Sun 23 Dec 22:22:46 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 1vk8-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-4.0-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/1vk8-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-4.0-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 22:22:56 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/1vk8-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-4.0-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 253 and 0 Target number of residues in the AU: 253 Target solvent content: 0.6385 Checking the provided sequence file Detected sequence length: 106 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 424 Adjusted target solvent content: 0.39 Input MTZ file: 1vk8-4.0-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: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3392 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: 41.711 4.001 Wilson plot Bfac: 70.82 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2973 reflections ( 96.18 % complete ) and 0 restraints for refining 3752 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3082 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2997 (Rfree = 0.000) for 3752 atoms. Found 17 (17 requested) and removed 79 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 4.11 Search for helices and strands: 0 residues in 0 chains, 3780 seeds are put forward NCS extension: 0 residues added, 3780 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 6 peptides. Score 0.231 Round 2: 141 peptides, 28 chains. Longest chain 9 peptides. Score 0.310 Round 3: 140 peptides, 27 chains. Longest chain 11 peptides. Score 0.325 Round 4: 144 peptides, 27 chains. Longest chain 11 peptides. Score 0.343 Round 5: 153 peptides, 29 chains. Longest chain 9 peptides. Score 0.345 Taking the results from Round 5 Chains 29, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 7722 restraints for refining 3063 atoms. 7255 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2370 (Rfree = 0.000) for 3063 atoms. Found 14 (14 requested) and removed 46 (7 requested) atoms. Cycle 2: After refmac, R = 0.2358 (Rfree = 0.000) for 2978 atoms. Found 14 (14 requested) and removed 34 (7 requested) atoms. Cycle 3: After refmac, R = 0.1679 (Rfree = 0.000) for 2921 atoms. Found 5 (14 requested) and removed 21 (7 requested) atoms. Cycle 4: After refmac, R = 0.1606 (Rfree = 0.000) for 2885 atoms. Found 1 (13 requested) and removed 14 (6 requested) atoms. Cycle 5: After refmac, R = 0.2152 (Rfree = 0.000) for 2861 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 4.12 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward NCS extension: 0 residues added, 2946 seeds are put forward Round 1: 123 peptides, 28 chains. Longest chain 8 peptides. Score 0.223 Round 2: 143 peptides, 26 chains. Longest chain 10 peptides. Score 0.357 Round 3: 152 peptides, 25 chains. Longest chain 11 peptides. Score 0.415 Round 4: 156 peptides, 25 chains. Longest chain 13 peptides. Score 0.432 Round 5: 148 peptides, 23 chains. Longest chain 16 peptides. Score 0.435 Taking the results from Round 5 Chains 23, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 6647 restraints for refining 2749 atoms. 6170 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2141 (Rfree = 0.000) for 2749 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 7: After refmac, R = 0.2027 (Rfree = 0.000) for 2709 atoms. Found 11 (12 requested) and removed 32 (6 requested) atoms. Cycle 8: After refmac, R = 0.1900 (Rfree = 0.000) for 2671 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 9: After refmac, R = 0.1987 (Rfree = 0.000) for 2650 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 10: After refmac, R = 0.1855 (Rfree = 0.000) for 2631 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 4.25 Search for helices and strands: 0 residues in 0 chains, 2751 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2776 seeds are put forward Round 1: 102 peptides, 20 chains. Longest chain 12 peptides. Score 0.286 Round 2: 131 peptides, 24 chains. Longest chain 17 peptides. Score 0.342 Round 3: 141 peptides, 23 chains. Longest chain 12 peptides. Score 0.406 Round 4: 134 peptides, 21 chains. Longest chain 17 peptides. Score 0.413 Round 5: 163 peptides, 25 chains. Longest chain 21 peptides. Score 0.460 Taking the results from Round 5 Chains 25, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 6102 restraints for refining 2623 atoms. 5575 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1861 (Rfree = 0.000) for 2623 atoms. Found 9 (12 requested) and removed 29 (6 requested) atoms. Cycle 12: After refmac, R = 0.1913 (Rfree = 0.000) for 2581 atoms. Found 12 (12 requested) and removed 31 (6 requested) atoms. Cycle 13: After refmac, R = 0.1972 (Rfree = 0.000) for 2547 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 14: After refmac, R = 0.1681 (Rfree = 0.000) for 2536 atoms. Found 11 (12 requested) and removed 16 (6 requested) atoms. Cycle 15: After refmac, R = 0.1182 (Rfree = 0.000) for 2523 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 4.21 Search for helices and strands: 0 residues in 0 chains, 2633 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 2665 seeds are put forward Round 1: 127 peptides, 27 chains. Longest chain 7 peptides. Score 0.263 Round 2: 151 peptides, 25 chains. Longest chain 13 peptides. Score 0.411 Round 3: 145 peptides, 21 chains. Longest chain 23 peptides. Score 0.459 Round 4: 153 peptides, 24 chains. Longest chain 12 peptides. Score 0.437 Round 5: 143 peptides, 24 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 3 Chains 21, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5993 restraints for refining 2579 atoms. 5518 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1814 (Rfree = 0.000) for 2579 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 17: After refmac, R = 0.1860 (Rfree = 0.000) for 2553 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 18: After refmac, R = 0.2082 (Rfree = 0.000) for 2536 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 19: After refmac, R = 0.1928 (Rfree = 0.000) for 2526 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 20: After refmac, R = 0.1855 (Rfree = 0.000) for 2516 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 4.16 Search for helices and strands: 0 residues in 0 chains, 2652 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 2689 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 10 peptides. Score 0.265 Round 2: 149 peptides, 28 chains. Longest chain 10 peptides. Score 0.346 Round 3: 145 peptides, 26 chains. Longest chain 14 peptides. Score 0.366 Round 4: 142 peptides, 22 chains. Longest chain 16 peptides. Score 0.428 Round 5: 150 peptides, 25 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 4 Chains 22, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5858 restraints for refining 2534 atoms. 