Mon 24 Dec 07:36:01 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 1vkh-2.3-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-2.3-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-2.3-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-2.3-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/1vkh-2.3-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-2.3-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 07:36:05 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-2.3-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-2.3-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 518 and 0 Target number of residues in the AU: 518 Target solvent content: 0.4436 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-2.3-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: 4 Cell parameters: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-2.3-parrot-noncs.fasta_lf Building free atoms model in initial map for 4368 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: 19.289 2.300 Wilson plot Bfac: 13.58 22067 reflections ( 99.75 % complete ) and 0 restraints for refining 4889 atoms. Observations/parameters ratio is 1.13 ------------------------------------------------------ Starting model: R = 0.3318 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2327 (Rfree = 0.000) for 4889 atoms. Found 98 (112 requested) and removed 77 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.90 2.14 NCS extension: 0 residues added, 4910 seeds are put forward Round 1: 344 peptides, 54 chains. Longest chain 20 peptides. Score 0.560 Round 2: 396 peptides, 36 chains. Longest chain 38 peptides. Score 0.800 Round 3: 428 peptides, 28 chains. Longest chain 59 peptides. Score 0.872 Round 4: 464 peptides, 18 chains. Longest chain 85 peptides. Score 0.929 Round 5: 462 peptides, 20 chains. Longest chain 91 peptides. Score 0.922 Taking the results from Round 4 Chains 21, Residues 446, Estimated correctness of the model 99.1 % 10 chains (373 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 140 B and 151 B Built loop between residues 174 B and 182 B 14 chains (454 residues) following loop building 8 chains (390 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 5142 restraints for refining 4435 atoms. 1679 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2814 (Rfree = 0.000) for 4435 atoms. Found 102 (102 requested) and removed 74 (51 requested) atoms. Cycle 2: After refmac, R = 0.2519 (Rfree = 0.000) for 4444 atoms. Found 74 (100 requested) and removed 52 (51 requested) atoms. Cycle 3: After refmac, R = 0.2426 (Rfree = 0.000) for 4451 atoms. Found 50 (98 requested) and removed 53 (51 requested) atoms. Cycle 4: After refmac, R = 0.2355 (Rfree = 0.000) for 4443 atoms. Found 41 (96 requested) and removed 52 (51 requested) atoms. Cycle 5: After refmac, R = 0.2286 (Rfree = 0.000) for 4420 atoms. Found 40 (93 requested) and removed 44 (50 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.88 2.12 NCS extension: 6 residues added (92 deleted due to clashes), 4430 seeds are put forward Round 1: 462 peptides, 13 chains. Longest chain 107 peptides. Score 0.942 Round 2: 467 peptides, 12 chains. Longest chain 157 peptides. Score 0.946 Round 3: 472 peptides, 11 chains. Longest chain 93 peptides. Score 0.951 Round 4: 463 peptides, 18 chains. Longest chain 86 peptides. Score 0.928 Round 5: 464 peptides, 12 chains. Longest chain 111 peptides. Score 0.945 Taking the results from Round 3 Chains 14, Residues 461, Estimated correctness of the model 99.6 % 8 chains (422 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 50 A and 55 A Built loop between residues 85 A and 95 A Built loop between residues 170 A and 180 A Built loop between residues 181 B and 187 B Built loop between residues 199 B and 202 B 5 chains (479 residues) following loop building 3 chains (451 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4639 restraints for refining 4439 atoms. 