null Sun 23 Dec 22:22:49 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 2fqp-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-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/2fqp-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-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 22:22:59 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/2fqp-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-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 244 and 0 Target number of residues in the AU: 244 Target solvent content: 0.6100 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-3.4-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: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3104 target number of atoms Had to go as low as 0.60 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: 50.895 3.400 Wilson plot Bfac: 56.75 3849 reflections ( 82.76 % complete ) and 0 restraints for refining 3439 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3231 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2098 (Rfree = 0.000) for 3439 atoms. Found 5 (25 requested) and removed 64 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.00 3.53 Search for helices and strands: 0 residues in 0 chains, 3408 seeds are put forward NCS extension: 0 residues added, 3408 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 7 peptides. Score 0.265 Round 2: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.368 Round 3: 125 peptides, 22 chains. Longest chain 9 peptides. Score 0.370 Round 4: 138 peptides, 24 chains. Longest chain 11 peptides. Score 0.391 Round 5: 144 peptides, 26 chains. Longest chain 16 peptides. Score 0.379 Taking the results from Round 4 Chains 24, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6722 restraints for refining 2820 atoms. 6290 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2089 (Rfree = 0.000) for 2820 atoms. Found 13 (21 requested) and removed 26 (10 requested) atoms. Cycle 2: After refmac, R = 0.1910 (Rfree = 0.000) for 2789 atoms. Found 8 (21 requested) and removed 13 (10 requested) atoms. Cycle 3: After refmac, R = 0.1886 (Rfree = 0.000) for 2778 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 4: After refmac, R = 0.2071 (Rfree = 0.000) for 2765 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 5: After refmac, R = 0.1847 (Rfree = 0.000) for 2758 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 3.57 Search for helices and strands: 0 residues in 0 chains, 2824 seeds are put forward NCS extension: 6 residues added (1 deleted due to clashes), 2830 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.256 Round 2: 127 peptides, 25 chains. Longest chain 10 peptides. Score 0.315 Round 3: 141 peptides, 25 chains. Longest chain 13 peptides. Score 0.385 Round 4: 147 peptides, 24 chains. Longest chain 18 peptides. Score 0.433 Round 5: 165 peptides, 27 chains. Longest chain 17 peptides. Score 0.455 Taking the results from Round 5 Chains 27, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6380 restraints for refining 2731 atoms. 5855 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2185 (Rfree = 0.000) for 2731 atoms. Found 9 (20 requested) and removed 17 (10 requested) atoms. Cycle 7: After refmac, R = 0.2037 (Rfree = 0.000) for 2711 atoms. Found 4 (20 requested) and removed 13 (10 requested) atoms. Cycle 8: After refmac, R = 0.1969 (Rfree = 0.000) for 2697 atoms. Found 1 (20 requested) and removed 10 (10 requested) atoms. Cycle 9: After refmac, R = 0.1930 (Rfree = 0.000) for 2686 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 10: After refmac, R = 0.1886 (Rfree = 0.000) for 2680 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.02 3.55 Search for helices and strands: 0 residues in 0 chains, 2710 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2736 seeds are put forward Round 1: 130 peptides, 26 chains. Longest chain 10 peptides. Score 0.309 Round 2: 145 peptides, 23 chains. Longest chain 12 peptides. Score 0.444 Round 3: 147 peptides, 23 chains. Longest chain 15 peptides. Score 0.453 Round 4: 147 peptides, 22 chains. Longest chain 11 peptides. Score 0.472 Round 5: 147 peptides, 21 chains. Longest chain 14 peptides. Score 0.491 Taking the results from Round 5 Chains 21, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6161 restraints for refining 2685 atoms. 5678 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2133 (Rfree = 0.000) for 2685 atoms. Found 15 (20 requested) and removed 18 (10 requested) atoms. Cycle 12: After refmac, R = 0.1762 (Rfree = 0.000) for 2674 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 13: After refmac, R = 0.1590 (Rfree = 0.000) for 2670 atoms. Found 6 (20 requested) and removed 13 (10 requested) atoms. Cycle 14: After refmac, R = 0.1532 (Rfree = 0.000) for 2661 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. Cycle 15: After refmac, R = 0.1506 (Rfree = 0.000) for 2651 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 3.60 Search for helices and strands: 0 residues in 0 chains, 2679 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2694 seeds are put forward Round 1: 118 peptides, 22 chains. Longest chain 9 peptides. Score 0.335 Round 2: 141 peptides, 24 chains. Longest chain 14 peptides. Score 0.405 Round 3: 147 peptides, 24 chains. Longest chain 16 peptides. Score 0.433 Round 4: 143 peptides, 23 chains. Longest chain 15 peptides. Score 0.435 Round 5: 149 peptides, 26 chains. Longest chain 15 peptides. Score 0.402 Taking the results from Round 4 Chains 23, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6230 restraints for refining 2677 atoms. 5773 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1843 (Rfree = 0.000) for 2677 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 17: After refmac, R = 0.1676 (Rfree = 0.000) for 2677 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 18: After refmac, R = 0.1643 (Rfree = 0.000) for 2669 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.1646 (Rfree = 0.000) for 2660 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.1678 (Rfree = 0.000) for 2652 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 2694 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2717 seeds are put forward Round 1: 121 peptides, 24 chains. Longest chain 10 peptides. Score 0.306 Round 2: 127 peptides, 19 chains. Longest chain 12 peptides. Score 0.442 Round 3: 129 peptides, 19 chains. Longest chain 14 peptides. Score 0.451 Round 4: 134 peptides, 19 chains. Longest chain 12 peptides. Score 0.474 Round 5: 127 peptides, 22 chains. Longest chain 10 peptides. Score 0.380 Taking the results from Round 4 Chains 21, Residues 115, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6115 restraints for refining 2703 atoms. 