null Mon 24 Dec 00:28:09 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkh-2.3-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-2.3-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-2.3-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-2.3-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-2.3-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-2.3-parrot-mrncs ############### 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 00:28:14 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-2.3-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-2.3-parrot-mrncs/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-mrncs.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-mrncs.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 4817 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Starting model: R = 0.3217 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2225 (Rfree = 0.000) for 4817 atoms. Found 104 (110 requested) and removed 63 (55 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.90 2.14 NCS extension: 0 residues added, 4858 seeds are put forward Round 1: 347 peptides, 50 chains. Longest chain 20 peptides. Score 0.608 Round 2: 418 peptides, 28 chains. Longest chain 40 peptides. Score 0.864 Round 3: 440 peptides, 23 chains. Longest chain 60 peptides. Score 0.900 Round 4: 448 peptides, 19 chains. Longest chain 97 peptides. Score 0.918 Round 5: 457 peptides, 14 chains. Longest chain 81 peptides. Score 0.937 Taking the results from Round 5 Chains 14, Residues 443, Estimated correctness of the model 99.3 % 9 chains (398 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 116 A and 120 A Built loop between residues 175 A and 181 A Built loop between residues 64 B and 67 B Built loop between residues 195 B and 198 B 10 chains (455 residues) following loop building 5 chains (410 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4962 restraints for refining 4389 atoms. 1397 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2659 (Rfree = 0.000) for 4389 atoms. Found 100 (100 requested) and removed 64 (50 requested) atoms. Cycle 2: After refmac, R = 0.2434 (Rfree = 0.000) for 4408 atoms. Found 77 (99 requested) and removed 50 (50 requested) atoms. Cycle 3: After refmac, R = 0.2304 (Rfree = 0.000) for 4422 atoms. Found 69 (98 requested) and removed 51 (51 requested) atoms. Cycle 4: After refmac, R = 0.2230 (Rfree = 0.000) for 4432 atoms. Found 64 (96 requested) and removed 53 (51 requested) atoms. Cycle 5: After refmac, R = 0.2185 (Rfree = 0.000) for 4441 atoms. Found 55 (94 requested) and removed 55 (51 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.90 2.14 NCS extension: 33 residues added (211 deleted due to clashes), 4478 seeds are put forward Round 1: 476 peptides, 13 chains. Longest chain 95 peptides. Score 0.947 Round 2: 478 peptides, 10 chains. Longest chain 178 peptides. Score 0.955 Round 3: 484 peptides, 11 chains. Longest chain 101 peptides. Score 0.954 Round 4: 477 peptides, 14 chains. Longest chain 122 peptides. Score 0.945 Round 5: 478 peptides, 13 chains. Longest chain 178 peptides. Score 0.948 Taking the results from Round 2 Chains 11, Residues 468, Estimated correctness of the model 99.6 % 8 chains (449 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 54 A Built loop between residues 88 A and 94 A Built loop between residues 113 A and 117 A Built loop between residues 170 A and 173 A Built loop between residues 208 A and 211 A Built loop between residues 88 B and 95 B 5 chains (488 residues) following loop building 2 chains (469 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4486 restraints for refining 4484 atoms. 535 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2380 (Rfree = 0.000) for 4484 atoms. Found 93 (93 requested) and removed 62 (51 requested) atoms. Cycle 7: After refmac, R = 0.2185 (Rfree = 0.000) for 4506 atoms. Found 56 (91 requested) and removed 51 (51 requested) atoms. Cycle 8: After refmac, R = 0.2150 (Rfree = 0.000) for 4505 atoms. Found 51 (89 requested) and removed 51 (51 requested) atoms. Cycle 9: After refmac, R = 0.2080 (Rfree = 0.000) for 4501 atoms. Found 65 (87 requested) and removed 52 (51 requested) atoms. Cycle 10: After refmac, R = 0.2040 (Rfree = 0.000) for 4509 atoms. Found 61 (84 requested) and removed 51 (51 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.88 2.12 NCS extension: 78 residues added (417 deleted due to clashes), 4602 seeds are