Sun 23 Dec 22:23:10 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 1vkb-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-1.9-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/1vkb-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-1.9-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 ============================================================ Sun 23 Dec 22:23:20 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/1vkb-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-1.9-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 187 and 0 Target number of residues in the AU: 187 Target solvent content: 0.4437 Checking the provided sequence file Detected sequence length: 161 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 161 Adjusted target solvent content: 0.52 Input MTZ file: 1vkb-1.9-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: 170 Cell parameters: 85.745 85.745 42.858 90.000 90.000 120.000 Input sequence file: 1vkb-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 1288 target number of atoms Had to go as low as 0.50 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 Loops will be built when appropriate and at the last cycle Resolution range: 74.257 1.901 Wilson plot Bfac: 13.53 14345 reflections ( 99.99 % complete ) and 0 restraints for refining 1436 atoms. Observations/parameters ratio is 2.50 ------------------------------------------------------ Starting model: R = 0.3448 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2956 (Rfree = 0.000) for 1436 atoms. Found 56 (56 requested) and removed 54 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.72 1.67 Round 1: 130 peptides, 7 chains. Longest chain 37 peptides. Score 0.855 Round 2: 142 peptides, 2 chains. Longest chain 102 peptides. Score 0.937 Round 3: 139 peptides, 5 chains. Longest chain 65 peptides. Score 0.901 Round 4: 143 peptides, 2 chains. Longest chain 103 peptides. Score 0.938 Round 5: 142 peptides, 3 chains. Longest chain 66 peptides. Score 0.927 Taking the results from Round 4 Chains 2, Residues 141, Estimated correctness of the model 99.6 % 2 chains (141 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 120 A 1 chains (147 residues) following loop building 1 chains (147 residues) in sequence following loop building ------------------------------------------------------ 14345 reflections ( 99.99 % complete ) and 1417 restraints for refining 1400 atoms. 191 conditional restraints added. Observations/parameters ratio is 2.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3133 (Rfree = 0.000) for 1400 atoms. Found 55 (55 requested) and removed 30 (27 requested) atoms. Cycle 2: After refmac, R = 0.2748 (Rfree = 0.000) for 1419 atoms. Found 55 (55 requested) and removed 30 (28 requested) atoms. Cycle 3: After refmac, R = 0.2494 (Rfree = 0.000) for 1431 atoms. Found 46 (55 requested) and removed 22 (28 requested) atoms. Cycle 4: After refmac, R = 0.2287 (Rfree = 0.000) for 1443 atoms. Found 47 (55 requested) and removed 16 (28 requested) atoms. Cycle 5: After refmac, R = 0.2162 (Rfree = 0.000) for 1467 atoms. Found 55 (56 requested) and removed 23 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.67 1.63 Round 1: 140 peptides, 3 chains. Longest chain 86 peptides. Score 0.924 Round 2: 139 peptides, 5 chains. Longest chain 57 peptides. Score 0.901 Round 3: 143 peptides, 3 chains. Longest chain 86 peptides. Score 0.929 Round 4: 143 peptides, 4 chains. Longest chain 66 peptides. Score 0.918 Round 5: 142 peptides, 3 chains. Longest chain 86 peptides. Score 0.927 Taking the results from Round 3 Chains 5, Residues 140, Estimated correctness of the model 99.5 % 3 chains (136 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 96 A and 99 A Built loop between residues 112 A and 121 A 2 chains (148 residues) following loop building 1 chains (146 residues) in sequence following loop building ------------------------------------------------------ 14345 reflections ( 99.99 % complete ) and 1392 restraints for refining 1409 atoms. 170 conditional restraints added. Observations/parameters ratio is 2.