Mon 24 Dec 08:03:08 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 2obn-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2obn-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2obn-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.6-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/2obn-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.6-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 08:03:13 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/2obn-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.6-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 879 and 0 Target number of residues in the AU: 879 Target solvent content: 0.6480 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-3.6-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: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 11168 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: 73.214 3.600 Wilson plot Bfac: 76.69 15421 reflections ( 99.62 % complete ) and 0 restraints for refining 12457 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3133 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2761 (Rfree = 0.000) for 12457 atoms. Found 79 (79 requested) and removed 100 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 12679 seeds are put forward NCS extension: 0 residues added, 12679 seeds are put forward Round 1: 519 peptides, 102 chains. Longest chain 15 peptides. Score 0.319 Round 2: 629 peptides, 107 chains. Longest chain 14 peptides. Score 0.426 Round 3: 689 peptides, 111 chains. Longest chain 18 peptides. Score 0.473 Round 4: 733 peptides, 109 chains. Longest chain 15 peptides. Score 0.528 Round 5: 732 peptides, 112 chains. Longest chain 18 peptides. Score 0.514 Taking the results from Round 4 Chains 111, Residues 624, Estimated correctness of the model 0.0 % 9 chains (53 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23250 restraints for refining 10123 atoms. 20724 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2276 (Rfree = 0.000) for 10123 atoms. Found 45 (64 requested) and removed 66 (32 requested) atoms. Cycle 2: After refmac, R = 0.2072 (Rfree = 0.000) for 9936 atoms. Found 38 (64 requested) and removed 52 (32 requested) atoms. Cycle 3: After refmac, R = 0.2007 (Rfree = 0.000) for 9860 atoms. Found 31 (63 requested) and removed 45 (31 requested) atoms. Cycle 4: After refmac, R = 0.1892 (Rfree = 0.000) for 9792 atoms. Found 20 (63 requested) and removed 43 (31 requested) atoms. Cycle 5: After refmac, R = 0.1853 (Rfree = 0.000) for 9749 atoms. Found 11 (62 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.74 Search for helices and strands: 0 residues in 0 chains, 10053 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10067 seeds are put forward Round 1: 603 peptides, 108 chains. Longest chain 12 peptides. Score 0.391 Round 2: 668 peptides, 102 chains. Longest chain 14 peptides. Score 0.493 Round 3: 663 peptides, 104 chains. Longest chain 17 peptides. Score 0.478 Round 4: 668 peptides, 95 chains. Longest chain 20 peptides. Score 0.524 Round 5: 696 peptides, 103 chains. Longest chain 22 peptides. Score 0.517 Taking the results from Round 4 Chains 97, Residues 573, Estimated correctness of the model 0.0 % 15 chains (99 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 22978 restraints for refining 10069 atoms. 20479 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1993 (Rfree = 0.000) for 10069 atoms. Found 49 (64 requested) and removed 81 (32 requested) atoms. Cycle 7: After refmac, R = 0.1941 (Rfree = 0.000) for 9945 atoms. Found 42 (64 requested) and removed 54 (32 requested) atoms. Cycle 8: After refmac, R = 0.1791 (Rfree = 0.000) for 9893 atoms. Found 35 (63 requested) and removed 43 (31 requested) atoms. Cycle 9: After refmac, R = 0.1721 (Rfree = 0.000) for 9853 atoms. Found 29 (63 requested) and removed 37 (31 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1668 (Rfree = 0.000) for 9819 atoms. Found 21 (63 requested) and removed 41 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.76 Search for helices and strands: 0 residues in 0 chains, 10123 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 10138 seeds are put forward Round 1: 611 peptides, 117 chains. Longest chain 12 peptides. Score 0.355 Round 2: 702 peptides, 105 chains. Longest chain 17 peptides. Score 0.514 Round 3: 724 peptides, 111 chains. Longest chain 17 peptides. Score 0.510 Round 4: 704 peptides, 102 chains. Longest chain 18 peptides. Score 0.529 Round 5: 702 peptides, 100 chains. Longest chain 20 peptides. Score 0.536 Taking the results from Round 5 Chains 106, Residues 602, Estimated correctness of the model 0.0 % 12 chains (88 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23090 restraints for refining 10121 atoms. 