Sun 23 Dec 22:22:43 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 1vkz-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:53 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/1vkz-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 721 and 0 Target number of residues in the AU: 721 Target solvent content: 0.5393 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 6592 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 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: 19.959 3.200 Wilson plot Bfac: 32.54 13478 reflections ( 96.64 % complete ) and 0 restraints for refining 7293 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.2896 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2608 (Rfree = 0.000) for 7293 atoms. Found 65 (65 requested) and removed 65 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.69 2.80 Search for helices and strands: 0 residues in 0 chains, 7408 seeds are put forward NCS extension: 0 residues added, 7408 seeds are put forward Round 1: 352 peptides, 66 chains. Longest chain 18 peptides. Score 0.355 Round 2: 469 peptides, 73 chains. Longest chain 19 peptides. Score 0.510 Round 3: 490 peptides, 66 chains. Longest chain 24 peptides. Score 0.589 Round 4: 514 peptides, 69 chains. Longest chain 23 peptides. Score 0.604 Round 5: 532 peptides, 63 chains. Longest chain 25 peptides. Score 0.662 Taking the results from Round 5 Chains 67, Residues 469, Estimated correctness of the model 56.7 % 12 chains (132 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11521 restraints for refining 6013 atoms. 9206 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2495 (Rfree = 0.000) for 6013 atoms. Found 54 (54 requested) and removed 77 (27 requested) atoms. Cycle 2: After refmac, R = 0.2308 (Rfree = 0.000) for 5868 atoms. Found 42 (53 requested) and removed 39 (26 requested) atoms. Cycle 3: After refmac, R = 0.2215 (Rfree = 0.000) for 5826 atoms. Found 16 (52 requested) and removed 34 (26 requested) atoms. Cycle 4: After refmac, R = 0.2208 (Rfree = 0.000) for 5775 atoms. Found 26 (52 requested) and removed 32 (26 requested) atoms. Cycle 5: After refmac, R = 0.2112 (Rfree = 0.000) for 5749 atoms. Found 29 (51 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.67 2.78 Search for helices and strands: 0 residues in 0 chains, 5901 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 5929 seeds are put forward Round 1: 474 peptides, 68 chains. Longest chain 21 peptides. Score 0.552 Round 2: 541 peptides, 66 chains. Longest chain 28 peptides. Score 0.656 Round 3: 559 peptides, 71 chains. Longest chain 25 peptides. Score 0.651 Round 4: 549 peptides, 64 chains. Longest chain 40 peptides. Score 0.676 Round 5: 524 peptides, 59 chains. Longest chain 27 peptides. Score 0.674 Taking the results from Round 4 Chains 68, Residues 485, Estimated correctness of the model 59.9 % 9 chains (107 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11874 restraints for refining 5988 atoms. 9599 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2535 (Rfree = 0.000) for 5988 atoms. Found 53 (53 requested) and removed 61 (26 requested) atoms. Cycle 7: After refmac, R = 0.2349 (Rfree = 0.000) for 5936 atoms. Found 25 (53 requested) and removed 36 (26 requested) atoms. Cycle 8: After refmac, R = 0.2254 (Rfree = 0.000) for 5891 atoms. Found 34 (53 requested) and removed 35 (26 requested) atoms. Cycle 9: After refmac, R = 0.2163 (Rfree = 0.000) for 5864 atoms. Found 20 (52 requested) and removed 37 (26 requested) atoms. Cycle 10: After refmac, R = 0.2095 (Rfree = 0.000) for 5830 atoms. Found 20 (52 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.67 2.78 Search for helices and strands: 0 residues in 0 chains, 5962 seeds are put forward NCS extension: 18 residues added (19 deleted due to clashes), 5980 seeds are put forward Round 1: 511 peptides, 71 chains. Longest chain 30 peptides. Score 