794 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2574 (Rfree = 0.000) for 4439 atoms. Found 92 (92 requested) and removed 63 (51 requested) atoms. Cycle 7: After refmac, R = 0.2363 (Rfree = 0.000) for 4463 atoms. Found 57 (90 requested) and removed 51 (51 requested) atoms. Cycle 8: After refmac, R = 0.2281 (Rfree = 0.000) for 4462 atoms. Found 46 (88 requested) and removed 49 (51 requested) atoms. Cycle 9: After refmac, R = 0.2187 (Rfree = 0.000) for 4452 atoms. Found 50 (86 requested) and removed 35 (51 requested) atoms. Cycle 10: After refmac, R = 0.2155 (Rfree = 0.000) for 4463 atoms. Found 39 (84 requested) and removed 40 (51 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.87 2.11 NCS extension: 31 residues added (179 deleted due to clashes), 4499 seeds are put forward Round 1: 470 peptides, 10 chains. Longest chain 155 peptides. Score 0.953 Round 2: 479 peptides, 9 chains. Longest chain 108 peptides. Score 0.958 Round 3: 469 peptides, 13 chains. Longest chain 78 peptides. Score 0.945 Round 4: 474 peptides, 11 chains. Longest chain 118 peptides. Score 0.951 Round 5: 474 peptides, 10 chains. Longest chain 178 peptides. Score 0.954 Taking the results from Round 2 Chains 9, Residues 470, Estimated correctness of the model 99.7 % 9 chains (470 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 95 A Built loop between residues 110 A and 117 A Built loop between residues 174 A and 177 A Built loop between residues 199 A and 202 A Built loop between residues 234 A and 237 A Built loop between residues 88 B and 94 B Built loop between residues 200 B and 203 B 2 chains (495 residues) following loop building 2 chains (495 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4409 restraints for refining 4587 atoms. 311 conditional restraints added. Observations/parameters ratio is 1.20 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2419 (Rfree = 0.000) for 4587 atoms. Found 84 (84 requested) and removed 63 (52 requested) atoms. Cycle 12: After refmac, R = 0.2244 (Rfree = 0.000) for 4601 atoms. Found 43 (82 requested) and removed 52 (52 requested) atoms. Cycle 13: After refmac, R = 0.2144 (Rfree = 0.000) for 4586 atoms. Found 48 (80 requested) and removed 52 (52 requested) atoms. Cycle 14: After refmac, R = 0.2061 (Rfree = 0.000) for 4575 atoms. Found 45 (78 requested) and removed 45 (52 requested) atoms. Cycle 15: After refmac, R = 0.2028 (Rfree = 0.000) for 4569 atoms. Found 45 (76 requested) and removed 30 (52 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.88 2.12 NCS extension: 30 residues added (237 deleted due to clashes), 4618 seeds are put forward Round 1: 469 peptides, 10 chains. Longest chain 91 peptides. Score 0.952 Round 2: 477 peptides, 10 chains. Longest chain 107 peptides. Score 0.955 Round 3: 476 peptides, 12 chains. Longest chain 142 peptides. Score 0.949 Round 4: 470 peptides, 13 chains. Longest chain 120 peptides. Score 0.945 Round 5: 473 peptides, 11 chains. Longest chain 139 peptides. Score 0.951 Taking the results from Round 2 Chains 11, Residues 467, Estimated correctness of the model 99.6 % 9 chains (456 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 88 A and 96 A Built loop between residues 110 A and 117 A Built loop between residues 51 B and 54 B Built loop between residues 88 B and 94 B Built loop between residues 184 B and 188 B 4 chains (491 residues) following loop building 3 chains (481 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4523 restraints for refining 4585 atoms. 498 conditional restraints added. Observations/parameters ratio is 1.20 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2363 (Rfree = 0.000) for 4585 atoms. Found 73 (73 requested) and removed 68 (52 requested) atoms. Cycle 17: After refmac, R = 0.2141 (Rfree = 0.000) for 4587 atoms. Found 61 (71 requested) and removed 52 (52 requested) atoms. Cycle 18: After refmac, R = 0.2063 (Rfree = 0.000) for 4589 atoms. Found 40 (69 requested) and removed 52 (52 requested) atoms. Cycle 19: After refmac, R = 0.2068 (Rfree = 0.000) for 4570 atoms. Found 47 (67 requested) and removed 48 (52 requested) atoms. Cycle 20: After refmac, R = 0.2047 (Rfree = 0.000) for 4563 atoms. Found 51 (65 requested) and removed 33 (52 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.87 2.11 NCS extension: 28 residues added (423 deleted due to clashes), 4615 seeds are put forward Round 1: 477 peptides, 9 chains. Longest chain 156 peptides. Score 0.957 Round 2: 476 peptides, 10 chains. Longest chain 86 peptides. Score 0.954 Round 3: 476 peptides, 11 chains. Longest chain 101 peptides. Score 0.952 Round 4: 478 peptides, 5 chains. Longest chain 178 peptides. Score 0.967 Round 5: 474 peptides, 9 chains. Longest chain 178 peptides. Score 0.956 Taking the results from Round 4 Chains 6, Residues 473, Estimated correctness of the model 99.8 % 5 chains (472 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 96 A Built loop between residues 110 A and 117 A Built loop between residues 88 B and 95 B 2 chains (491 residues) following loop building 2 chains (491 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4392 restraints for refining 4575 atoms. 