 2806 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2002 (Rfree = 0.000) for 5558 atoms. Found 50 (50 requested) and removed 58 (50 requested) atoms. Cycle 37: After refmac, R = 0.1858 (Rfree = 0.000) for 5546 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. Cycle 38: After refmac, R = 0.1804 (Rfree = 0.000) for 5538 atoms. Found 43 (50 requested) and removed 50 (50 requested) atoms. Cycle 39: After refmac, R = 0.1805 (Rfree = 0.000) for 5529 atoms. Found 40 (50 requested) and removed 50 (50 requested) atoms. Cycle 40: After refmac, R = 0.1774 (Rfree = 0.000) for 5518 atoms. Found 45 (50 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.44 2.61 NCS extension: 397 residues added (809 deleted due to clashes), 5913 seeds are put forward Round 1: 579 peptides, 28 chains. Longest chain 99 peptides. Score 0.887 Round 2: 586 peptides, 26 chains. Longest chain 111 peptides. Score 0.896 Round 3: 579 peptides, 24 chains. Longest chain 99 peptides. Score 0.899 Round 4: 574 peptides, 25 chains. Longest chain 76 peptides. Score 0.893 Round 5: 576 peptides, 25 chains. Longest chain 93 peptides. Score 0.894 Taking the results from Round 3 Chains 32, Residues 555, Estimated correctness of the model 97.9 % 15 chains (445 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 104 A Built loop between residues 114 A and 117 A Built loop between residues 145 A and 152 A Built loop between residues 176 A and 186 A Built loop between residues 200 A and 203 A Built loop between residues 39 C and 43 C Built loop between residues 200 C and 206 C 21 chains (576 residues) following loop building 8 chains (474 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6852 restraints for refining 5558 atoms. 2768 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2108 (Rfree = 0.000) for 5558 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. Cycle 42: After refmac, R = 0.1949 (Rfree = 0.000) for 5546 atoms. Found 50 (50 requested) and removed 50 (50 requested) atoms. Cycle 43: After refmac, R = 0.1886 (Rfree = 0.000) for 5541 atoms. Found 36 (50 requested) and removed 50 (50 requested) atoms. Cycle 44: After refmac, R = 0.1855 (Rfree = 0.000) for 5520 atoms. Found 41 (50 requested) and removed 50 (50 requested) atoms. Cycle 45: After refmac, R = 0.1816 (Rfree = 0.000) for 5507 atoms. Found 50 (50 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.44 2.61 NCS extension: 376 residues added (499 deleted due to clashes), 5889 seeds are put forward Round 1: 560 peptides, 24 chains. Longest chain 97 peptides. Score 0.889 Round 2: 583 peptides, 17 chains. Longest chain 216 peptides. Score 0.919 Round 3: 571 peptides, 21 chains. Longest chain 93 peptides. Score 0.903 Round 4: 577 peptides, 21 chains. Longest chain 111 peptides. Score 0.906 Round 5: 562 peptides, 23 chains. Longest chain 81 peptides. Score 0.893 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 566, Estimated correctness of the model 98.6 % 10 chains (489 residues) have been docked in sequence Sequence coverage is 86 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 41 A and 47 A Built loop between residues 145 A and 151 A Built loop between residues 178 A and 186 A Built loop between residues 200 A and 213 A Built loop between residues 232 A and 235 A Built loop between residues 145 C and 151 C 13 chains (592 residues) following loop building 4 chains (525 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22751 reflections ( 85.61 % complete ) and 4373 restraints for refining 4340 atoms. Observations/parameters ratio is 1.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3190 (Rfree = 0.000) for 4340 atoms. Found 36 (39 requested) and removed 0 (39 requested) atoms. Cycle 47: After refmac, R = 0.2971 (Rfree = 0.000) for 4340 atoms. Found 18 (40 requested) and removed 4 (40 requested) atoms. Cycle 48: After refmac, R = 0.2873 (Rfree = 0.000) for 4340 atoms. Found 6 (40 requested) and removed 2 (40 requested) atoms. Cycle 49: After refmac, R = 0.2827 (Rfree = 0.000) for 4340 atoms. TimeTaking 80.52