0.587 Round 2: 557 peptides, 60 chains. Longest chain 29 peptides. Score 0.706 Round 3: 557 peptides, 67 chains. Longest chain 26 peptides. Score 0.670 Round 4: 565 peptides, 62 chains. Longest chain 32 peptides. Score 0.705 Round 5: 572 peptides, 65 chains. Longest chain 22 peptides. Score 0.697 Taking the results from Round 2 Chains 65, Residues 497, Estimated correctness of the model 66.4 % 13 chains (146 residues) have been docked in sequence Building loops using Loopy2018 65 chains (497 residues) following loop building 13 chains (146 residues) in sequence following loop building ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11439 restraints for refining 6017 atoms. 8939 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2394 (Rfree = 0.000) for 6017 atoms. Found 53 (54 requested) and removed 62 (27 requested) atoms. Cycle 12: After refmac, R = 0.2268 (Rfree = 0.000) for 5975 atoms. Found 19 (52 requested) and removed 31 (26 requested) atoms. Cycle 13: After refmac, R = 0.2182 (Rfree = 0.000) for 5937 atoms. Found 27 (51 requested) and removed 35 (26 requested) atoms. Cycle 14: After refmac, R = 0.2089 (Rfree = 0.000) for 5912 atoms. Found 23 (50 requested) and removed 30 (26 requested) atoms. Cycle 15: After refmac, R = 0.2016 (Rfree = 0.000) for 5888 atoms. Found 18 (48 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.65 2.76 Search for helices and strands: 0 residues in 0 chains, 6003 seeds are put forward NCS extension: 14 residues added (28 deleted due to clashes), 6017 seeds are put forward Round 1: 487 peptides, 68 chains. Longest chain 35 peptides. Score 0.572 Round 2: 551 peptides, 66 chains. Longest chain 29 peptides. Score 0.668 Round 3: 573 peptides, 63 chains. Longest chain 27 peptides. Score 0.708 Round 4: 558 peptides, 63 chains. Longest chain 32 peptides. Score 0.692 Round 5: 564 peptides, 66 chains. Longest chain 25 peptides. Score 0.683 Taking the results from Round 3 Chains 68, Residues 510, Estimated correctness of the model 66.9 % 12 chains (142 residues) have been docked in sequence Building loops using Loopy2018 68 chains (510 residues) following loop building 12 chains (142 residues) in sequence following loop building ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11511 restraints for refining 6018 atoms. 9000 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2383 (Rfree = 0.000) for 6018 atoms. Found 49 (49 requested) and removed 56 (27 requested) atoms. Cycle 17: After refmac, R = 0.2170 (Rfree = 0.000) for 5984 atoms. Found 25 (47 requested) and removed 36 (26 requested) atoms. Cycle 18: After refmac, R = 0.2127 (Rfree = 0.000) for 5953 atoms. Found 27 (46 requested) and removed 38 (26 requested) atoms. Cycle 19: After refmac, R = 0.2112 (Rfree = 0.000) for 5928 atoms. Found 27 (45 requested) and removed 35 (26 requested) atoms. Cycle 20: After refmac, R = 0.2046 (Rfree = 0.000) for 5904 atoms. Found 20 (43 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.69 2.80 Search for helices and strands: 0 residues in 0 chains, 6010 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 6042 seeds are put forward Round 1: 489 peptides, 65 chains. Longest chain 28 peptides. Score 0.594 Round 2: 537 peptides, 58 chains. Longest chain 40 peptides. Score 0.694 Round 3: 549 peptides, 59 chains. Longest chain 40 peptides. Score 0.702 Round 4: 529 peptides, 64 chains. Longest chain 31 peptides. Score 0.653 Round 5: 541 peptides, 58 chains. Longest chain 42 peptides. Score 0.699 Taking the results from Round 3 Chains 62, Residues 490, Estimated correctness of the model 65.6 % 8 chains (107 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 276 A and 279 A 61 chains (492 residues) following loop building 7 chains (109 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 13478 reflections ( 96.64 % complete ) and 11764 restraints for refining 6012 atoms. 