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2122 (Rfree = 0.000) for 1409 atoms. Found 53 (53 requested) and removed 28 (27 requested) atoms. Cycle 7: After refmac, R = 0.1952 (Rfree = 0.000) for 1431 atoms. Found 52 (53 requested) and removed 28 (28 requested) atoms. Cycle 8: After refmac, R = 0.1825 (Rfree = 0.000) for 1453 atoms. Found 42 (52 requested) and removed 22 (28 requested) atoms. Cycle 9: After refmac, R = 0.1748 (Rfree = 0.000) for 1469 atoms. Found 46 (52 requested) and removed 25 (29 requested) atoms. Cycle 10: After refmac, R = 0.1718 (Rfree = 0.000) for 1487 atoms. Found 50 (51 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.69 1.65 Round 1: 143 peptides, 3 chains. Longest chain 86 peptides. Score 0.929 Round 2: 140 peptides, 4 chains. Longest chain 77 peptides. Score 0.914 Round 3: 143 peptides, 4 chains. Longest chain 66 peptides. Score 0.918 Round 4: 144 peptides, 3 chains. Longest chain 86 peptides. Score 0.930 Round 5: 143 peptides, 4 chains. Longest chain 66 peptides. Score 0.918 Taking the results from Round 4 Chains 4, Residues 141, Estimated correctness of the model 99.5 % 3 chains (139 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 96 A and 99 A Built loop between residues 112 A and 120 A 1 chains (148 residues) following loop building 1 chains (148 residues) in sequence following loop building ------------------------------------------------------ 14345 reflections ( 99.99 % complete ) and 1407 restraints for refining 1417 atoms. 172 conditional restraints added. Observations/parameters ratio is 2.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1924 (Rfree = 0.000) for 1417 atoms. Found 48 (48 requested) and removed 28 (28 requested) atoms. Cycle 12: After refmac, R = 0.1768 (Rfree = 0.000) for 1436 atoms. Found 47 (47 requested) and removed 14 (28 requested) atoms. Cycle 13: After refmac, R = 0.1688 (Rfree = 0.000) for 1466 atoms. Found 44 (49 requested) and removed 29 (29 requested) atoms. Cycle 14: After refmac, R = 0.1668 (Rfree = 0.000) for 1480 atoms. Found 48 (48 requested) and removed 24 (29 requested) atoms. Cycle 15: After refmac, R = 0.1645 (Rfree = 0.000) for 1501 atoms. Found 37 (48 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.70 1.66 Round 1: 145 peptides, 3 chains. Longest chain 86 peptides. Score 0.931 Round 2: 141 peptides, 3 chains. Longest chain 86 peptides. Score 0.926 Round 3: 144 peptides, 4 chains. Longest chain 66 peptides. Score 0.920 Round 4: 141 peptides, 3 chains. Longest chain 86 peptides. Score 0.926 Round 5: 144 peptides, 4 chains. Longest chain 66 peptides. Score 0.920 Taking the results from Round 1 Chains 4, Residues 142, Estimated correctness of the model 99.5 % 3 chains (141 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 99 A Built loop between residues 112 A and 118 A 1 chains (149 residues) following loop building 1 chains (149 residues) in sequence following loop building ------------------------------------------------------ 14345 reflections ( 99.99 % complete ) and 1362 restraints for refining 1419 atoms. 119 conditional restraints added. Observations/parameters ratio is 2.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1834 (Rfree = 0.000) for 1419 atoms. Found 45 (45 requested) and removed 27 (28 requested) atoms. Cycle 17: After refmac, R = 0.1691 (Rfree = 0.000) for 1437 atoms. Found 44 (44 requested) and removed 15 (28 requested) atoms. Cycle 18: After refmac, R = 0.1641 (Rfree = 0.000) for 1466 atoms. Found 39 (45 requested) and removed 19 (29 requested) atoms. Cycle 19: After refmac, R = 0.1586 (Rfree = 0.000) for 1484 atoms. Found 41 (45 requested) and removed 25 (29 requested) atoms. Cycle 20: After refmac, R = 0.1605 (Rfree = 0.000) for 1499 atoms. Found 43 (45 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.69 1.65 Round 1: 145 peptides, 3 chains. Longest chain 86 peptides. Score 0.931 Round 2: 145 peptides, 3 chains. Longest chain 86 peptides. Score 0.931 Round 3: 141 peptides, 3 chains. Longest chain 86 peptides. Score 0.926 Round 4: 144 peptides, 4 chains. Longest chain 66 peptides. Score 0.920 Round 5: 145 peptides, 3 chains. Longest chain 86 peptides. Score 0.931 Taking the results from Round 5 Chains 6, Residues 142, Estimated correctness of the model 99.5 % 3 chains (138 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 99 A Built loop between residues 112 A and 120 A 2 chains (149 residues) following loop building 1 chains (148 residues) in sequence following loop building ------------------------------------------------------ 14345 reflections ( 99.99 % complete ) and 1383 restraints for refining 1428 atoms. 