null Mon 24 Dec 07:36:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2od4-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2od4-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2od4-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-parrot-noncs ############### 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 07:36:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-parrot-noncs/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 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.6198 Checking the provided sequence file Detected sequence length: 101 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 202 Adjusted target solvent content: 0.48 Input MTZ file: 2od4-3.2-parrot-noncs.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: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 1616 target number of atoms Had to go as low as 0.65 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: 28.889 3.200 Wilson plot Bfac: 61.23 3433 reflections ( 98.54 % complete ) and 0 restraints for refining 1779 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3169 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2631 (Rfree = 0.000) for 1779 atoms. Found 13 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward NCS extension: 0 residues added, 1823 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 14 peptides. Score 0.330 Round 2: 93 peptides, 16 chains. Longest chain 15 peptides. Score 0.409 Round 3: 112 peptides, 20 chains. Longest chain 13 peptides. Score 0.424 Round 4: 117 peptides, 21 chains. Longest chain 10 peptides. Score 0.429 Round 5: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.486 Taking the results from Round 5 Chains 20, Residues 101, Estimated correctness of the model 6.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3215 restraints for refining 1475 atoms. 2831 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2294 (Rfree = 0.000) for 1475 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 2: After refmac, R = 0.2083 (Rfree = 0.000) for 1455 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2028 (Rfree = 0.000) for 1437 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2059 (Rfree = 0.000) for 1428 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.1915 (Rfree = 0.000) for 1418 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 1485 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1491 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.364 Round 2: 113 peptides, 18 chains. Longest chain 18 peptides. Score 0.490 Round 3: 114 peptides, 17 chains. Longest chain 13 peptides. Score 0.524 Round 4: 112 peptides, 15 chains. Longest chain 24 peptides. Score 0.567 Round 5: 111 peptides, 17 chains. Longest chain 12 peptides. Score 0.505 Taking the results from Round 4 Chains 15, Residues 97, Estimated correctness of the model 31.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3263 restraints for refining 1476 atoms. 2890 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2263 (Rfree = 0.000) for 1476 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. Cycle 7: After refmac, R = 0.2101 (Rfree = 0.000) for 1470 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.2091 (Rfree = 0.000) for 1463 atoms. Found 2 (13 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.2018 (Rfree = 0.000) for 1453 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.1939 (Rfree = 0.000) for 1444 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 3.19 Search for helices and strands: 0 residues in 0 chains, 1490 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 1520 seeds are put forward Round 1: 98 peptides, 15 chains. Longest chain 14 peptides. Score 0.476 Round 2: 104 peptides, 17 chains. Longest chain 14 peptides. Score 0.458 Round 3: 95 peptides, 16 chains. Longest chain 12 peptides. Score 0.424 Round 4: 92 peptides, 13 chains. Longest chain 15 peptides. Score 0.496 Round 5: 100 peptides, 16 chains. Longest chain 16 peptides. Score 0.460 Taking the results from Round 4 Chains 13, Residues 79, Estimated correctness of the model 10.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3342 restraints for refining 1467 atoms. 3039 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2148 (Rfree = 0.000) for 1467 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 12: After refmac, R = 0.2081 (Rfree = 0.000) for 1468 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.2082 (Rfree = 0.000) for 1462 atoms. Found 7 (13 requested) and removed 16 (6 requested) atoms. Cycle 14: After refmac, R = 0.2461 (Rfree = 0.000) for 1452 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2342 (Rfree = 0.000) for 1450 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.31 Search for helices and strands: 0 residues in 0 chains, 1504 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1525 seeds are put forward Round 1: 87 peptides, 15 chains. Longest chain 11 peptides. Score 0.397 Round 2: 99 peptides, 16 chains. Longest chain 15 peptides. Score 0.453 Round 3: 103 peptides, 18 chains. Longest chain 9 peptides. Score 0.420 Round 4: 101 peptides, 13 chains. Longest chain 15 peptides. Score 0.554 Round 5: 99 peptides, 16 chains. Longest chain 14 peptides. Score 0.453 Taking the results from Round 4 Chains 13, Residues 88, Estimated correctness of the model 28.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3317 restraints for refining 1468 atoms. 2978 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2190 (Rfree = 0.000) for 1468 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 17: After refmac, R = 0.2020 (Rfree = 0.000) for 1469 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2347 (Rfree = 0.000) for 1467 atoms. Found 7 (13 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.1914 (Rfree = 0.000) for 1462 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.1997 (Rfree = 0.000) for 1457 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 1511 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1527 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.343 Round 2: 117 peptides, 20 chains. Longest chain 13 peptides. Score 0.459 Round 3: 125 peptides, 17 chains. Longest chain 18 peptides. Score 0.590 Round 4: 118 peptides, 17 chains. Longest chain 12 peptides. Score 0.549 Round 5: 119 peptides, 14 chains. Longest chain 25 peptides. Score 0.631 Taking the results from Round 5 Chains 14, Residues 105, Estimated correctness of the model 49.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3270 restraints for refining 1476 atoms. 