null 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 2nyh-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-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/2nyh-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-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 22:22:55 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/2nyh-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-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 191 and 0 Target number of residues in the AU: 191 Target solvent content: 0.6279 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 234 Adjusted target solvent content: 0.54 Input MTZ file: 2nyh-3.6-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: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.85 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: 55.335 3.600 Wilson plot Bfac: 64.85 3363 reflections ( 98.05 % complete ) and 0 restraints for refining 2063 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3564 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2700 (Rfree = 0.000) for 2063 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 2092 seeds are put forward NCS extension: 0 residues added, 2092 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.291 Round 2: 112 peptides, 19 chains. Longest chain 13 peptides. Score 0.402 Round 3: 136 peptides, 21 chains. Longest chain 12 peptides. Score 0.485 Round 4: 128 peptides, 18 chains. Longest chain 16 peptides. Score 0.512 Round 5: 132 peptides, 18 chains. Longest chain 15 peptides. Score 0.532 Taking the results from Round 5 Chains 19, Residues 114, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3704 restraints for refining 1696 atoms. 3210 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3055 (Rfree = 0.000) for 1696 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 2: After refmac, R = 0.2855 (Rfree = 0.000) for 1689 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.2734 (Rfree = 0.000) for 1679 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2633 (Rfree = 0.000) for 1664 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2544 (Rfree = 0.000) for 1661 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 1694 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 1706 seeds are put forward Round 1: 122 peptides, 24 chains. Longest chain 9 peptides. Score 0.335 Round 2: 126 peptides, 21 chains. Longest chain 10 peptides. Score 0.432 Round 3: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.392 Round 4: 133 peptides, 21 chains. Longest chain 13 peptides. Score 0.470 Round 5: 140 peptides, 22 chains. Longest chain 16 peptides. Score 0.484 Taking the results from Round 5 Chains 22, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3902 restraints for refining 1697 atoms. 3452 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2965 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 7: After refmac, R = 0.2776 (Rfree = 0.000) for 1699 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 8: After refmac, R = 0.2634 (Rfree = 0.000) for 1694 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2547 (Rfree = 0.000) for 1687 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2459 (Rfree = 0.000) for 1682 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1726 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1748 seeds are put forward Round 1: 109 peptides, 21 chains. Longest chain 14 peptides. Score 0.333 Round 2: 127 peptides, 21 chains. Longest chain 16 peptides. Score 0.437 Round 3: 132 peptides, 23 chains. Longest chain 14 peptides. Score 0.417 Round 4: 128 peptides, 21 chains. Longest chain 16 peptides. Score 0.443 Round 5: 133 peptides, 21 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 5 Chains 21, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3887 restraints for refining 1695 atoms. 3460 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2693 (Rfree = 0.000) for 1695 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 12: After refmac, R = 0.2529 (Rfree = 0.000) for 1693 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 13: After refmac, R = 0.2464 (Rfree = 0.000) for 1691 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.2449 (Rfree = 0.000) for 1687 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2435 (Rfree = 0.000) for 1682 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 1714 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1725 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.308 Round 2: 118 peptides, 20 chains. Longest chain 10 peptides. Score 0.411 Round 3: 123 peptides, 19 chains. Longest chain 11 peptides. Score 0.463 Round 4: 122 peptides, 19 chains. Longest chain 11 peptides. Score 0.458 Round 5: 133 peptides, 20 chains. Longest chain 13 peptides. Score 0.493 Taking the results from Round 5 Chains 20, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3884 restraints for refining 1697 atoms. 3452 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2797 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 17: After refmac, R = 0.2640 (Rfree = 0.000) for 1695 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.2569 (Rfree = 0.000) for 1690 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.2524 (Rfree = 0.000) for 1683 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.2490 (Rfree = 0.000) for 1676 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 1703 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1717 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.310 Round 2: 114 peptides, 18 chains. Longest chain 13 peptides. Score 0.438 Round 3: 127 peptides, 22 chains. Longest chain 11 peptides. Score 0.413 Round 4: 121 peptides, 17 chains. Longest chain 13 peptides. Score 0.499 Round 5: 108 peptides, 16 chains. Longest chain 12 peptides. Score 0.454 Taking the results from Round 4 Chains 17, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3850 restraints for refining 1697 atoms. 