put forward Round 1: 483 peptides, 11 chains. Longest chain 157 peptides. Score 0.954 Round 2: 483 peptides, 7 chains. Longest chain 178 peptides. Score 0.963 Round 3: 480 peptides, 10 chains. Longest chain 142 peptides. Score 0.956 Round 4: 478 peptides, 12 chains. Longest chain 91 peptides. Score 0.950 Round 5: 481 peptides, 10 chains. Longest chain 153 peptides. Score 0.956 Taking the results from Round 2 Chains 7, Residues 476, Estimated correctness of the model 99.7 % 6 chains (472 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 95 A Built loop between residues 112 A and 116 A Built loop between residues 169 A and 172 A Built loop between residues 88 B and 95 B 3 chains (493 residues) following loop building 2 chains (489 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4425 restraints for refining 4533 atoms. 364 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2192 (Rfree = 0.000) for 4533 atoms. Found 83 (83 requested) and removed 61 (52 requested) atoms. Cycle 12: After refmac, R = 0.2065 (Rfree = 0.000) for 4555 atoms. Found 43 (81 requested) and removed 52 (52 requested) atoms. Cycle 13: After refmac, R = 0.2022 (Rfree = 0.000) for 4542 atoms. Found 45 (79 requested) and removed 53 (52 requested) atoms. Cycle 14: After refmac, R = 0.2019 (Rfree = 0.000) for 4531 atoms. Found 52 (77 requested) and removed 48 (52 requested) atoms. Cycle 15: After refmac, R = 0.2000 (Rfree = 0.000) for 4532 atoms. Found 54 (75 requested) and removed 50 (52 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.86 2.10 NCS extension: 66 residues added (689 deleted due to clashes), 4608 seeds are put forward Round 1: 483 peptides, 10 chains. Longest chain 178 peptides. Score 0.956 Round 2: 484 peptides, 10 chains. Longest chain 164 peptides. Score 0.957 Round 3: 482 peptides, 8 chains. Longest chain 131 peptides. Score 0.961 Round 4: 484 peptides, 8 chains. Longest chain 129 peptides. Score 0.961 Round 5: 483 peptides, 8 chains. Longest chain 172 peptides. Score 0.961 Taking the results from Round 5 Chains 8, Residues 475, Estimated correctness of the model 99.7 % 6 chains (468 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 75 A Built loop between residues 88 A and 95 A Built loop between residues 88 B and 95 B Built loop between residues 228 B and 231 B 4 chains (491 residues) following loop building 2 chains (484 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4421 restraints for refining 4533 atoms. 398 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2319 (Rfree = 0.000) for 4533 atoms. Found 73 (73 requested) and removed 64 (52 requested) atoms. Cycle 17: After refmac, R = 0.2097 (Rfree = 0.000) for 4539 atoms. Found 48 (71 requested) and removed 52 (52 requested) atoms. Cycle 18: After refmac, R = 0.2023 (Rfree = 0.000) for 4530 atoms. Found 42 (69 requested) and removed 48 (52 requested) atoms. Cycle 19: After refmac, R = 0.2005 (Rfree = 0.000) for 4520 atoms. Found 42 (67 requested) and removed 35 (52 requested) atoms. Cycle 20: After refmac, R = 0.1982 (Rfree = 0.000) for 4523 atoms. Found 45 (64 requested) and removed 37 (52 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.87 2.11 NCS extension: 36 residues added (449 deleted due to clashes), 4572 seeds are put forward Round 1: 475 peptides, 10 chains. Longest chain 173 peptides. Score 0.954 Round 2: 483 peptides, 8 chains. Longest chain 102 peptides. Score 0.961 Round 3: 476 peptides, 12 chains. Longest chain 129 peptides. Score 0.949 Round 4: 476 peptides, 13 chains. Longest chain 151 peptides. Score 0.947 Round 5: 472 peptides, 15 chains. Longest chain 108 peptides. Score 0.940 Taking the results from Round 2 Chains 9, Residues 475, Estimated correctness of the model 99.7 % 8 chains (474 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 54 A Built loop between residues 88 A and 95 A Built loop between residues 177 A and 180 A Built loop between residues 88 B and 96 B Built loop between residues 112 B and 116 B Built loop between residues 169 B and 172 B 2 chains (496 residues) following loop building 2 chains (496 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4328 restraints for refining 4573 atoms. 