2864 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2092 (Rfree = 0.000) for 1476 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 22: After refmac, R = 0.2118 (Rfree = 0.000) for 1472 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2102 (Rfree = 0.000) for 1474 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.1676 (Rfree = 0.000) for 1474 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1577 (Rfree = 0.000) for 1473 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.17 Search for helices and strands: 0 residues in 0 chains, 1521 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 1563 seeds are put forward Round 1: 107 peptides, 19 chains. Longest chain 11 peptides. Score 0.418 Round 2: 108 peptides, 16 chains. Longest chain 13 peptides. Score 0.514 Round 3: 112 peptides, 17 chains. Longest chain 14 peptides. Score 0.512 Round 4: 104 peptides, 15 chains. Longest chain 13 peptides. Score 0.517 Round 5: 103 peptides, 15 chains. Longest chain 10 peptides. Score 0.510 Taking the results from Round 4 Chains 15, Residues 89, Estimated correctness of the model 16.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3349 restraints for refining 1476 atoms. 3008 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2030 (Rfree = 0.000) for 1476 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.2071 (Rfree = 0.000) for 1474 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.1869 (Rfree = 0.000) for 1471 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.1651 (Rfree = 0.000) for 1466 atoms. Found 1 (13 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.1731 (Rfree = 0.000) for 1457 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 3.17 Search for helices and strands: 0 residues in 0 chains, 1495 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1501 seeds are put forward Round 1: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.448 Round 2: 104 peptides, 15 chains. Longest chain 19 peptides. Score 0.517 Round 3: 112 peptides, 14 chains. Longest chain 22 peptides. Score 0.593 Round 4: 102 peptides, 15 chains. Longest chain 10 peptides. Score 0.503 Round 5: 99 peptides, 12 chains. Longest chain 22 peptides. Score 0.570 Taking the results from Round 3 Chains 14, Residues 98, Estimated correctness of the model 39.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3241 restraints for refining 1476 atoms. 2863 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1881 (Rfree = 0.000) for 1476 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 32: After refmac, R = 0.1825 (Rfree = 0.000) for 1470 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.1685 (Rfree = 0.000) for 1465 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1637 (Rfree = 0.000) for 1460 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1611 (Rfree = 0.000) for 1458 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 1479 seeds are put forward NCS extension: 32 residues added (5 deleted due to clashes), 1511 seeds are put forward Round 1: 88 peptides, 13 chains. Longest chain 18 peptides. Score 0.468 Round 2: 104 peptides, 14 chains. Longest chain 20 peptides. Score 0.545 Round 3: 99 peptides, 13 chains. Longest chain 22 peptides. Score 0.542 Round 4: 109 peptides, 15 chains. Longest chain 20 peptides. Score 0.548 Round 5: 114 peptides, 16 chains. Longest chain 20 peptides. Score 0.552 Taking the results from Round 5 Chains 16, Residues 98, Estimated correctness of the model 27.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3308 restraints for refining 1476 atoms. 2932 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2064 (Rfree = 0.000) for 1476 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 37: After refmac, R = 0.1778 (Rfree = 0.000) for 1475 atoms. Found 9 (13 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.2061 (Rfree = 0.000) for 1477 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2186 (Rfree = 0.000) for 1480 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 40: After refmac, R = 0.1482 (Rfree = 0.000) for 1481 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 1520 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 1550 seeds are put forward Round 1: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.394 Round 2: 110 peptides, 14 chains. Longest chain 21 peptides. Score 0.581 Round 3: 104 peptides, 15 chains. Longest chain 14 peptides. Score 0.517 Round 4: 93 peptides, 12 chains. Longest chain 12 peptides. Score 0.532 Round 5: 82 peptides, 13 chains. Longest chain 12 peptides. Score 0.425 Taking the results from Round 2 Chains 14, Residues 96, Estimated correctness of the model 35.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3264 restraints for refining 1476 atoms. 2894 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1738 (Rfree = 0.000) for 1476 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.1505 (Rfree = 0.000) for 1482 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.1421 (Rfree = 0.000) for 1477 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1380 (Rfree = 0.000) for 1472 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1351 (Rfree = 0.000) for 1466 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.17 Search for helices and strands: 0 residues in 0 chains, 1511 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 1544 seeds are put forward Round 1: 90 peptides, 14 chains. Longest chain 10 peptides. Score 0.451 Round 2: 96 peptides, 16 chains. Longest chain 10 peptides. Score 0.431 Round 3: 109 peptides, 16 chains. Longest chain 11 peptides. Score 0.520 Round 4: 111 peptides, 16 chains. Longest chain 12 peptides. Score 0.533 Round 5: 94 peptides, 14 chains. Longest chain 10 peptides. Score 0.479 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 95, Estimated correctness of the model 21.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2od4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3433 reflections ( 98.54 % complete ) and 3232 restraints for refining 1476 atoms. 2868 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1728 (Rfree = 0.000) for 1476 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1612 (Rfree = 0.000) for 1470 atoms. Found 0 (13 requested) and removed 0 (6 requested) atoms. Cycle 48: After refmac, R = 0.1491 (Rfree = 0.000) for 1468 atoms. Found 0 (13 requested) and removed 1 (6 requested) atoms. Cycle 49: After refmac, R = 0.1432 (Rfree = 0.000) for 1467 atoms. Found 0 (13 requested) and removed 0 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:59:16 GMT 2018 Job finished. TimeTaking 22.36 Used memory is bytes: 6640856