Mon 24 Dec 00:43:33 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 2ooc-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ooc-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ooc-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-3.4-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/2ooc-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-3.4-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 00:43:37 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/2ooc-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-3.4-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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6431 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.53 Input MTZ file: 2ooc-3.4-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: 154 Cell parameters: 62.597 62.597 115.277 90.000 90.000 120.000 Input sequence file: 2ooc-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1808 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: 54.211 3.400 Wilson plot Bfac: 73.43 3879 reflections ( 99.77 % complete ) and 0 restraints for refining 2001 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3367 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2975 (Rfree = 0.000) for 2001 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 2056 seeds are put forward NCS extension: 0 residues added, 2056 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 11 peptides. Score 0.338 Round 2: 115 peptides, 18 chains. Longest chain 18 peptides. Score 0.456 Round 3: 111 peptides, 16 chains. Longest chain 20 peptides. Score 0.483 Round 4: 106 peptides, 15 chains. Longest chain 20 peptides. Score 0.480 Round 5: 106 peptides, 16 chains. Longest chain 20 peptides. Score 0.454 Taking the results from Round 3 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3673 restraints for refining 1644 atoms. 3189 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2685 (Rfree = 0.000) for 1644 atoms. Found 11 (12 requested) and removed 24 (6 requested) atoms. Cycle 2: After refmac, R = 0.2593 (Rfree = 0.000) for 1598 atoms. Found 8 (12 requested) and removed 17 (6 requested) atoms. Cycle 3: After refmac, R = 0.2587 (Rfree = 0.000) for 1578 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2558 (Rfree = 0.000) for 1576 atoms. Found 2 (11 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.2573 (Rfree = 0.000) for 1564 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 1657 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 1677 seeds are put forward Round 1: 103 peptides, 19 chains. Longest chain 11 peptides. Score 0.356 Round 2: 107 peptides, 15 chains. Longest chain 18 peptides. Score 0.486 Round 3: 106 peptides, 14 chains. Longest chain 17 peptides. Score 0.505 Round 4: 101 peptides, 12 chains. Longest chain 22 peptides. Score 0.528 Round 5: 105 peptides, 13 chains. Longest chain 14 peptides. Score 0.524 Taking the results from Round 4 Chains 14, Residues 89, Estimated correctness of the model 3.4 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3608 restraints for refining 1576 atoms. 3219 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2548 (Rfree = 0.000) for 1576 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 7: After refmac, R = 0.2397 (Rfree = 0.000) for 1561 atoms. Found 10 (11 requested) and removed 11 (5 requested) atoms. Cycle 8: After refmac, R = 0.2313 (Rfree = 0.000) for 1558 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2255 (Rfree = 0.000) for 1555 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2247 (Rfree = 0.000) for 1541 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 1631 seeds are put forward NCS extension: 0 residues added, 1631 seeds are put forward Round 1: 99 peptides, 16 chains. Longest chain 13 peptides. Score 0.413 Round 2: 107 peptides, 17 chains. Longest chain 14 peptides. Score 0.434 Round 3: 112 peptides, 18 chains. Longest chain 16 peptides. Score 0.438 Round 4: 110 peptides, 15 chains. Longest chain 21 peptides. Score 0.502 Round 5: 112 peptides, 15 chains. Longest chain 16 peptides. Score 0.513 Taking the results from Round 5 Chains 15, Residues 97, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3625 restraints for refining 1599 atoms. 3214 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2631 (Rfree = 0.000) for 1599 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 12: After refmac, R = 0.2433 (Rfree = 0.000) for 1582 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2345 (Rfree = 0.000) for 1579 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2342 (Rfree = 0.000) for 1567 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. Cycle 15: After refmac, R = 0.2353 (Rfree = 0.000) for 1555 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 1652 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1674 seeds are put forward Round 1: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.390 Round 2: 110 peptides, 17 chains. Longest chain 13 peptides. Score 0.452 Round 3: 127 peptides, 21 chains. Longest chain 13 peptides. Score 0.450 Round 4: 119 peptides, 18 chains. Longest chain 16 peptides. Score 0.478 Round 5: 117 peptides, 16 chains. Longest chain 21 peptides. Score 0.516 Taking the results from Round 5 Chains 16, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3658 restraints for refining 1603 atoms. 3270 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2686 (Rfree = 0.000) for 1603 atoms. Found 4 (12 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2554 (Rfree = 0.000) for 1587 atoms. Found 0 (12 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.2522 (Rfree = 0.000) for 1578 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2473 (Rfree = 0.000) for 1570 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2432 (Rfree = 0.000) for 1564 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 1659 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1679 seeds are put forward Round 1: 110 peptides, 21 chains. Longest chain 9 peptides. Score 0.347 Round 2: 122 peptides, 20 chains. Longest chain 13 peptides. Score 0.446 Round 3: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.406 Round 4: 106 peptides, 15 chains. Longest chain 16 peptides. Score 0.480 Round 5: 109 peptides, 16 chains. Longest chain 12 peptides. Score 0.472 Taking the results from Round 4 Chains 15, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3672 restraints for refining 1598 atoms. 