329 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2230 (Rfree = 0.000) for 4575 atoms. Found 63 (63 requested) and removed 67 (52 requested) atoms. Cycle 22: After refmac, R = 0.2113 (Rfree = 0.000) for 4562 atoms. Found 61 (61 requested) and removed 52 (52 requested) atoms. Cycle 23: After refmac, R = 0.2051 (Rfree = 0.000) for 4568 atoms. Found 53 (59 requested) and removed 53 (52 requested) atoms. Cycle 24: After refmac, R = 0.2026 (Rfree = 0.000) for 4567 atoms. Found 49 (57 requested) and removed 44 (52 requested) atoms. Cycle 25: After refmac, R = 0.1998 (Rfree = 0.000) for 4568 atoms. Found 49 (55 requested) and removed 38 (52 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.88 2.12 NCS extension: 14 residues added (222 deleted due to clashes), 4600 seeds are put forward Round 1: 475 peptides, 9 chains. Longest chain 178 peptides. Score 0.957 Round 2: 477 peptides, 12 chains. Longest chain 107 peptides. Score 0.950 Round 3: 482 peptides, 8 chains. Longest chain 109 peptides. Score 0.961 Round 4: 475 peptides, 9 chains. Longest chain 178 peptides. Score 0.957 Round 5: 474 peptides, 12 chains. Longest chain 101 peptides. Score 0.949 Taking the results from Round 3 Chains 9, Residues 474, Estimated correctness of the model 99.7 % 8 chains (473 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 95 A Built loop between residues 178 A and 181 A Built loop between residues 73 B and 77 B Built loop between residues 88 B and 95 B Built loop between residues 114 B and 117 B Built loop between residues 224 B and 227 B 2 chains (495 residues) following loop building 2 chains (495 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4368 restraints for refining 4566 atoms. 270 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2158 (Rfree = 0.000) for 4566 atoms. Found 52 (52 requested) and removed 62 (52 requested) atoms. Cycle 27: After refmac, R = 0.2043 (Rfree = 0.000) for 4552 atoms. Found 52 (52 requested) and removed 52 (52 requested) atoms. Cycle 28: After refmac, R = 0.2003 (Rfree = 0.000) for 4547 atoms. Found 43 (52 requested) and removed 52 (52 requested) atoms. Cycle 29: After refmac, R = 0.1979 (Rfree = 0.000) for 4536 atoms. Found 44 (52 requested) and removed 39 (52 requested) atoms. Cycle 30: After refmac, R = 0.1972 (Rfree = 0.000) for 4540 atoms. Found 52 (52 requested) and removed 45 (52 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.87 2.11 NCS extension: 9 residues added (188 deleted due to clashes), 4563 seeds are put forward Round 1: 478 peptides, 9 chains. Longest chain 116 peptides. Score 0.957 Round 2: 480 peptides, 8 chains. Longest chain 156 peptides. Score 0.960 Round 3: 477 peptides, 10 chains. Longest chain 128 peptides. Score 0.955 Round 4: 476 peptides, 12 chains. Longest chain 156 peptides. Score 0.949 Round 5: 475 peptides, 12 chains. Longest chain 107 peptides. Score 0.949 Taking the results from Round 2 Chains 9, Residues 472, Estimated correctness of the model 99.7 % 8 chains (471 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 88 A and 95 A Built loop between residues 218 A and 221 A Built loop between residues 73 B and 77 B Built loop between residues 88 B and 95 B Built loop between residues 113 B and 117 B 2 chains (493 residues) following loop building 2 chains (493 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4373 restraints for refining 4559 atoms. 291 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2173 (Rfree = 0.000) for 4559 atoms. Found 52 (52 requested) and removed 66 (52 requested) atoms. Cycle 32: After refmac, R = 0.2061 (Rfree = 0.000) for 4539 atoms. Found 51 (52 requested) and removed 52 (52 requested) atoms. Cycle 33: After refmac, R = 0.2037 (Rfree = 0.000) for 4535 atoms. Found 49 (52 requested) and removed 48 (52 requested) atoms. Cycle 34: After refmac, R = 0.1997 (Rfree = 0.000) for 4534 atoms. Found 48 (52 requested) and removed 39 (52 requested) atoms. Cycle 35: After refmac, R = 0.1976 (Rfree = 0.000) for 4541 atoms. Found 36 (52 requested) and removed 36 (52 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.88 2.12 NCS extension: 10 residues added (291 deleted due to clashes), 4556 seeds are put forward Round 1: 481 peptides, 9 chains. Longest chain 142 peptides. Score 0.958 Round 2: 484 peptides, 9 chains. Longest chain 155 peptides. Score 0.959 Round 3: 478 peptides, 10 