9456 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2313 (Rfree = 0.000) for 6012 atoms. Found 43 (43 requested) and removed 51 (27 requested) atoms. Cycle 22: After refmac, R = 0.2199 (Rfree = 0.000) for 5967 atoms. Found 26 (41 requested) and removed 37 (26 requested) atoms. Cycle 23: After refmac, R = 0.2137 (Rfree = 0.000) for 5935 atoms. Found 31 (40 requested) and removed 35 (26 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2115 (Rfree = 0.000) for 5918 atoms. Found 28 (39 requested) and removed 28 (26 requested) atoms. Cycle 25: After refmac, R = 0.2046 (Rfree = 0.000) for 5908 atoms. Found 15 (38 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.69 2.80 Search for helices and strands: 0 residues in 0 chains, 6038 seeds are put forward NCS extension: 43 residues added (12 deleted due to clashes), 6081 seeds are put forward Round 1: 478 peptides, 68 chains. Longest chain 23 peptides. Score 0.558 Round 2: 540 peptides, 62 chains. Longest chain 30 peptides. Score 0.677 Round 3: 493 peptides, 65 chains. Longest chain 21 peptides. Score 0.599 Round 4: 496 peptides, 58 chains. Longest chain 35 peptides. Score 0.645 Round 5: 504 peptides, 56 chains. Longest chain 28 peptides. Score 0.667 Taking the results from Round 2 Chains 67, Residues 478, Estimated correctness of the model 60.1 % 10 chains (115 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 11793 restraints for refining 6018 atoms. 9529 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2302 (Rfree = 0.000) for 6018 atoms. Found 38 (38 requested) and removed 56 (27 requested) atoms. Cycle 27: After refmac, R = 0.2171 (Rfree = 0.000) for 5979 atoms. Found 23 (37 requested) and removed 32 (26 requested) atoms. Cycle 28: After refmac, R = 0.2087 (Rfree = 0.000) for 5950 atoms. Found 20 (37 requested) and removed 36 (26 requested) atoms. Cycle 29: After refmac, R = 0.2051 (Rfree = 0.000) for 5921 atoms. Found 21 (37 requested) and removed 30 (26 requested) atoms. Cycle 30: After refmac, R = 0.2009 (Rfree = 0.000) for 5906 atoms. Found 14 (37 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.67 2.78 Search for helices and strands: 0 residues in 0 chains, 6027 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 6055 seeds are put forward Round 1: 478 peptides, 71 chains. Longest chain 21 peptides. Score 0.538 Round 2: 491 peptides, 59 chains. Longest chain 25 peptides. Score 0.633 Round 3: 505 peptides, 65 chains. Longest chain 29 peptides. Score 0.616 Round 4: 526 peptides, 64 chains. Longest chain 34 peptides. Score 0.649 Round 5: 526 peptides, 69 chains. Longest chain 23 peptides. Score 0.620 Taking the results from Round 4 Chains 67, Residues 462, Estimated correctness of the model 53.6 % 5 chains (80 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12238 restraints for refining 6016 atoms. 10155 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2216 (Rfree = 0.000) for 6016 atoms. Found 37 (38 requested) and removed 48 (27 requested) atoms. Cycle 32: After refmac, R = 0.2089 (Rfree = 0.000) for 5988 atoms. Found 24 (37 requested) and removed 36 (26 requested) atoms. Cycle 33: After refmac, R = 0.2039 (Rfree = 0.000) for 5968 atoms. Found 28 (37 requested) and removed 28 (26 requested) atoms. Cycle 34: After refmac, R = 0.1976 (Rfree = 0.000) for 5957 atoms. Found 19 (37 requested) and removed 31 (26 requested) atoms. Cycle 35: After refmac, R = 0.1943 (Rfree = 0.000) for 5938 atoms. Found 11 (37 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.70 2.81 Search for helices and strands: 0 residues in 0 chains, 6044 seeds are put forward NCS extension: 36 residues added (16 deleted due to clashes), 6080 seeds are put forward Round 1: 451 peptides, 69 chains. Longest chain 23 peptides. Score 0.509 Round 2: 514 peptides, 64 chains. Longest chain 27 peptides. Score 0.634 Round 3: 526 peptides, 67 chains. Longest chain 31 peptides. Score 0.632 Round 4: 525 peptides, 60 chains. Longest chain 38 peptides. Score 0.670 Round 5: 504 peptides, 62 chains. Longest chain 26 peptides. Score 0.632 Taking the results from Round 4 Chains 60, Residues 465, Estimated correctness of the model 58.5 % 5 chains (80 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12151 restraints for refining 6018 atoms. 