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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-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/2ozj-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-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 22:22:53 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.6503 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-3.4-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: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-3.4-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 3.400 Wilson plot Bfac: 77.77 3159 reflections ( 99.37 % complete ) and 0 restraints for refining 2017 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3255 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3605 (Rfree = 0.000) for 2017 atoms. Found 13 (15 requested) and removed 35 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.77 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: 89 peptides, 15 chains. Longest chain 11 peptides. Score 0.409 Round 2: 116 peptides, 17 chains. Longest chain 13 peptides. Score 0.533 Round 3: 136 peptides, 19 chains. Longest chain 14 peptides. Score 0.598 Round 4: 135 peptides, 18 chains. Longest chain 14 peptides. Score 0.616 Round 5: 140 peptides, 16 chains. Longest chain 19 peptides. Score 0.685 Taking the results from Round 5 Chains 17, Residues 124, Estimated correctness of the model 53.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3639 restraints for refining 1658 atoms. 3126 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3290 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.3144 (Rfree = 0.000) for 1623 atoms. Found 10 (12 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2733 (Rfree = 0.000) for 1586 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2857 (Rfree = 0.000) for 1567 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.2483 (Rfree = 0.000) for 1561 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 1603 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 1619 seeds are put forward Round 1: 110 peptides, 19 chains. Longest chain 9 peptides. Score 0.436 Round 2: 122 peptides, 16 chains. Longest chain 20 peptides. Score 0.594 Round 3: 120 peptides, 15 chains. Longest chain 21 peptides. Score 0.608 Round 4: 125 peptides, 15 chains. Longest chain 17 peptides. Score 0.634 Round 5: 116 peptides, 14 chains. Longest chain 14 peptides. Score 0.611 Taking the results from Round 4 Chains 15, Residues 110, Estimated correctness of the model 39.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3621 restraints for refining 1607 atoms. 3196 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3054 (Rfree = 0.000) for 1607 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.2567 (Rfree = 0.000) for 1591 atoms. Found 11 (12 requested) and removed 12 (6 requested) atoms. Cycle 8: After refmac, R = 0.2296 (Rfree = 0.000) for 1585 atoms. Found 4 (12 requested) and removed 14 (6 requested) atoms. Cycle 9: After refmac, R = 0.2332 (Rfree = 0.000) for 1571 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.2262 (Rfree = 0.000) for 1572 atoms. Found 7 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.83 Search for helices and strands: 0 residues in 0 chains, 1623 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1642 seeds are put forward Round 1: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.403 Round 2: 117 peptides, 19 chains. Longest chain 15 peptides. Score 0.484 Round 3: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.473 Round 4: 116 peptides, 16 chains. Longest chain 15 peptides. Score 0.560 Round 5: 119 peptides, 16 chains. Longest chain 25 peptides. Score 0.577 Taking the results from Round 5 Chains 16, Residues 103, Estimated correctness of the model 21.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3870 restraints for refining 1658 atoms. 3474 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2602 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 12: After refmac, R = 0.2210 (Rfree = 0.000) for 1636 atoms. Found 8 (12 requested) and removed 13 (6 requested) atoms. Cycle 13: After refmac, R = 0.2278 (Rfree = 0.000) for 1617 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2496 (Rfree = 0.000) for 1613 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.2362 (Rfree = 0.000) for 1608 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.73 Search for helices and strands: 0 residues in 0 chains, 1666 seeds are put forward NCS extension: 46 residues added (3 deleted due to clashes), 1712 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.320 Round 2: 100 peptides, 15 chains. Longest chain 11 peptides. Score 0.487 Round 3: 115 peptides, 16 chains. Longest chain 14 peptides. Score 0.554 Round 4: 116 peptides, 16 chains. Longest chain 17 peptides. Score 0.560 Round 5: 120 peptides, 16 chains. Longest chain 18 peptides. Score 0.583 Taking the results from Round 5 Chains 17, Residues 104, Estimated correctness of the model 23.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3588 restraints for refining 1636 atoms. 3136 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2724 (Rfree = 0.000) for 1636 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 17: After refmac, R = 0.2853 (Rfree = 0.000) for 1612 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 18: After refmac, R = 0.2870 (Rfree = 0.000) for 1591 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 19: After refmac, R = 0.2785 (Rfree = 0.000) for 1578 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.2306 (Rfree = 0.000) for 1573 atoms. Found 7 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.76 Search for helices and strands: 0 residues in 0 chains, 1618 seeds are put forward NCS extension: 0 residues added, 1618 seeds are put forward Round 1: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.322 Round 2: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.422 Round 3: 121 peptides, 17 chains. Longest chain 15 peptides. Score 0.563 Round 4: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.473 Round 5: 127 peptides, 19 chains. Longest chain 12 peptides. Score 0.547 Taking the results from Round 3 Chains 17, Residues 104, Estimated correctness of the model 16.