3323 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2631 (Rfree = 0.000) for 1598 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 22: After refmac, R = 0.2507 (Rfree = 0.000) for 1585 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.2383 (Rfree = 0.000) for 1580 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2331 (Rfree = 0.000) for 1574 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2311 (Rfree = 0.000) for 1568 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 1620 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 1639 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Round 2: 87 peptides, 14 chains. Longest chain 13 peptides. Score 0.393 Round 3: 90 peptides, 16 chains. Longest chain 8 peptides. Score 0.355 Round 4: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.360 Round 5: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.419 Taking the results from Round 5 Chains 16, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3821 restraints for refining 1627 atoms. 3501 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2459 (Rfree = 0.000) for 1627 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.2307 (Rfree = 0.000) for 1624 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2250 (Rfree = 0.000) for 1615 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2253 (Rfree = 0.000) for 1610 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2213 (Rfree = 0.000) for 1603 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 1683 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 1685 seeds are put forward Round 1: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.351 Round 2: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.366 Round 3: 108 peptides, 17 chains. Longest chain 11 peptides. Score 0.440 Round 4: 110 peptides, 13 chains. Longest chain 18 peptides. Score 0.551 Round 5: 111 peptides, 20 chains. Longest chain 14 peptides. Score 0.380 Taking the results from Round 4 Chains 13, Residues 97, Estimated correctness of the model 11.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3658 restraints for refining 1602 atoms. 3283 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2474 (Rfree = 0.000) for 1602 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2345 (Rfree = 0.000) for 1594 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2282 (Rfree = 0.000) for 1586 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2225 (Rfree = 0.000) for 1582 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.2160 (Rfree = 0.000) for 1573 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 1652 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1668 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 8 peptides. Score 0.248 Round 2: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.375 Round 3: 96 peptides, 16 chains. Longest chain 10 peptides. Score 0.394 Round 4: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.362 Round 5: 95 peptides, 17 chains. Longest chain 8 peptides. Score 0.360 Taking the results from Round 3 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3875 restraints for refining 1627 atoms. 3571 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2316 (Rfree = 0.000) for 1627 atoms. Found 10 (12 requested) and removed 13 (6 requested) atoms. Cycle 37: After refmac, R = 0.2484 (Rfree = 0.000) for 1614 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 38: After refmac, R = 0.2113 (Rfree = 0.000) for 1609 atoms. Found 8 (12 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2560 (Rfree = 0.000) for 1599 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 40: After refmac, R = 0.2439 (Rfree = 0.000) for 1591 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 1676 seeds are put forward NCS extension: 0 residues added, 1676 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 8 peptides. Score 0.248 Round 2: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.312 Round 3: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.345 Round 4: 101 peptides, 18 chains. Longest chain 12 peptides. Score 0.371 Round 5: 100 peptides, 15 chains. Longest chain 15 peptides. Score 0.445 Taking the results from Round 5 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3599 restraints for refining 1583 atoms. 3274 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2248 (Rfree = 0.000) for 1583 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2013 (Rfree = 0.000) for 1578 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.1929 (Rfree = 0.000) for 1575 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.1867 (Rfree = 0.000) for 1577 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.1822 (Rfree = 0.000) for 1569 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 1654 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1667 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 12 peptides. Score 0.300 Round 2: 85 peptides, 14 chains. Longest chain 14 peptides. Score 0.380 Round 3: 91 peptides, 14 chains. Longest chain 12 peptides. Score 0.418 Round 4: 92 peptides, 14 chains. Longest chain 16 peptides. Score 0.424 Round 5: 92 peptides, 14 chains. Longest chain 19 peptides. Score 0.424 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ooc-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3879 reflections ( 99.77 % complete ) and 3720 restraints for refining 1607 atoms. 3422 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2130 (Rfree = 0.000) for 1607 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1972 (Rfree = 0.000) for 1598 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2016 (Rfree = 0.000) for 1591 atoms. Found 0 (12 requested) and removed 0 (6 requested) atoms. Cycle 49: After refmac, R = 0.1929 (Rfree = 0.000) for 1591 atoms. TimeTaking 27.55