null 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 2ozj-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-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/2ozj-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-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 22:22:52 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/2ozj-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-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 141 and 0 Target number of residues in the AU: 141 Target solvent content: 0.6453 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.43 Input MTZ file: 2ozj-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: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1824 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: 75.275 3.200 Wilson plot Bfac: 74.11 3785 reflections ( 99.45 % complete ) and 0 restraints for refining 2026 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3245 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3475 (Rfree = 0.000) for 2026 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.90 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 0 residues added, 2035 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.299 Round 2: 126 peptides, 20 chains. Longest chain 11 peptides. Score 0.514 Round 3: 134 peptides, 20 chains. Longest chain 13 peptides. Score 0.562 Round 4: 150 peptides, 21 chains. Longest chain 21 peptides. Score 0.626 Round 5: 149 peptides, 17 chains. Longest chain 23 peptides. Score 0.704 Taking the results from Round 5 Chains 18, Residues 132, Estimated correctness of the model 66.0 % 2 chains (33 residues) have been docked in sequence Building loops using Loopy2018 18 chains (132 residues) following loop building 2 chains (33 residues) in sequence following loop building ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3247 restraints for refining 1663 atoms. 2609 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3205 (Rfree = 0.000) for 1663 atoms. Found 9 (14 requested) and removed 49 (7 requested) atoms. Cycle 2: After refmac, R = 0.2786 (Rfree = 0.000) for 1593 atoms. Found 6 (14 requested) and removed 23 (7 requested) atoms. Cycle 3: After refmac, R = 0.2574 (Rfree = 0.000) for 1567 atoms. Found 4 (13 requested) and removed 7 (7 requested) atoms. Cycle 4: After refmac, R = 0.2458 (Rfree = 0.000) for 1560 atoms. Found 4 (13 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2373 (Rfree = 0.000) for 1552 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.57 Search for helices and strands: 0 residues in 0 chains, 1581 seeds are put forward NCS extension: 38 residues added (4 deleted due to clashes), 1619 seeds are put forward Round 1: 113 peptides, 16 chains. Longest chain 15 peptides. Score 0.542 Round 2: 136 peptides, 14 chains. Longest chain 20 peptides. Score 0.707 Round 3: 138 peptides, 15 chains. Longest chain 29 peptides. Score 0.696 Round 4: 132 peptides, 16 chains. Longest chain 20 peptides. Score 0.647 Round 5: 136 peptides, 13 chains. Longest chain 30 peptides. Score 0.727 Taking the results from Round 5 Chains 13, Residues 123, Estimated correctness of the model 70.7 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3391 restraints for refining 1665 atoms. 2803 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2614 (Rfree = 0.000) for 1665 atoms. Found 10 (13 requested) and removed 18 (7 requested) atoms. Cycle 7: After refmac, R = 0.2391 (Rfree = 0.000) for 1643 atoms. Found 2 (12 requested) and removed 12 (7 requested) atoms. Cycle 8: After refmac, R = 0.2972 (Rfree = 0.000) for 1614 atoms. Found 6 (12 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.2398 (Rfree = 0.000) for 1592 atoms. Found 4 (12 requested) and removed 8 (7 requested) atoms. Cycle 10: After refmac, R = 0.2510 (Rfree = 0.000) for 1583 atoms. Found 11 (11 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.55 Search for helices and strands: 0 residues in 0 chains, 1614 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 1644 seeds are put forward Round 1: 137 peptides, 21 chains. Longest chain 21 peptides. Score 0.555 Round 2: 143 peptides, 17 chains. Longest chain 24 peptides. Score 0.677 Round 3: 153 peptides, 16 chains. Longest chain 23 peptides. Score 0.738 Round 4: 148 peptides, 17 chains. Longest chain 26 peptides. Score 0.699 Round 5: 149 peptides, 15 chains. Longest chain 23 peptides. Score 0.740 Taking the results from Round 5 Chains 15, Residues 134, Estimated correctness of the model 73.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3529 restraints for refining 1632 atoms. 