chains. Longest chain 95 peptides. Score 0.955 Round 4: 470 peptides, 13 chains. Longest chain 107 peptides. Score 0.945 Round 5: 480 peptides, 7 chains. Longest chain 156 peptides. Score 0.963 Taking the results from Round 5 Chains 7, Residues 473, Estimated correctness of the model 99.7 % 7 chains (473 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 94 A Built loop between residues 167 A and 172 A Built loop between residues 194 A and 196 A Built loop between residues 88 B and 95 B Built loop between residues 113 B and 117 B 2 chains (493 residues) following loop building 2 chains (493 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4374 restraints for refining 4549 atoms. 292 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2187 (Rfree = 0.000) for 4549 atoms. Found 52 (52 requested) and removed 57 (52 requested) atoms. Cycle 37: After refmac, R = 0.2070 (Rfree = 0.000) for 4541 atoms. Found 52 (52 requested) and removed 52 (52 requested) atoms. Cycle 38: After refmac, R = 0.2001 (Rfree = 0.000) for 4540 atoms. Found 52 (52 requested) and removed 54 (52 requested) atoms. Cycle 39: After refmac, R = 0.1985 (Rfree = 0.000) for 4536 atoms. Found 52 (52 requested) and removed 44 (52 requested) atoms. Cycle 40: After refmac, R = 0.1957 (Rfree = 0.000) for 4542 atoms. Found 52 (52 requested) and removed 43 (52 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.87 2.11 NCS extension: 36 residues added (477 deleted due to clashes), 4594 seeds are put forward Round 1: 485 peptides, 10 chains. Longest chain 157 peptides. Score 0.957 Round 2: 489 peptides, 10 chains. Longest chain 101 peptides. Score 0.958 Round 3: 488 peptides, 10 chains. Longest chain 92 peptides. Score 0.958 Round 4: 488 peptides, 11 chains. Longest chain 101 peptides. Score 0.955 Round 5: 487 peptides, 8 chains. Longest chain 164 peptides. Score 0.962 Taking the results from Round 5 Chains 8, Residues 479, Estimated correctness of the model 99.7 % 6 chains (469 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 90 A Built loop between residues 195 A and 198 A Built loop between residues 213 A and 216 A Built loop between residues 88 B and 95 B 4 chains (491 residues) following loop building 2 chains (481 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4495 restraints for refining 4537 atoms. 479 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2175 (Rfree = 0.000) for 4537 atoms. Found 52 (52 requested) and removed 61 (52 requested) atoms. Cycle 42: After refmac, R = 0.2069 (Rfree = 0.000) for 4524 atoms. Found 52 (52 requested) and removed 53 (52 requested) atoms. Cycle 43: After refmac, R = 0.2020 (Rfree = 0.000) for 4523 atoms. Found 52 (52 requested) and removed 47 (52 requested) atoms. Cycle 44: After refmac, R = 0.2004 (Rfree = 0.000) for 4528 atoms. Found 46 (52 requested) and removed 43 (52 requested) atoms. Cycle 45: After refmac, R = 0.1994 (Rfree = 0.000) for 4529 atoms. Found 49 (52 requested) and removed 38 (52 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.89 2.13 NCS extension: 6 residues added (216 deleted due to clashes), 4551 seeds are put forward Round 1: 486 peptides, 8 chains. Longest chain 179 peptides. Score 0.962 Round 2: 483 peptides, 8 chains. Longest chain 102 peptides. Score 0.961 Round 3: 483 peptides, 9 chains. Longest chain 107 peptides. Score 0.959 Round 4: 482 peptides, 9 chains. Longest chain 179 peptides. Score 0.959 Round 5: 480 peptides, 10 chains. Longest chain 148 peptides. Score 0.956 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 478, Estimated correctness of the model 99.7 % 7 chains (474 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 87 A and 96 A Built loop between residues 113 A and 117 A Built loop between residues 51 B and 54 B Built loop between residues 87 B and 95 B 2 chains (496 residues) following loop building 2 chains (496 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22067 reflections ( 99.75 % complete ) and 4106 restraints for refining 4024 atoms. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2668 (Rfree = 0.000) for 4024 atoms. Found 33 (46 requested) and removed 0 (46 requested) atoms. Cycle 47: After refmac, R = 0.2528 (Rfree = 0.000) for 4024 atoms. Found 10 (46 requested) and removed 3 (46 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2495 (Rfree = 0.000) for 4024 atoms. Found 3 (46 requested) and removed 0 (46 requested) atoms. Cycle 49: After refmac, R = 0.2467 (Rfree = 0.000) for 4024 atoms. TimeTaking 57.83