145 conditional restraints added. Observations/parameters ratio is 2.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1815 (Rfree = 0.000) for 1428 atoms. Found 41 (41 requested) and removed 29 (28 requested) atoms. Cycle 22: After refmac, R = 0.1657 (Rfree = 0.000) for 1439 atoms. Found 41 (41 requested) and removed 15 (28 requested) atoms. Cycle 23: After refmac, R = 0.1610 (Rfree = 0.000) for 1465 atoms. Found 40 (42 requested) and removed 19 (29 requested) atoms. Cycle 24: After refmac, R = 0.1604 (Rfree = 0.000) for 1483 atoms. Found 36 (42 requested) and removed 25 (29 requested) atoms. Cycle 25: After refmac, R = 0.1562 (Rfree = 0.000) for 1492 atoms. Found 41 (41 requested) and removed 23 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.71 1.67 Round 1: 146 peptides, 3 chains. Longest chain 86 peptides. Score 0.933 Round 2: 146 peptides, 3 chains. Longest chain 86 peptides. Score 0.933 Round 3: 141 peptides, 4 chains. Longest chain 66 peptides. Score 0.915 Round 4: 146 peptides, 3 chains. Longest chain 86 peptides. Score 0.933 Round 5: 146 peptides, 4 chains. Longest chain 66 peptides. Score 0.923 Taking the results from Round 4 Chains 5, Residues 143, Estimated correctness of the model 99.6 % 3 chains (140 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 96 A and 99 A Built loop between residues 113 A and 120 A 2 chains (149 residues) following loop building 1 chains (148 residues) in sequence following loop building ------------------------------------------------------ 14345 reflections ( 99.99 % complete ) and 1379 restraints for refining 1424 atoms. 141 conditional restraints added. Observations/parameters ratio is 2.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1818 (Rfree = 0.000) for 1424 atoms. Found 38 (38 requested) and removed 28 (28 requested) atoms. Cycle 27: After refmac, R = 0.1668 (Rfree = 0.000) for 1434 atoms. Found 37 (37 requested) and removed 8 (28 requested) atoms. Cycle 28: After refmac, R = 0.1615 (Rfree = 0.000) for 1462 atoms. Found 38 (38 requested) and removed 22 (28 requested) atoms. Cycle 29: After refmac, R = 0.1613 (Rfree = 0.000) for 1477 atoms. Found 37 (37 requested) and removed 31 (29 requested) atoms. Cycle 30: After refmac, R = 0.1558 (Rfree = 0.000) for 1479 atoms. Found 36 (36 requested) and removed 24 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.69 1.65 Round 1: 145 peptides, 3 chains. Longest chain 85 peptides. Score 0.931 Round 2: 145 peptides, 3 chains. Longest chain 85 peptides. Score 0.931 Round 3: 141 peptides, 4 chains. Longest chain 66 peptides. Score 0.915 Round 4: 145 peptides, 3 chains. Longest chain 86 peptides. Score 0.931 Round 5: 144 peptides, 4 chains. Longest chain 76 peptides. Score 0.920 Taking the results from Round 4 Chains 6, Residues 142, Estimated correctness of the model 99.5 % 3 chains (138 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 96 A and 100 A Built loop between residues 112 A and 120 A 2 chains (149 residues) following loop building 1 chains (148 residues) in sequence following loop building ------------------------------------------------------ 14345 reflections ( 99.99 % complete ) and 1389 restraints for refining 1436 atoms. 151 conditional restraints added. Observations/parameters ratio is 2.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1839 (Rfree = 0.000) for 1436 atoms. Found 34 (34 requested) and removed 30 (28 requested) atoms. Cycle 32: After refmac, R = 0.1651 (Rfree = 0.000) for 1437 atoms. Found 33 (33 requested) and removed 18 (28 requested) atoms. Cycle 33: After refmac, R = 0.1578 (Rfree = 0.000) for 1451 atoms. Found 32 (32 requested) and removed 13 (28 requested) atoms. Cycle 34: After refmac, R = 0.1544 (Rfree = 0.000) for 1468 atoms. Found 28 (32 requested) and removed 25 (29 requested) atoms. Cycle 35: After refmac, R = 0.1533 (Rfree = 0.000) for 1469 atoms. Found 31 (31 requested) and removed 24 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.70 1.66 Round 1: 145 peptides, 3 chains. Longest chain 86 peptides. Score 0.931 Round 2: 144 peptides, 4 chains. Longest chain 77 peptides. Score 0.920 Round 3: 141 peptides, 3 chains. Longest