3008 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2921 (Rfree = 0.000) for 1632 atoms. Found 6 (11 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.2961 (Rfree = 0.000) for 1611 atoms. Found 11 (11 requested) and removed 9 (7 requested) atoms. Cycle 13: After refmac, R = 0.3106 (Rfree = 0.000) for 1603 atoms. Found 11 (11 requested) and removed 15 (7 requested) atoms. Cycle 14: After refmac, R = 0.2629 (Rfree = 0.000) for 1592 atoms. Found 8 (10 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.2579 (Rfree = 0.000) for 1582 atoms. Found 3 (10 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.62 Search for helices and strands: 0 residues in 0 chains, 1608 seeds are put forward NCS extension: 0 residues added, 1608 seeds are put forward Round 1: 115 peptides, 20 chains. Longest chain 16 peptides. Score 0.442 Round 2: 121 peptides, 16 chains. Longest chain 17 peptides. Score 0.589 Round 3: 126 peptides, 18 chains. Longest chain 18 peptides. Score 0.567 Round 4: 138 peptides, 15 chains. Longest chain 28 peptides. Score 0.696 Round 5: 140 peptides, 18 chains. Longest chain 19 peptides. Score 0.642 Taking the results from Round 4 Chains 15, Residues 123, Estimated correctness of the model 64.3 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3269 restraints for refining 1626 atoms. 2695 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3294 (Rfree = 0.000) for 1626 atoms. Found 10 (10 requested) and removed 32 (7 requested) atoms. Cycle 17: After refmac, R = 0.2649 (Rfree = 0.000) for 1597 atoms. Found 4 (10 requested) and removed 10 (7 requested) atoms. Cycle 18: After refmac, R = 0.2599 (Rfree = 0.000) for 1586 atoms. Found 8 (10 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.3065 (Rfree = 0.000) for 1576 atoms. Found 10 (10 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.2679 (Rfree = 0.000) for 1567 atoms. Found 10 (10 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 1593 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 1616 seeds are put forward Round 1: 114 peptides, 16 chains. Longest chain 20 peptides. Score 0.548 Round 2: 124 peptides, 13 chains. Longest chain 23 peptides. Score 0.675 Round 3: 126 peptides, 14 chains. Longest chain 18 peptides. Score 0.662 Round 4: 132 peptides, 13 chains. Longest chain 23 peptides. Score 0.710 Round 5: 136 peptides, 16 chains. Longest chain 23 peptides. Score 0.666 Taking the results from Round 4 Chains 15, Residues 119, Estimated correctness of the model 67.3 % 2 chains (23 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 29 A 13 chains (120 residues) following loop building 1 chains (25 residues) in sequence following loop building ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3147 restraints for refining 1590 atoms. 2589 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2580 (Rfree = 0.000) for 1590 atoms. Found 6 (10 requested) and removed 15 (7 requested) atoms. Cycle 22: After refmac, R = 0.2347 (Rfree = 0.000) for 1574 atoms. Found 3 (10 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.2258 (Rfree = 0.000) for 1569 atoms. Found 1 (9 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.2205 (Rfree = 0.000) for 1560 atoms. Found 2 (9 requested) and removed 8 (7 requested) atoms. Cycle 25: After refmac, R = 0.2192 (Rfree = 0.000) for 1553 atoms. Found 2 (8 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.68 Search for helices and strands: 0 residues in 0 chains, 1577 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1596 seeds are put forward Round 1: 117 peptides, 15 chains. Longest chain 28 peptides. Score 0.591 Round 2: 118 peptides, 12 chains. Longest chain 35 peptides. Score 0.668 Round 3: 124 peptides, 16 chains. Longest chain 21 peptides. Score 0.605 Round 4: 131 peptides, 15 chains. Longest chain 20 peptides. Score 0.664 Round 5: 127 peptides, 14 chains. Longest chain 21 peptides. Score 0.667 Taking the results from Round 2 Chains 12, Residues 106, Estimated correctness of the model 58.1 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3197 restraints for refining 1612 atoms. 2651 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2287 (Rfree = 0.000) for 1612 atoms. Found 3 (8 requested) and removed 18 (7 requested) atoms. Cycle 27: After refmac, R = 0.2185 (Rfree = 0.000) for 1596 atoms. Found 2 (8 requested) and removed 11 (7 requested) atoms. Cycle 28: After refmac, R = 0.2124 (Rfree = 0.000) for 1582 atoms. Found 3 (8 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.2104 (Rfree = 0.000) for 1574 atoms. Found 1 (8 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.2181 (Rfree = 0.000) for 1566 atoms. Found 4 (8 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.62 Search for helices and strands: 0 residues in 0 chains, 1578 seeds are put forward NCS extension: 43 residues added (7 deleted due to clashes), 1621 seeds are put forward Round 1: 107 peptides, 16 chains. Longest chain 17 peptides. Score 0.504 Round 2: 120 peptides, 12 chains. Longest chain 37 peptides. Score 0.678 Round 3: 118 peptides, 16 chains. Longest chain 16 peptides. Score 0.572 Round 4: 124 peptides, 14 chains. Longest chain 24 peptides. Score 0.652 Round 5: 130 peptides, 16 chains. Longest chain 24 peptides. Score 0.637 Taking the results from Round 2 Chains 12, Residues 108, Estimated correctness of the model 60.4 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3085 restraints for refining 1604 atoms. 