3451 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2866 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 22: After refmac, R = 0.2722 (Rfree = 0.000) for 1697 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 23: After refmac, R = 0.2636 (Rfree = 0.000) for 1698 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2575 (Rfree = 0.000) for 1695 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2533 (Rfree = 0.000) for 1691 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 1711 seeds are put forward NCS extension: 0 residues added, 1711 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.299 Round 2: 93 peptides, 16 chains. Longest chain 9 peptides. Score 0.366 Round 3: 100 peptides, 18 chains. Longest chain 12 peptides. Score 0.356 Round 4: 101 peptides, 16 chains. Longest chain 13 peptides. Score 0.414 Round 5: 110 peptides, 17 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 5 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3980 restraints for refining 1697 atoms. 3625 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2766 (Rfree = 0.000) for 1697 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 27: After refmac, R = 0.2614 (Rfree = 0.000) for 1694 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2536 (Rfree = 0.000) for 1688 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2490 (Rfree = 0.000) for 1686 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2462 (Rfree = 0.000) for 1678 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1699 seeds are put forward NCS extension: 0 residues added, 1699 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 7 peptides. Score 0.250 Round 2: 97 peptides, 18 chains. Longest chain 13 peptides. Score 0.337 Round 3: 114 peptides, 19 chains. Longest chain 12 peptides. Score 0.413 Round 4: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.384 Round 5: 106 peptides, 17 chains. Longest chain 11 peptides. Score 0.417 Taking the results from Round 5 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 4101 restraints for refining 1697 atoms. 3762 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2808 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2646 (Rfree = 0.000) for 1701 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.2519 (Rfree = 0.000) for 1699 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2451 (Rfree = 0.000) for 1694 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2383 (Rfree = 0.000) for 1686 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 1712 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1721 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 10 peptides. Score 0.264 Round 2: 105 peptides, 18 chains. Longest chain 14 peptides. Score 0.386 Round 3: 94 peptides, 18 chains. Longest chain 11 peptides. Score 0.318 Round 4: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.366 Round 5: 114 peptides, 20 chains. Longest chain 16 peptides. Score 0.388 Taking the results from Round 5 Chains 20, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3943 restraints for refining 1697 atoms. 3587 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2697 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.2629 (Rfree = 0.000) for 1695 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.2581 (Rfree = 0.000) for 1690 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2589 (Rfree = 0.000) for 1686 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2547 (Rfree = 0.000) for 1678 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1697 seeds are put forward NCS extension: 0 residues added, 1697 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 8 peptides. Score 0.291 Round 2: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.345 Round 3: 94 peptides, 16 chains. Longest chain 11 peptides. Score 0.372 Round 4: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.362 Round 5: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.358 Taking the results from Round 3 Chains 16, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 4028 restraints for refining 1668 atoms. 3732 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2828 (Rfree = 0.000) for 1668 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2729 (Rfree = 0.000) for 1672 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.2690 (Rfree = 0.000) for 1675 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2603 (Rfree = 0.000) for 1674 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2487 (Rfree = 0.000) for 1671 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1696 seeds are put forward NCS extension: 0 residues added, 1696 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 11 peptides. Score 0.314 Round 2: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.354 Round 3: 103 peptides, 17 chains. Longest chain 11 peptides. Score 0.400 Round 4: 107 peptides, 18 chains. Longest chain 9 peptides. Score 0.398 Round 5: 105 peptides, 16 chains. Longest chain 11 peptides. Score 0.437 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 89, 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 2nyh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3363 reflections ( 98.05 % complete ) and 4085 restraints for refining 1689 atoms. 3745 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2719 (Rfree = 0.000) for 1689 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2624 (Rfree = 0.000) for 1683 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2610 (Rfree = 0.000) for 1678 atoms. Found 0 (10 requested) and removed 3 (5 requested) atoms. Cycle 49: After refmac, R = 0.2596 (Rfree = 0.000) for 1673 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:26 GMT 2018 Job finished. TimeTaking 30.66 Used memory is bytes: 19253552