20564 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1931 (Rfree = 0.000) for 10121 atoms. Found 49 (64 requested) and removed 72 (32 requested) atoms. Cycle 12: After refmac, R = 0.1820 (Rfree = 0.000) for 10050 atoms. Found 30 (64 requested) and removed 50 (32 requested) atoms. Cycle 13: After refmac, R = 0.1749 (Rfree = 0.000) for 10007 atoms. Found 34 (64 requested) and removed 39 (32 requested) atoms. Cycle 14: After refmac, R = 0.1691 (Rfree = 0.000) for 9991 atoms. Found 26 (64 requested) and removed 43 (32 requested) atoms. Cycle 15: After refmac, R = 0.1677 (Rfree = 0.000) for 9964 atoms. Found 23 (63 requested) and removed 43 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 10283 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 10301 seeds are put forward Round 1: 568 peptides, 104 chains. Longest chain 17 peptides. Score 0.369 Round 2: 640 peptides, 100 chains. Longest chain 17 peptides. Score 0.472 Round 3: 653 peptides, 103 chains. Longest chain 17 peptides. Score 0.472 Round 4: 678 peptides, 101 chains. Longest chain 26 peptides. Score 0.508 Round 5: 686 peptides, 97 chains. Longest chain 23 peptides. Score 0.533 Taking the results from Round 5 Chains 103, Residues 589, Estimated correctness of the model 0.0 % 15 chains (111 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 15421 reflections ( 99.62 % complete ) and 22452 restraints for refining 10121 atoms. 19883 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1875 (Rfree = 0.000) for 10121 atoms. Found 43 (64 requested) and removed 59 (32 requested) atoms. Cycle 17: After refmac, R = 0.1789 (Rfree = 0.000) for 10061 atoms. Found 32 (64 requested) and removed 51 (32 requested) atoms. Cycle 18: After refmac, R = 0.1718 (Rfree = 0.000) for 10020 atoms. Found 29 (64 requested) and removed 40 (32 requested) atoms. Cycle 19: After refmac, R = 0.1660 (Rfree = 0.000) for 9987 atoms. Found 28 (64 requested) and removed 40 (32 requested) atoms. Cycle 20: After refmac, R = 0.1610 (Rfree = 0.000) for 9952 atoms. Found 25 (63 requested) and removed 37 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 10273 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 10293 seeds are put forward Round 1: 561 peptides, 110 chains. Longest chain 10 peptides. Score 0.329 Round 2: 591 peptides, 95 chains. Longest chain 15 peptides. Score 0.442 Round 3: 624 peptides, 103 chains. Longest chain 13 peptides. Score 0.440 Round 4: 607 peptides, 91 chains. Longest chain 25 peptides. Score 0.479 Round 5: 602 peptides, 86 chains. Longest chain 25 peptides. Score 0.497 Taking the results from Round 5 Chains 87, Residues 516, Estimated correctness of the model 0.0 % 10 chains (50 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23903 restraints for refining 10123 atoms. 21790 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1914 (Rfree = 0.000) for 10123 atoms. Found 33 (64 requested) and removed 44 (32 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1806 (Rfree = 0.000) for 10065 atoms. Found 44 (64 requested) and removed 41 (32 requested) atoms. Cycle 23: After refmac, R = 0.1672 (Rfree = 0.000) for 10040 atoms. Found 33 (64 requested) and removed 41 (32 requested) atoms. Cycle 24: After refmac, R = 0.1579 (Rfree = 0.000) for 10011 atoms. Found 35 (64 requested) and removed 36 (32 requested) atoms. Cycle 25: After refmac, R = 0.1607 (Rfree = 0.000) for 9994 atoms. Found 40 (64 requested) and removed 43 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 10260 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 10276 seeds are put forward Round 1: 527 peptides, 108 chains. Longest chain 14 peptides. Score 0.297 Round 2: 577 peptides, 94 chains. Longest chain 14 peptides. Score 0.431 Round 3: 567 peptides, 94 chains. Longest chain 14 peptides. Score 0.419 Round 4: 580 peptides, 91 chains. Longest chain 17 peptides. Score 0.449 Round 5: 598 peptides, 97 chains. Longest chain 15 peptides. Score 0.440 Taking the results from Round 4 Chains 93, Residues 489, Estimated correctness of the model 0.0 % 10 chains (68 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23640 restraints for refining 10124 atoms. 21593 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1807 (Rfree = 0.000) for 10124 atoms. Found 37 (64 requested) and removed 44 (32 requested) atoms. Cycle 27: After refmac, R = 0.1737 (Rfree = 0.000) for 10091 atoms. Found 32 (64 requested) and removed 41 (32 requested) atoms. Cycle 28: After refmac, R = 0.1685 (Rfree = 0.000) for 10057 atoms. Found 44 (64 requested) and removed 38 (32 requested) atoms. Cycle 29: After refmac, R = 0.1640 (Rfree = 0.000) for 10039 atoms. Found 29 (64 requested) and removed 38 (32 requested) atoms. Cycle 30: After refmac, R = 0.1615 (Rfree = 0.000) for 10020 atoms. Found 34 (64 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 10316 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 10336 seeds are put forward Round 1: 427 peptides, 88 chains. Longest chain 13 peptides. Score 0.275 Round 2: 512 peptides, 88 chains. Longest chain 16 peptides. Score 0.385 Round 3: 518 peptides, 87 chains. Longest chain 17 peptides. Score 0.397 Round 4: 511 peptides, 86 chains. Longest chain 14 peptides. Score 0.394 Round 5: 536 peptides, 88 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 5 Chains 88, Residues 448, Estimated correctness of the model 0.0 % 6 chains (37 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 24102 restraints for refining 10124 atoms. 