2521 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2887 (Rfree = 0.000) for 1604 atoms. Found 8 (8 requested) and removed 21 (7 requested) atoms. Cycle 32: After refmac, R = 0.2427 (Rfree = 0.000) for 1585 atoms. Found 3 (8 requested) and removed 11 (7 requested) atoms. Cycle 33: After refmac, R = 0.2829 (Rfree = 0.000) for 1569 atoms. Found 8 (8 requested) and removed 11 (7 requested) atoms. Cycle 34: After refmac, R = 0.2756 (Rfree = 0.000) for 1564 atoms. Found 8 (8 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.2245 (Rfree = 0.000) for 1552 atoms. Found 8 (8 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.62 Search for helices and strands: 0 residues in 0 chains, 1568 seeds are put forward NCS extension: 40 residues added (7 deleted due to clashes), 1608 seeds are put forward Round 1: 100 peptides, 15 chains. Longest chain 23 peptides. Score 0.487 Round 2: 113 peptides, 15 chains. Longest chain 24 peptides. Score 0.568 Round 3: 120 peptides, 12 chains. Longest chain 25 peptides. Score 0.678 Round 4: 118 peptides, 12 chains. Longest chain 26 peptides. Score 0.668 Round 5: 121 peptides, 15 chains. Longest chain 17 peptides. Score 0.613 Taking the results from Round 3 Chains 13, Residues 108, Estimated correctness of the model 60.4 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3023 restraints for refining 1549 atoms. 2534 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2608 (Rfree = 0.000) for 1549 atoms. Found 6 (8 requested) and removed 16 (6 requested) atoms. Cycle 37: After refmac, R = 0.2733 (Rfree = 0.000) for 1538 atoms. Found 8 (8 requested) and removed 14 (6 requested) atoms. Cycle 38: After refmac, R = 0.2693 (Rfree = 0.000) for 1527 atoms. Found 8 (8 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.2039 (Rfree = 0.000) for 1520 atoms. Found 8 (8 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1892 (Rfree = 0.000) for 1520 atoms. Found 3 (8 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 1543 seeds are put forward NCS extension: 32 residues added (6 deleted due to clashes), 1575 seeds are put forward Round 1: 97 peptides, 17 chains. Longest chain 18 peptides. Score 0.405 Round 2: 112 peptides, 13 chains. Longest chain 23 peptides. Score 0.614 Round 3: 109 peptides, 12 chains. Longest chain 24 peptides. Score 0.623 Round 4: 117 peptides, 14 chains. Longest chain 26 peptides. Score 0.616 Round 5: 126 peptides, 13 chains. Longest chain 26 peptides. Score 0.684 Taking the results from Round 5 Chains 14, Residues 113, Estimated correctness of the model 61.7 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3058 restraints for refining 1577 atoms. 2541 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2602 (Rfree = 0.000) for 1577 atoms. Found 8 (8 requested) and removed 16 (7 requested) atoms. Cycle 42: After refmac, R = 0.2166 (Rfree = 0.000) for 1563 atoms. Found 7 (8 requested) and removed 10 (7 requested) atoms. Cycle 43: After refmac, R = 0.2113 (Rfree = 0.000) for 1556 atoms. Found 3 (8 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2086 (Rfree = 0.000) for 1552 atoms. Found 2 (8 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.2074 (Rfree = 0.000) for 1547 atoms. Found 4 (8 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 1578 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 1618 seeds are put forward Round 1: 89 peptides, 13 chains. Longest chain 18 peptides. Score 0.472 Round 2: 92 peptides, 12 chains. Longest chain 20 peptides. Score 0.522 Round 3: 99 peptides, 13 chains. Longest chain 21 peptides. Score 0.538 Round 4: 106 peptides, 17 chains. Longest chain 13 peptides. Score 0.468 Round 5: 104 peptides, 13 chains. Longest chain 20 peptides. Score 0.568 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 91, Estimated correctness of the model 32.1 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ozj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3785 reflections ( 99.45 % complete ) and 3688 restraints for refining 1628 atoms. 3337 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2581 (Rfree = 0.000) for 1628 atoms. Found 0 (8 requested) and removed 4 (7 requested) atoms. Cycle 47: After refmac, R = 0.2368 (Rfree = 0.000) for 1624 atoms. Found 0 (8 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2337 (Rfree = 0.000) for 1613 atoms. Found 0 (8 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2318 (Rfree = 0.000) for 1605 atoms. Found 0 (8 requested) and removed 5 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:24 GMT 2018 Job finished. TimeTaking 31.69 Used memory is bytes: 19379200