10067 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2273 (Rfree = 0.000) for 6018 atoms. Found 38 (38 requested) and removed 43 (27 requested) atoms. Cycle 37: After refmac, R = 0.2218 (Rfree = 0.000) for 5998 atoms. Found 37 (37 requested) and removed 38 (26 requested) atoms. Cycle 38: After refmac, R = 0.2141 (Rfree = 0.000) for 5986 atoms. Found 35 (37 requested) and removed 30 (26 requested) atoms. Cycle 39: After refmac, R = 0.2094 (Rfree = 0.000) for 5978 atoms. Found 19 (37 requested) and removed 38 (26 requested) atoms. Cycle 40: After refmac, R = 0.2054 (Rfree = 0.000) for 5946 atoms. Found 22 (37 requested) and removed 36 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.67 2.78 Search for helices and strands: 0 residues in 0 chains, 6063 seeds are put forward NCS extension: 33 residues added (22 deleted due to clashes), 6096 seeds are put forward Round 1: 434 peptides, 70 chains. Longest chain 14 peptides. Score 0.474 Round 2: 477 peptides, 60 chains. Longest chain 24 peptides. Score 0.608 Round 3: 496 peptides, 67 chains. Longest chain 18 peptides. Score 0.591 Round 4: 497 peptides, 67 chains. Longest chain 25 peptides. Score 0.593 Round 5: 481 peptides, 63 chains. Longest chain 24 peptides. Score 0.595 Taking the results from Round 2 Chains 61, Residues 417, Estimated correctness of the model 43.2 % 7 chains (73 residues) have been docked in sequence ------------------------------------------------------ 13478 reflections ( 96.64 % complete ) and 12583 restraints for refining 6018 atoms. 10726 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2158 (Rfree = 0.000) for 6018 atoms. Found 38 (38 requested) and removed 53 (27 requested) atoms. Cycle 42: After refmac, R = 0.2083 (Rfree = 0.000) for 5989 atoms. Found 32 (37 requested) and removed 36 (26 requested) atoms. Cycle 43: After refmac, R = 0.1999 (Rfree = 0.000) for 5976 atoms. Found 21 (37 requested) and removed 34 (26 requested) atoms. Cycle 44: After refmac, R = 0.1938 (Rfree = 0.000) for 5958 atoms. Found 18 (37 requested) and removed 28 (26 requested) atoms. Cycle 45: After refmac, R = 0.1901 (Rfree = 0.000) for 5945 atoms. Found 25 (37 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.69 2.80 Search for helices and strands: 0 residues in 0 chains, 6075 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 6103 seeds are put forward Round 1: 443 peptides, 67 chains. Longest chain 15 peptides. Score 0.511 Round 2: 480 peptides, 61 chains. Longest chain 26 peptides. Score 0.606 Round 3: 476 peptides, 66 chains. Longest chain 16 peptides. Score 0.569 Round 4: 471 peptides, 64 chains. Longest chain 25 peptides. Score 0.574 Round 5: 488 peptides, 63 chains. Longest chain 25 peptides. Score 0.605 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 419, Estimated correctness of the model 42.7 % 6 chains (73 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 358 A and 363 A 60 chains (422 residues) following loop building 5 chains (77 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13478 reflections ( 96.64 % complete ) and 12398 restraints for refining 6018 atoms. 10512 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2222 (Rfree = 0.000) for 6018 atoms. Found 0 (38 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2177 (Rfree = 0.000) for 5978 atoms. Found 0 (37 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2117 (Rfree = 0.000) for 5947 atoms. Found 0 (37 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2067 (Rfree = 0.000) for 5913 atoms. TimeTaking 78.53