222 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2126 (Rfree = 0.000) for 4573 atoms. Found 63 (63 requested) and removed 64 (52 requested) atoms. Cycle 22: After refmac, R = 0.2010 (Rfree = 0.000) for 4569 atoms. Found 61 (61 requested) and removed 52 (52 requested) atoms. Cycle 23: After refmac, R = 0.1968 (Rfree = 0.000) for 4576 atoms. Found 42 (59 requested) and removed 52 (52 requested) atoms. Cycle 24: After refmac, R = 0.1955 (Rfree = 0.000) for 4565 atoms. Found 52 (57 requested) and removed 49 (52 requested) atoms. Cycle 25: After refmac, R = 0.1963 (Rfree = 0.000) for 4563 atoms. Found 55 (55 requested) and removed 44 (52 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.89 2.13 NCS extension: 18 residues added (303 deleted due to clashes), 4598 seeds are put forward Round 1: 478 peptides, 7 chains. Longest chain 99 peptides. Score 0.962 Round 2: 481 peptides, 8 chains. Longest chain 176 peptides. Score 0.961 Round 3: 473 peptides, 11 chains. Longest chain 99 peptides. Score 0.951 Round 4: 474 peptides, 12 chains. Longest chain 155 peptides. Score 0.949 Round 5: 472 peptides, 12 chains. Longest chain 144 peptides. Score 0.948 Taking the results from Round 1 Chains 8, Residues 471, Estimated correctness of the model 99.7 % 7 chains (470 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 55 A Built loop between residues 88 A and 95 A Built loop between residues 177 A and 180 A Built loop between residues 87 B and 95 B Built loop between residues 169 B and 172 B 2 chains (493 residues) following loop building 2 chains (493 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4365 restraints for refining 4572 atoms. 283 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2104 (Rfree = 0.000) for 4572 atoms. Found 52 (52 requested) and removed 60 (52 requested) atoms. Cycle 27: After refmac, R = 0.1998 (Rfree = 0.000) for 4559 atoms. Found 50 (52 requested) and removed 52 (52 requested) atoms. Cycle 28: After refmac, R = 0.1965 (Rfree = 0.000) for 4556 atoms. Found 48 (52 requested) and removed 52 (52 requested) atoms. Cycle 29: After refmac, R = 0.1954 (Rfree = 0.000) for 4550 atoms. Found 52 (52 requested) and removed 43 (52 requested) atoms. Cycle 30: After refmac, R = 0.1948 (Rfree = 0.000) for 4557 atoms. Found 52 (52 requested) and removed 44 (52 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.87 2.11 NCS extension: 24 residues added (489 deleted due to clashes), 4596 seeds are put forward Round 1: 479 peptides, 10 chains. Longest chain 156 peptides. Score 0.955 Round 2: 478 peptides, 11 chains. Longest chain 91 peptides. Score 0.953 Round 3: 466 peptides, 14 chains. Longest chain 75 peptides. Score 0.941 Round 4: 471 peptides, 13 chains. Longest chain 107 peptides. Score 0.945 Round 5: 472 peptides, 9 chains. Longest chain 134 peptides. Score 0.956 Taking the results from Round 5 Chains 9, Residues 463, Estimated correctness of the model 99.6 % 7 chains (451 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 95 A Built loop between residues 112 A and 115 A Built loop between residues 177 A and 180 A Built loop between residues 88 B and 95 B Built loop between residues 227 B and 230 B 4 chains (481 residues) following loop building 2 chains (469 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4565 restraints for refining 4551 atoms. 643 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2183 (Rfree = 0.000) for 4551 atoms. Found 52 (52 requested) and removed 59 (52 requested) atoms. Cycle 32: After refmac, R = 0.2057 (Rfree = 0.000) for 4543 atoms. Found 52 (52 requested) and removed 52 (52 requested) atoms. Cycle 33: After refmac, R = 0.1993 (Rfree = 0.000) for 4538 atoms. Found 52 (52 requested) and removed 45 (52 requested) atoms. Cycle 34: After refmac, R = 0.1968 (Rfree = 0.000) for 4542 atoms. Found 50 (52 requested) and removed 35 (52 requested) atoms. Cycle 35: After refmac, R = 0.1947 (Rfree = 0.000) for 4554 atoms. Found 44 (52 requested) and removed 26 (52 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.87 2.11 NCS extension: 17 residues added (297 deleted due to clashes), 4592 seeds are put forward Round 1: 476 peptides, 14 chains. Longest chain 157 peptides. Score 0.944 Round 2: 483 peptides, 9 chains. Longest chain 176 peptides. Score 0.959 Round 3: 475 peptides, 14 chains. Longest chain 91 peptides. Score 0.944 Round 4: 483 peptides, 12 chains. Longest chain 178 peptides. Score 0.952 Round 5: 476 peptides, 15 chains. Longest chain 82 peptides. Score 0.942 Taking the results from Round 2 Chains 9, Residues 474, Estimated correctness of the model 99.7 % 6 chains (463 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 95 A Built loop between residues 112 A and 115 A Built loop between residues 175 A and 179 A Built loop between residues 87 B and 95 B 3 chains (487 residues) following loop building 2 chains (482 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4487 restraints for refining 4562 atoms. 