Sun 23 Dec 22:23:02 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 2nlv-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-3.2-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/2nlv-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-3.2-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 22:23:12 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/2nlv-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-3.2-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 155 and 0 Target number of residues in the AU: 155 Target solvent content: 0.6190 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 224 Adjusted target solvent content: 0.45 Input MTZ file: 2nlv-3.2-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: 4 Cell parameters: 46.793 37.359 63.476 90.000 97.240 90.000 Input sequence file: 2nlv-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1792 target number of atoms Had to go as low as 0.70 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: 29.104 3.200 Wilson plot Bfac: 60.11 3736 reflections ( 99.84 % complete ) and 0 restraints for refining 1983 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3517 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3202 (Rfree = 0.000) for 1983 atoms. Found 16 (17 requested) and removed 27 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.01 3.22 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward NCS extension: 0 residues added, 2006 seeds are put forward Round 1: 80 peptides, 15 chains. Longest chain 7 peptides. Score 0.337 Round 2: 99 peptides, 18 chains. Longest chain 11 peptides. Score 0.384 Round 3: 106 peptides, 17 chains. Longest chain 12 peptides. Score 0.463 Round 4: 116 peptides, 19 chains. Longest chain 13 peptides. Score 0.472 Round 5: 105 peptides, 16 chains. Longest chain 18 peptides. Score 0.485 Taking the results from Round 5 Chains 16, Residues 89, Estimated correctness of the model 6.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3689 restraints for refining 1635 atoms. 3349 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2457 (Rfree = 0.000) for 1635 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 2: After refmac, R = 0.2600 (Rfree = 0.000) for 1615 atoms. Found 11 (14 requested) and removed 8 (7 requested) atoms. Cycle 3: After refmac, R = 0.2438 (Rfree = 0.000) for 1613 atoms. Found 8 (14 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.2429 (Rfree = 0.000) for 1610 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 5: After refmac, R = 0.2332 (Rfree = 0.000) for 1604 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 1656 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1676 seeds are put forward Round 1: 113 peptides, 21 chains. Longest chain 10 peptides. Score 0.393 Round 2: 122 peptides, 18 chains. Longest chain 18 peptides. Score 0.537 Round 3: 126 peptides, 17 chains. Longest chain 19 peptides. Score 0.585 Round 4: 129 peptides, 19 chains. Longest chain 23 peptides. Score 0.552 Round 5: 128 peptides, 18 chains. Longest chain 23 peptides. Score 0.571 Taking the results from Round 3 Chains 17, Residues 109, Estimated correctness of the model 37.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3599 restraints for refining 1631 atoms. 3180 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2517 (Rfree = 0.000) for 1631 atoms. Found 10 (14 requested) and removed 15 (7 requested) atoms. Cycle 7: After refmac, R = 0.2433 (Rfree = 0.000) for 1625 atoms. Found 10 (14 requested) and removed 9 (7 requested) atoms. Cycle 8: After refmac, R = 0.2447 (Rfree = 0.000) for 1626 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.2299 (Rfree = 0.000) for 1627 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.2365 (Rfree = 0.000) for 1624 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.28 Search for helices and strands: 0 residues in 0 chains, 1683 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 1712 seeds are put forward Round 1: 100 peptides, 17 chains. Longest chain 11 peptides. Score 0.422 Round 2: 124 peptides, 17 chains. Longest chain 22 peptides. Score 0.574 Round 3: 127 peptides, 17 chains. Longest chain 23 peptides. Score 0.590 Round 4: 125 peptides, 17 chains. Longest chain 16 peptides. Score 0.579 Round 5: 126 peptides, 16 chains. Longest chain 23 peptides. Score 0.609 Taking the results from Round 5 Chains 16, Residues 110, Estimated correctness of the model 43.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3623 restraints for refining 1636 atoms. 3199 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2271 (Rfree = 0.000) for 1636 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 12: After refmac, R = 0.2242 (Rfree = 0.000) for 1628 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2163 (Rfree = 0.000) for 1625 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 14: After refmac, R = 0.2153 (Rfree = 0.000) for 1622 atoms. Found 13 (14 requested) and removed 9 (7 requested) atoms. Cycle 15: After refmac, R = 0.2039 (Rfree = 0.000) for 1626 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 1683 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1704 seeds are put forward Round 1: 116 peptides, 22 chains. Longest chain 11 peptides. Score 0.385 Round 2: 127 peptides, 20 chains. Longest chain 19 peptides. Score 0.514 Round 3: 135 peptides, 20 chains. Longest chain 27 peptides. Score 0.561 Round 4: 123 peptides, 19 chains. Longest chain 16 peptides. Score 0.516 Round 5: 123 peptides, 17 chains. Longest chain 20 peptides. Score 0.568 Taking the results from Round 5 Chains 17, Residues 106, Estimated correctness of the model 32.