5608 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1829 (Rfree = 0.000) for 2703 atoms. Found 15 (20 requested) and removed 14 (10 requested) atoms. Cycle 22: After refmac, R = 0.1713 (Rfree = 0.000) for 2703 atoms. Found 3 (20 requested) and removed 12 (10 requested) atoms. Cycle 23: After refmac, R = 0.1704 (Rfree = 0.000) for 2691 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.1682 (Rfree = 0.000) for 2685 atoms. Found 2 (20 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.1680 (Rfree = 0.000) for 2674 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 3.61 Search for helices and strands: 0 residues in 0 chains, 2728 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2741 seeds are put forward Round 1: 122 peptides, 26 chains. Longest chain 9 peptides. Score 0.267 Round 2: 142 peptides, 25 chains. Longest chain 17 peptides. Score 0.390 Round 3: 138 peptides, 27 chains. Longest chain 10 peptides. Score 0.328 Round 4: 156 peptides, 28 chains. Longest chain 11 peptides. Score 0.395 Round 5: 160 peptides, 28 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 28, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6138 restraints for refining 2699 atoms. 5638 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1911 (Rfree = 0.000) for 2699 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 27: After refmac, R = 0.1766 (Rfree = 0.000) for 2702 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.1708 (Rfree = 0.000) for 2695 atoms. Found 1 (20 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.1696 (Rfree = 0.000) for 2685 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1675 (Rfree = 0.000) for 2675 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 3.60 Search for helices and strands: 0 residues in 0 chains, 2706 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2724 seeds are put forward Round 1: 129 peptides, 26 chains. Longest chain 9 peptides. Score 0.304 Round 2: 116 peptides, 20 chains. Longest chain 12 peptides. Score 0.368 Round 3: 126 peptides, 22 chains. Longest chain 10 peptides. Score 0.375 Round 4: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.328 Round 5: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.378 Taking the results from Round 5 Chains 21, Residues 98, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6411 restraints for refining 2754 atoms. 5980 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1795 (Rfree = 0.000) for 2754 atoms. Found 15 (20 requested) and removed 12 (10 requested) atoms. Cycle 32: After refmac, R = 0.1645 (Rfree = 0.000) for 2754 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.1604 (Rfree = 0.000) for 2743 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.1575 (Rfree = 0.000) for 2736 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1528 (Rfree = 0.000) for 2729 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.04 3.58 Search for helices and strands: 0 residues in 0 chains, 2774 seeds are put forward NCS extension: 0 residues added, 2774 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 9 peptides. Score 0.279 Round 2: 126 peptides, 23 chains. Longest chain 10 peptides. Score 0.353 Round 3: 122 peptides, 21 chains. Longest chain 13 peptides. Score 0.376 Round 4: 131 peptides, 24 chains. Longest chain 11 peptides. Score 0.357 Round 5: 130 peptides, 21 chains. Longest chain 12 peptides. Score 0.415 Taking the results from Round 5 Chains 21, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6605 restraints for refining 2756 atoms. 6190 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1698 (Rfree = 0.000) for 2756 atoms. Found 13 (20 requested) and removed 12 (10 requested) atoms. Cycle 37: After refmac, R = 0.1645 (Rfree = 0.000) for 2753 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 38: After refmac, R = 0.1573 (Rfree = 0.000) for 2746 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1587 (Rfree = 0.000) for 2735 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1537 (Rfree = 0.000) for 2726 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 3.57 Search for helices and strands: 0 residues in 0 chains, 2744 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2757 seeds are put forward Round 1: 117 peptides, 25 chains. Longest chain 10 peptides. Score 0.263 Round 2: 111 peptides, 19 chains. Longest chain 12 peptides. Score 0.365 Round 3: 121 peptides, 20 chains. Longest chain 13 peptides. Score 0.393 Round 4: 126 peptides, 21 chains. Longest chain 13 peptides. Score 0.396 Round 5: 135 peptides, 23 chains. Longest chain 12 peptides. Score 0.397 Taking the results from Round 5 Chains 23, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6479 restraints for refining 2711 atoms. 6054 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1962 (Rfree = 0.000) for 2711 atoms. Found 12 (20 requested) and removed 12 (10 requested) atoms. Cycle 42: After refmac, R = 0.1625 (Rfree = 0.000) for 2699 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.1509 (Rfree = 0.000) for 2686 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.1423 (Rfree = 0.000) for 2678 atoms. Found 1 (20 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1333 (Rfree = 0.000) for 2669 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.98 3.51 Search for helices and strands: 0 residues in 0 chains, 2690 seeds are put forward NCS extension: 0 residues added, 2690 seeds are put forward Round 1: 110 peptides, 21 chains. Longest chain 10 peptides. Score 0.315 Round 2: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.358 Round 3: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.414 Round 4: 101 peptides, 16 chains. Longest chain 11 peptides. Score 0.382 Round 5: 98 peptides, 16 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 95, 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 2fqp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3849 reflections ( 82.76 % complete ) and 6181 restraints for refining 2625 atoms. 5818 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1595 (Rfree = 0.000) for 2625 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2452 (Rfree = 0.000) for 2613 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1671 (Rfree = 0.000) for 2600 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1614 (Rfree = 0.000) for 2587 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:10 GMT 2018 Job finished. TimeTaking 47.34 Used memory is bytes: 5942680