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3467 restraints for refining 1556 atoms. 3068 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2384 (Rfree = 0.000) for 1556 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 22: After refmac, R = 0.2388 (Rfree = 0.000) for 1545 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.2666 (Rfree = 0.000) for 1531 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 24: After refmac, R = 0.2444 (Rfree = 0.000) for 1527 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2195 (Rfree = 0.000) for 1530 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.72 Search for helices and strands: 0 residues in 0 chains, 1554 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 1570 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.336 Round 2: 105 peptides, 18 chains. Longest chain 13 peptides. Score 0.431 Round 3: 113 peptides, 18 chains. Longest chain 12 peptides. Score 0.486 Round 4: 122 peptides, 18 chains. Longest chain 16 peptides. Score 0.543 Round 5: 112 peptides, 17 chains. Longest chain 12 peptides. Score 0.508 Taking the results from Round 4 Chains 18, Residues 104, Estimated correctness of the model 9.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3230 restraints for refining 1497 atoms. 2832 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2865 (Rfree = 0.000) for 1497 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 27: After refmac, R = 0.3251 (Rfree = 0.000) for 1488 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.2582 (Rfree = 0.000) for 1477 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2745 (Rfree = 0.000) for 1470 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2404 (Rfree = 0.000) for 1472 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 1524 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 1548 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.330 Round 2: 91 peptides, 14 chains. Longest chain 12 peptides. Score 0.455 Round 3: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.461 Round 4: 103 peptides, 17 chains. Longest chain 12 peptides. Score 0.448 Round 5: 115 peptides, 16 chains. Longest chain 13 peptides. Score 0.554 Taking the results from Round 5 Chains 16, Residues 99, Estimated correctness of the model 13.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3192 restraints for refining 1470 atoms. 2812 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3051 (Rfree = 0.000) for 1470 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 32: After refmac, R = 0.2822 (Rfree = 0.000) for 1455 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.2751 (Rfree = 0.000) for 1452 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2666 (Rfree = 0.000) for 1452 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2570 (Rfree = 0.000) for 1455 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.71 Search for helices and strands: 0 residues in 0 chains, 1496 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1511 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 11 peptides. Score 0.296 Round 2: 104 peptides, 19 chains. Longest chain 14 peptides. Score 0.393 Round 3: 104 peptides, 18 chains. Longest chain 17 peptides. Score 0.424 Round 4: 101 peptides, 18 chains. Longest chain 13 peptides. Score 0.403 Round 5: 93 peptides, 16 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 3 Chains 18, Residues 86, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3133 restraints for refining 1431 atoms. 2790 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2900 (Rfree = 0.000) for 1431 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 37: After refmac, R = 0.2791 (Rfree = 0.000) for 1421 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2711 (Rfree = 0.000) for 1410 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2750 (Rfree = 0.000) for 1405 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2653 (Rfree = 0.000) for 1403 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.72 Search for helices and strands: 0 residues in 0 chains, 1440 seeds are put forward NCS extension: 0 residues added, 1440 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.239 Round 2: 85 peptides, 16 chains. Longest chain 13 peptides. Score 0.346 Round 3: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.382 Round 4: 96 peptides, 16 chains. Longest chain 16 peptides. Score 0.429 Round 5: 91 peptides, 15 chains. Longest chain 17 peptides. Score 0.424 Taking the results from Round 4 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3055 restraints for refining 1423 atoms. 2725 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2560 (Rfree = 0.000) for 1423 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.2460 (Rfree = 0.000) for 1415 atoms. Found 5 (10 requested) and removed 12 (5 requested) atoms. Cycle 43: After refmac, R = 0.2772 (Rfree = 0.000) for 1404 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2558 (Rfree = 0.000) for 1407 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.2479 (Rfree = 0.000) for 1401 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.71 Search for helices and strands: 0 residues in 0 chains, 1430 seeds are put forward NCS extension: 0 residues added, 1430 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 10 peptides. Score 0.266 Round 2: 79 peptides, 15 chains. Longest chain 12 peptides. Score 0.332 Round 3: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.301 Round 4: 84 peptides, 14 chains. Longest chain 13 peptides. Score 0.404 Round 5: 79 peptides, 14 chains. Longest chain 13 peptides. Score 0.366 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 70, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2ozj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3159 reflections ( 99.37 % complete ) and 3035 restraints for refining 1421 atoms. 2743 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2735 (Rfree = 0.000) for 1421 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2631 (Rfree = 0.000) for 1408 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2499 (Rfree = 0.000) for 1397 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2467 (Rfree = 0.000) for 1390 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 30.67