22311 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1825 (Rfree = 0.000) for 10124 atoms. Found 64 (64 requested) and removed 45 (32 requested) atoms. Cycle 32: After refmac, R = 0.1640 (Rfree = 0.000) for 10101 atoms. Found 47 (65 requested) and removed 38 (32 requested) atoms. Cycle 33: After refmac, R = 0.1640 (Rfree = 0.000) for 10083 atoms. Found 42 (64 requested) and removed 39 (32 requested) atoms. Cycle 34: After refmac, R = 0.1597 (Rfree = 0.000) for 10071 atoms. Found 59 (64 requested) and removed 35 (32 requested) atoms. Cycle 35: After refmac, R = 0.1574 (Rfree = 0.000) for 10081 atoms. Found 46 (64 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.78 Search for helices and strands: 0 residues in 0 chains, 10377 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 10394 seeds are put forward Round 1: 458 peptides, 97 chains. Longest chain 11 peptides. Score 0.266 Round 2: 505 peptides, 93 chains. Longest chain 11 peptides. Score 0.350 Round 3: 500 peptides, 87 chains. Longest chain 16 peptides. Score 0.375 Round 4: 505 peptides, 89 chains. Longest chain 17 peptides. Score 0.371 Round 5: 498 peptides, 85 chains. Longest chain 17 peptides. Score 0.384 Taking the results from Round 5 Chains 85, Residues 413, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 24732 restraints for refining 10124 atoms. 23151 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1707 (Rfree = 0.000) for 10124 atoms. Found 63 (64 requested) and removed 37 (32 requested) atoms. Cycle 37: After refmac, R = 0.1654 (Rfree = 0.000) for 10110 atoms. Found 54 (65 requested) and removed 36 (32 requested) atoms. Cycle 38: After refmac, R = 0.1643 (Rfree = 0.000) for 10117 atoms. Found 56 (64 requested) and removed 41 (32 requested) atoms. Cycle 39: After refmac, R = 0.1580 (Rfree = 0.000) for 10116 atoms. Found 52 (65 requested) and removed 34 (32 requested) atoms. Cycle 40: After refmac, R = 0.1521 (Rfree = 0.000) for 10119 atoms. Found 46 (65 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.78 Search for helices and strands: 0 residues in 0 chains, 10426 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 10454 seeds are put forward Round 1: 407 peptides, 84 chains. Longest chain 10 peptides. Score 0.271 Round 2: 469 peptides, 87 chains. Longest chain 10 peptides. Score 0.336 Round 3: 463 peptides, 84 chains. Longest chain 11 peptides. Score 0.345 Round 4: 468 peptides, 81 chains. Longest chain 12 peptides. Score 0.368 Round 5: 481 peptides, 83 chains. Longest chain 14 peptides. Score 0.373 Taking the results from Round 5 Chains 83, Residues 398, Estimated correctness of the model 0.0 % 10 chains (43 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 24477 restraints for refining 10124 atoms. 22877 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1667 (Rfree = 0.000) for 10124 atoms. Found 41 (64 requested) and removed 40 (32 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1650 (Rfree = 0.000) for 10088 atoms. Found 43 (64 requested) and removed 37 (32 requested) atoms. Cycle 43: After refmac, R = 0.1604 (Rfree = 0.000) for 10081 atoms. Found 51 (64 requested) and removed 33 (32 requested) atoms. Cycle 44: After refmac, R = 0.1528 (Rfree = 0.000) for 10085 atoms. Found 42 (64 requested) and removed 38 (32 requested) atoms. Cycle 45: After refmac, R = 0.1175 (Rfree = 0.000) for 10075 atoms. Found 8 (64 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.76 Search for helices and strands: 0 residues in 0 chains, 10363 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 10381 seeds are put forward Round 1: 352 peptides, 76 chains. Longest chain 8 peptides. Score 0.240 Round 2: 414 peptides, 80 chains. Longest chain 14 peptides. Score 0.304 Round 3: 427 peptides, 77 chains. Longest chain 14 peptides. Score 0.338 Round 4: 427 peptides, 76 chains. Longest chain 16 peptides. Score 0.343 Round 5: 423 peptides, 78 chains. Longest chain 11 peptides. Score 0.327 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 76, Residues 351, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 76 chains (351 residues) following loop building 6 chains (30 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15421 reflections ( 99.62 % complete ) and 24909 restraints for refining 10122 atoms. 23515 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1598 (Rfree = 0.000) for 10122 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.1654 (Rfree = 0.000) for 10067 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.1555 (Rfree = 0.000) for 10023 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1553 (Rfree = 0.000) for 9984 atoms. TimeTaking 94.45