null Mon 24 Dec 00:04:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ozj-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ozj-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ozj-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.2-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:04:47 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 2011 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3196 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3730 (Rfree = 0.000) for 2011 atoms. Found 11 (18 requested) and removed 36 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.94 4.33 Search for helices and strands: 0 residues in 0 chains, 2015 seeds are put forward NCS extension: 0 residues added, 2015 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 9 peptides. Score 0.307 Round 2: 123 peptides, 19 chains. Longest chain 13 peptides. Score 0.522 Round 3: 116 peptides, 18 chains. Longest chain 15 peptides. Score 0.506 Round 4: 139 peptides, 21 chains. Longest chain 17 peptides. Score 0.566 Round 5: 137 peptides, 17 chains. Longest chain 15 peptides. Score 0.649 Taking the results from Round 5 Chains 17, Residues 120, Estimated correctness of the model 53.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3672 restraints for refining 1665 atoms. 3209 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3101 (Rfree = 0.000) for 1665 atoms. Found 10 (14 requested) and removed 18 (7 requested) atoms. Cycle 2: After refmac, R = 0.3106 (Rfree = 0.000) for 1623 atoms. Found 12 (14 requested) and removed 14 (7 requested) atoms. Cycle 3: After refmac, R = 0.2761 (Rfree = 0.000) for 1600 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 4: After refmac, R = 0.2685 (Rfree = 0.000) for 1576 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Cycle 5: After refmac, R = 0.2570 (Rfree = 0.000) for 1569 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 1621 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1638 seeds are put forward Round 1: 100 peptides, 18 chains. Longest chain 11 peptides. Score 0.395 Round 2: 117 peptides, 19 chains. Longest chain 13 peptides. Score 0.484 Round 3: 133 peptides, 19 chains. Longest chain 15 peptides. Score 0.582 Round 4: 150 peptides, 19 chains. Longest chain 29 peptides. Score 0.668 Round 5: 126 peptides, 18 chains. Longest chain 16 peptides. Score 0.567 Taking the results from Round 4 Chains 19, Residues 131, Estimated correctness of the model 58.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3315 restraints for refining 1572 atoms. 2810 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2833 (Rfree = 0.000) for 1572 atoms. Found 12 (14 requested) and removed 15 (7 requested) atoms. Cycle 7: After refmac, R = 0.2768 (Rfree = 0.000) for 1554 atoms. Found 10 (14 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.3107 (Rfree = 0.000) for 1544 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.3288 (Rfree = 0.000) for 1531 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 10: After refmac, R = 0.2892 (Rfree = 0.000) for 1518 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.70 Search for helices and strands: 0 residues in 0 chains, 1590 seeds are put forward NCS extension: 61 residues added (5 deleted due to clashes), 1651 seeds are put forward Round 1: 116 peptides, 20 chains. Longest chain 13 peptides. Score 0.449 Round 2: 113 peptides, 17 chains. Longest chain 14 peptides. Score 0.514 Round 3: 125 peptides, 16 chains. Longest chain 22 peptides. Score 0.611 Round 4: 126 peptides, 15 chains. Longest chain 29 peptides. Score 0.640 Round 5: 133 peptides, 16 chains. Longest chain 20 peptides. Score 0.652 Taking the results from Round 5 Chains 16, Residues 117, Estimated correctness of the model 54.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3315 restraints for refining 1554 atoms. 2863 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2802 (Rfree = 0.000) for 1554 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. Cycle 12: After refmac, R = 0.2671 (Rfree = 0.000) for 1550 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 13: After refmac, R = 0.2426 (Rfree = 0.000) for 1540 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2278 (Rfree = 0.000) for 1535 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2266 (Rfree = 0.000) for 1528 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.65 Search for helices and strands: 0 residues in 0 chains, 1563 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 1586 seeds are put forward Round 1: 120 peptides, 20 chains. Longest chain 14 peptides. Score 0.475 Round 2: 132 peptides, 17 chains. Longest chain 22 peptides. Score 0.624 Round 3: 132 peptides, 14 chains. Longest chain 34 peptides. Score 0.690 Round 4: 135 peptides, 14 chains. Longest chain 20 peptides. Score 0.703 Round 5: 142 peptides, 14 chains. Longest chain 35 peptides. Score 0.732 Taking the results from Round 5 Chains 16, Residues 128, Estimated correctness of the model 71.7 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3359 restraints for refining 1613 atoms. 2797 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2991 (Rfree = 0.000) for 1613 atoms. Found 8 (14 requested) and removed 17 (7 requested) atoms. Cycle 17: After refmac, R = 0.2838 (Rfree = 0.000) for 1593 atoms. Found 8 (14 requested) and removed 13 (7 requested) atoms. Cycle 18: After refmac, R = 0.2701 (Rfree = 0.000) for 1579 atoms. Found 8 (13 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.3037 (Rfree = 0.000) for 1566 atoms. Found 13 (13 requested) and removed 14 (7 requested) atoms. Cycle 20: After refmac, R = 0.3014 (Rfree = 0.000) for 1555 atoms. Found 10 (13 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.65 Search for helices and strands: 0 residues in 0 chains, 1583 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 1623 seeds are put forward Round 1: 108 peptides, 17 chains. Longest chain 13 peptides. Score 0.482 Round 2: 121 peptides, 17 chains. Longest chain 15 peptides. Score 0.563 Round 3: 132 peptides, 16 chains. Longest chain 25 peptides. Score 0.647 Round 4: 132 peptides, 16 chains. Longest chain 15 peptides. Score 0.647 Round 5: 121 peptides, 15 chains. Longest chain 17 peptides. Score 0.613 Taking the results from Round 4 Chains 17, Residues 116, Estimated correctness of the model 53.1 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3357 restraints for refining 1567 atoms. 