480 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2141 (Rfree = 0.000) for 4562 atoms. Found 52 (52 requested) and removed 61 (52 requested) atoms. Cycle 37: After refmac, R = 0.2047 (Rfree = 0.000) for 4549 atoms. Found 52 (52 requested) and removed 52 (52 requested) atoms. Cycle 38: After refmac, R = 0.2030 (Rfree = 0.000) for 4546 atoms. Found 52 (52 requested) and removed 45 (52 requested) atoms. Cycle 39: After refmac, R = 0.1969 (Rfree = 0.000) for 4549 atoms. Found 52 (52 requested) and removed 40 (52 requested) atoms. Cycle 40: After refmac, R = 0.1958 (Rfree = 0.000) for 4558 atoms. Found 52 (52 requested) and removed 35 (52 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.88 2.12 NCS extension: 51 residues added (296 deleted due to clashes), 4634 seeds are put forward Round 1: 477 peptides, 11 chains. Longest chain 164 peptides. Score 0.952 Round 2: 484 peptides, 9 chains. Longest chain 101 peptides. Score 0.959 Round 3: 468 peptides, 14 chains. Longest chain 109 peptides. Score 0.942 Round 4: 474 peptides, 12 chains. Longest chain 122 peptides. Score 0.949 Round 5: 466 peptides, 14 chains. Longest chain 164 peptides. Score 0.941 Taking the results from Round 2 Chains 9, Residues 475, Estimated correctness of the model 99.7 % 7 chains (469 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 51 A Built loop between residues 87 A and 95 A Built loop between residues 177 A and 180 A Built loop between residues 86 B and 95 B Built loop between residues 167 B and 170 B 2 chains (490 residues) following loop building 2 chains (490 residues) in sequence following loop building ------------------------------------------------------ 22067 reflections ( 99.75 % complete ) and 4395 restraints for refining 4571 atoms. 336 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2166 (Rfree = 0.000) for 4571 atoms. Found 52 (52 requested) and removed 64 (52 requested) atoms. Cycle 42: After refmac, R = 0.2074 (Rfree = 0.000) for 4556 atoms. Found 52 (52 requested) and removed 52 (52 requested) atoms. Cycle 43: After refmac, R = 0.2021 (Rfree = 0.000) for 4555 atoms. Found 50 (52 requested) and removed 52 (52 requested) atoms. Cycle 44: After refmac, R = 0.2013 (Rfree = 0.000) for 4549 atoms. Found 51 (52 requested) and removed 27 (52 requested) atoms. Cycle 45: After refmac, R = 0.1980 (Rfree = 0.000) for 4569 atoms. Found 41 (52 requested) and removed 28 (52 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.87 2.11 NCS extension: 2 residues added (70 deleted due to clashes), 4592 seeds are put forward Round 1: 472 peptides, 10 chains. Longest chain 99 peptides. Score 0.953 Round 2: 472 peptides, 11 chains. Longest chain 157 peptides. Score 0.951 Round 3: 459 peptides, 13 chains. Longest chain 79 peptides. Score 0.941 Round 4: 466 peptides, 13 chains. Longest chain 104 peptides. Score 0.943 Round 5: 466 peptides, 10 chains. Longest chain 102 peptides. Score 0.951 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 462, Estimated correctness of the model 99.6 % 9 chains (456 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 49 A and 55 A Built loop between residues 88 A and 95 A Built loop between residues 178 A and 181 A Built loop between residues 222 A and 225 A Built loop between residues 257 A and 260 A Built loop between residues 88 B and 95 B Built loop between residues 169 B and 172 B 3 chains (487 residues) following loop building 2 chains (481 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22067 reflections ( 99.75 % complete ) and 4001 restraints for refining 3922 atoms. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2835 (Rfree = 0.000) for 3922 atoms. Found 36 (45 requested) and removed 0 (45 requested) atoms. Cycle 47: After refmac, R = 0.2677 (Rfree = 0.000) for 3922 atoms. Found 13 (45 requested) and removed 4 (45 requested) atoms. Cycle 48: After refmac, R = 0.2632 (Rfree = 0.000) for 3922 atoms. Found 7 (45 requested) and removed 3 (45 requested) atoms. Cycle 49: After refmac, R = 0.2609 (Rfree = 0.000) for 3922 atoms. Found 5 (45 requested) and removed 5 (45 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:34:36 GMT 2018 Job finished. TimeTaking 66.45 Used memory is bytes: 14274512