5400 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1719 (Rfree = 0.000) for 2534 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 22: After refmac, R = 0.1775 (Rfree = 0.000) for 2520 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 23: After refmac, R = 0.1783 (Rfree = 0.000) for 2506 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 24: After refmac, R = 0.1648 (Rfree = 0.000) for 2495 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 25: After refmac, R = 0.1704 (Rfree = 0.000) for 2487 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 4.20 Search for helices and strands: 0 residues in 0 chains, 2585 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 2598 seeds are put forward Round 1: 123 peptides, 27 chains. Longest chain 7 peptides. Score 0.244 Round 2: 147 peptides, 28 chains. Longest chain 10 peptides. Score 0.337 Round 3: 149 peptides, 23 chains. Longest chain 13 peptides. Score 0.439 Round 4: 143 peptides, 23 chains. Longest chain 12 peptides. Score 0.414 Round 5: 146 peptides, 24 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 3 Chains 23, Residues 126, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5883 restraints for refining 2582 atoms. 5390 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1668 (Rfree = 0.000) for 2582 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 27: After refmac, R = 0.1995 (Rfree = 0.000) for 2561 atoms. Found 12 (12 requested) and removed 31 (6 requested) atoms. Cycle 28: After refmac, R = 0.1700 (Rfree = 0.000) for 2532 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.1677 (Rfree = 0.000) for 2515 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1747 (Rfree = 0.000) for 2504 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 4.22 Search for helices and strands: 0 residues in 0 chains, 2606 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2619 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 8 peptides. Score 0.240 Round 2: 127 peptides, 24 chains. Longest chain 9 peptides. Score 0.324 Round 3: 127 peptides, 25 chains. Longest chain 10 peptides. Score 0.304 Round 4: 135 peptides, 24 chains. Longest chain 11 peptides. Score 0.360 Round 5: 130 peptides, 23 chains. Longest chain 12 peptides. Score 0.357 Taking the results from Round 4 Chains 24, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5791 restraints for refining 2532 atoms. 5371 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1689 (Rfree = 0.000) for 2532 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 32: After refmac, R = 0.1773 (Rfree = 0.000) for 2514 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 33: After refmac, R = 0.1623 (Rfree = 0.000) for 2497 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 34: After refmac, R = 0.1692 (Rfree = 0.000) for 2492 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 35: After refmac, R = 0.1654 (Rfree = 0.000) for 2483 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 4.24 Search for helices and strands: 0 residues in 0 chains, 2550 seeds are put forward NCS extension: 0 residues added, 2550 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 7 peptides. Score 0.262 Round 2: 117 peptides, 20 chains. Longest chain 11 peptides. Score 0.357 Round 3: 122 peptides, 22 chains. Longest chain 9 peptides. Score 0.340 Round 4: 138 peptides, 26 chains. Longest chain 9 peptides. Score 0.335 Round 5: 132 peptides, 18 chains. Longest chain 24 peptides. Score 0.461 Taking the results from Round 5 Chains 18, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5946 restraints for refining 2594 atoms. 5508 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1807 (Rfree = 0.000) for 2594 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 37: After refmac, R = 0.1684 (Rfree = 0.000) for 2580 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 38: After refmac, R = 0.1783 (Rfree = 0.000) for 2562 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 39: After refmac, R = 0.1629 (Rfree = 0.000) for 2549 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 40: After refmac, R = 0.1818 (Rfree = 0.000) for 2544 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 4.17 Search for helices and strands: 0 residues in 0 chains, 2646 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 2683 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 8 peptides. Score 0.238 Round 2: 131 peptides, 24 chains. Longest chain 10 peptides. Score 0.342 Round 3: 134 peptides, 25 chains. Longest chain 8 peptides. Score 0.336 Round 4: 135 peptides, 24 chains. Longest chain 13 peptides. Score 0.360 Round 5: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 5 Chains 23, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 6275 restraints for refining 2661 atoms. 5846 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1723 (Rfree = 0.000) for 2661 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 42: After refmac, R = 0.1890 (Rfree = 0.000) for 2634 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 43: After refmac, R = 0.1764 (Rfree = 0.000) for 2611 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 44: After refmac, R = 0.1706 (Rfree = 0.000) for 2594 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 45: After refmac, R = 0.1776 (Rfree = 0.000) for 2580 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 4.21 Search for helices and strands: 0 residues in 0 chains, 2675 seeds are put forward NCS extension: 0 residues added, 2675 seeds are put forward Round 1: 93 peptides, 22 chains. Longest chain 7 peptides. Score 0.195 Round 2: 100 peptides, 20 chains. Longest chain 8 peptides. Score 0.275 Round 3: 108 peptides, 19 chains. Longest chain 16 peptides. Score 0.336 Round 4: 113 peptides, 21 chains. Longest chain 9 peptides. Score 0.318 Round 5: 120 peptides, 20 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vk8-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2973 reflections ( 96.18 % complete ) and 5960 restraints for refining 2554 atoms. 5580 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1697 (Rfree = 0.000) for 2554 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1899 (Rfree = 0.000) for 2529 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1852 (Rfree = 0.000) for 2519 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1722 (Rfree = 0.000) for 2508 atoms. TimeTaking 50.12