chain 86 peptides. Score 0.926 Round 4: 145 peptides, 3 chains. Longest chain 86 peptides. Score 0.931 Round 5: 145 peptides, 3 chains. Longest chain 86 peptides. Score 0.931 Taking the results from Round 5 Chains 5, Residues 142, Estimated correctness of the model 99.5 % 3 chains (139 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 96 A and 99 A Built loop between residues 112 A and 120 A 2 chains (149 residues) following loop building 1 chains (148 residues) in sequence following loop building ------------------------------------------------------ 14345 reflections ( 99.99 % complete ) and 1365 restraints for refining 1411 atoms. 127 conditional restraints added. Observations/parameters ratio is 2.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1804 (Rfree = 0.000) for 1411 atoms. Found 29 (29 requested) and removed 27 (27 requested) atoms. Cycle 37: After refmac, R = 0.1650 (Rfree = 0.000) for 1412 atoms. Found 27 (27 requested) and removed 13 (27 requested) atoms. Cycle 38: After refmac, R = 0.1576 (Rfree = 0.000) for 1424 atoms. Found 28 (28 requested) and removed 10 (28 requested) atoms. Cycle 39: After refmac, R = 0.1522 (Rfree = 0.000) for 1440 atoms. Found 28 (28 requested) and removed 15 (28 requested) atoms. Cycle 40: After refmac, R = 0.1519 (Rfree = 0.000) for 1452 atoms. Found 27 (28 requested) and removed 14 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.70 1.66 Round 1: 146 peptides, 3 chains. Longest chain 86 peptides. Score 0.933 Round 2: 146 peptides, 3 chains. Longest chain 86 peptides. Score 0.933 Round 3: 145 peptides, 4 chains. Longest chain 66 peptides. Score 0.921 Round 4: 141 peptides, 3 chains. Longest chain 86 peptides. Score 0.926 Round 5: 143 peptides, 4 chains. Longest chain 66 peptides. Score 0.918 Taking the results from Round 2 Chains 4, Residues 143, Estimated correctness of the model 99.6 % 3 chains (142 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 99 A Built loop between residues 113 A and 118 A 1 chains (149 residues) following loop building 1 chains (149 residues) in sequence following loop building ------------------------------------------------------ 14345 reflections ( 99.99 % complete ) and 1370 restraints for refining 1420 atoms. 127 conditional restraints added. Observations/parameters ratio is 2.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1787 (Rfree = 0.000) for 1420 atoms. Found 28 (28 requested) and removed 28 (28 requested) atoms. Cycle 42: After refmac, R = 0.1645 (Rfree = 0.000) for 1419 atoms. Found 28 (28 requested) and removed 11 (28 requested) atoms. Cycle 43: After refmac, R = 0.1596 (Rfree = 0.000) for 1436 atoms. Found 28 (28 requested) and removed 11 (28 requested) atoms. Cycle 44: After refmac, R = 0.1581 (Rfree = 0.000) for 1453 atoms. Found 21 (28 requested) and removed 17 (28 requested) atoms. Cycle 45: After refmac, R = 0.1538 (Rfree = 0.000) for 1455 atoms. Found 28 (28 requested) and removed 8 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.71 1.67 Round 1: 144 peptides, 3 chains. Longest chain 86 peptides. Score 0.930 Round 2: 144 peptides, 3 chains. Longest chain 86 peptides. Score 0.930 Round 3: 139 peptides, 5 chains. Longest chain 57 peptides. Score 0.901 Round 4: 144 peptides, 3 chains. Longest chain 86 peptides. Score 0.930 Round 5: 143 peptides, 4 chains. Longest chain 66 peptides. Score 0.918 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 141, Estimated correctness of the model 99.5 % 3 chains (139 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 96 A and 99 A Built loop between residues 112 A and 121 A 1 chains (149 residues) following loop building 1 chains (149 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14345 reflections ( 99.99 % complete ) and 1243 restraints for refining 1203 atoms. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2477 (Rfree = 0.000) for 1203 atoms. Found 23 (23 requested) and removed 0 (23 requested) atoms. Cycle 47: After refmac, R = 0.2160 (Rfree = 0.000) for 1203 atoms. Found 24 (24 requested) and removed 0 (24 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2012 (Rfree = 0.000) for 1203 atoms. Found 24 (24 requested) and removed 0 (24 requested) atoms. Cycle 49: After refmac, R = 0.1858 (Rfree = 0.000) for 1203 atoms. TimeTaking 42.72