2875 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3246 (Rfree = 0.000) for 1567 atoms. Found 10 (13 requested) and removed 17 (7 requested) atoms. Cycle 22: After refmac, R = 0.3848 (Rfree = 0.000) for 1546 atoms. Found 10 (13 requested) and removed 32 (7 requested) atoms. Cycle 23: After refmac, R = 0.3335 (Rfree = 0.000) for 1506 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 24: After refmac, R = 0.2540 (Rfree = 0.000) for 1494 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.2228 (Rfree = 0.000) for 1484 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.60 Search for helices and strands: 0 residues in 0 chains, 1535 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1554 seeds are put forward Round 1: 111 peptides, 21 chains. Longest chain 12 peptides. Score 0.383 Round 2: 135 peptides, 21 chains. Longest chain 14 peptides. Score 0.543 Round 3: 117 peptides, 18 chains. Longest chain 16 peptides. Score 0.512 Round 4: 116 peptides, 18 chains. Longest chain 17 peptides. Score 0.506 Round 5: 127 peptides, 17 chains. Longest chain 17 peptides. Score 0.597 Taking the results from Round 5 Chains 17, Residues 110, Estimated correctness of the model 40.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3417 restraints for refining 1572 atoms. 2994 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3195 (Rfree = 0.000) for 1572 atoms. Found 13 (13 requested) and removed 19 (7 requested) atoms. Cycle 27: After refmac, R = 0.2818 (Rfree = 0.000) for 1552 atoms. Found 13 (13 requested) and removed 13 (7 requested) atoms. Cycle 28: After refmac, R = 0.2299 (Rfree = 0.000) for 1544 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.2062 (Rfree = 0.000) for 1539 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2064 (Rfree = 0.000) for 1531 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.57 Search for helices and strands: 0 residues in 0 chains, 1572 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1593 seeds are put forward Round 1: 103 peptides, 18 chains. Longest chain 12 peptides. Score 0.417 Round 2: 115 peptides, 16 chains. Longest chain 17 peptides. Score 0.554 Round 3: 112 peptides, 15 chains. Longest chain 13 peptides. Score 0.562 Round 4: 116 peptides, 15 chains. Longest chain 14 peptides. Score 0.586 Round 5: 107 peptides, 14 chains. Longest chain 16 peptides. Score 0.559 Taking the results from Round 4 Chains 15, Residues 101, Estimated correctness of the model 37.2 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3036 restraints for refining 1553 atoms. 2592 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3001 (Rfree = 0.000) for 1553 atoms. Found 4 (12 requested) and removed 23 (6 requested) atoms. Cycle 32: After refmac, R = 0.2833 (Rfree = 0.000) for 1528 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.2363 (Rfree = 0.000) for 1516 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2170 (Rfree = 0.000) for 1508 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1895 (Rfree = 0.000) for 1506 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.64 Search for helices and strands: 0 residues in 0 chains, 1545 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1560 seeds are put forward Round 1: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.382 Round 2: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.450 Round 3: 115 peptides, 14 chains. Longest chain 17 peptides. Score 0.605 Round 4: 117 peptides, 16 chains. Longest chain 14 peptides. Score 0.566 Round 5: 116 peptides, 15 chains. Longest chain 15 peptides. Score 0.586 Taking the results from Round 3 Chains 14, Residues 101, Estimated correctness of the model 42.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3029 restraints for refining 1493 atoms. 2639 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2642 (Rfree = 0.000) for 1493 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 37: After refmac, R = 0.2248 (Rfree = 0.000) for 1491 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2299 (Rfree = 0.000) for 1485 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2641 (Rfree = 0.000) for 1479 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.2863 (Rfree = 0.000) for 1478 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.64 Search for helices and strands: 0 residues in 0 chains, 1512 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1539 seeds are put forward Round 1: 80 peptides, 14 chains. Longest chain 10 peptides. Score 0.374 Round 2: 94 peptides, 15 chains. Longest chain 13 peptides. Score 0.445 Round 3: 98 peptides, 16 chains. Longest chain 14 peptides. Score 0.443 Round 4: 100 peptides, 15 chains. Longest chain 12 peptides. Score 0.487 Round 5: 107 peptides, 16 chains. Longest chain 12 peptides. Score 0.504 Taking the results from Round 5 Chains 16, Residues 91, Estimated correctness of the model 12.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 2938 restraints for refining 1454 atoms. 2555 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2795 (Rfree = 0.000) for 1454 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2528 (Rfree = 0.000) for 1454 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2073 (Rfree = 0.000) for 1459 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2129 (Rfree = 0.000) for 1449 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1971 (Rfree = 0.000) for 1444 atoms. Found 3 (11 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, 1467 seeds are put forward NCS extension: 0 residues added, 1467 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 10 peptides. Score 0.344 Round 2: 98 peptides, 16 chains. Longest chain 11 peptides. Score 0.443 Round 3: 100 peptides, 15 chains. Longest chain 11 peptides. Score 0.487 Round 4: 90 peptides, 14 chains. Longest chain 11 peptides. Score 0.448 Round 5: 87 peptides, 12 chains. Longest chain 15 peptides. Score 0.489 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 75, Estimated correctness of the model 7.7 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 11 % 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 3262 restraints for refining 1502 atoms. 2945 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2452 (Rfree = 0.000) for 1502 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2231 (Rfree = 0.000) for 1494 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2268 (Rfree = 0.000) for 1485 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2764 (Rfree = 0.000) for 1479 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:31:03 GMT 2018 Job finished. TimeTaking 26.35 Used memory is bytes: 8210896