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3642 restraints for refining 1636 atoms. 3235 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2336 (Rfree = 0.000) for 1636 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. Cycle 17: After refmac, R = 0.2242 (Rfree = 0.000) for 1628 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 18: After refmac, R = 0.2151 (Rfree = 0.000) for 1624 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.2132 (Rfree = 0.000) for 1622 atoms. Found 9 (14 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.2015 (Rfree = 0.000) for 1623 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 1676 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 1711 seeds are put forward Round 1: 106 peptides, 17 chains. Longest chain 18 peptides. Score 0.463 Round 2: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.445 Round 3: 110 peptides, 17 chains. Longest chain 18 peptides. Score 0.489 Round 4: 120 peptides, 18 chains. Longest chain 20 peptides. Score 0.525 Round 5: 119 peptides, 16 chains. Longest chain 16 peptides. Score 0.571 Taking the results from Round 5 Chains 16, Residues 103, Estimated correctness of the model 33.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3640 restraints for refining 1635 atoms. 3244 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2327 (Rfree = 0.000) for 1635 atoms. Found 11 (14 requested) and removed 14 (7 requested) atoms. Cycle 22: After refmac, R = 0.2023 (Rfree = 0.000) for 1631 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.1884 (Rfree = 0.000) for 1626 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.1775 (Rfree = 0.000) for 1619 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 25: After refmac, R = 0.1790 (Rfree = 0.000) for 1614 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.29 Search for helices and strands: 0 residues in 0 chains, 1666 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1688 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 12 peptides. Score 0.360 Round 2: 107 peptides, 17 chains. Longest chain 12 peptides. Score 0.469 Round 3: 114 peptides, 16 chains. Longest chain 19 peptides. Score 0.541 Round 4: 103 peptides, 15 chains. Longest chain 19 peptides. Score 0.501 Round 5: 110 peptides, 16 chains. Longest chain 19 peptides. Score 0.517 Taking the results from Round 3 Chains 16, Residues 98, Estimated correctness of the model 24.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3707 restraints for refining 1636 atoms. 3331 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2088 (Rfree = 0.000) for 1636 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.2009 (Rfree = 0.000) for 1635 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.1890 (Rfree = 0.000) for 1634 atoms. Found 9 (14 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1927 (Rfree = 0.000) for 1635 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1887 (Rfree = 0.000) for 1627 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 1660 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 1693 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.350 Round 2: 103 peptides, 17 chains. Longest chain 11 peptides. Score 0.443 Round 3: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.400 Round 4: 105 peptides, 18 chains. Longest chain 11 peptides. Score 0.427 Round 5: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.375 Taking the results from Round 2 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3619 restraints for refining 1635 atoms. 3292 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2024 (Rfree = 0.000) for 1635 atoms. Found 11 (14 requested) and removed 8 (7 requested) atoms. Cycle 32: After refmac, R = 0.1959 (Rfree = 0.000) for 1634 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.1949 (Rfree = 0.000) for 1630 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1939 (Rfree = 0.000) for 1625 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1972 (Rfree = 0.000) for 1620 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 1653 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1667 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.245 Round 2: 82 peptides, 14 chains. Longest chain 11 peptides. Score 0.385 Round 3: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.307 Round 4: 92 peptides, 16 chains. Longest chain 13 peptides. Score 0.395 Round 5: 95 peptides, 16 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 5 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3752 restraints for refining 1636 atoms. 3452 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2173 (Rfree = 0.000) for 1636 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 37: After refmac, R = 0.2266 (Rfree = 0.000) for 1633 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.1981 (Rfree = 0.000) for 1637 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.2523 (Rfree = 0.000) for 1631 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 40: After refmac, R = 0.2455 (Rfree = 0.000) for 1633 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.02 3.23 Search for helices and strands: 0 residues in 0 chains, 1678 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1696 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 6 peptides. Score 0.247 Round 2: 80 peptides, 14 chains. Longest chain 15 peptides. Score 0.370 Round 3: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.378 Round 4: 82 peptides, 14 chains. Longest chain 17 peptides. Score 0.385 Round 5: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.393 Taking the results from Round 5 Chains 14, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3767 restraints for refining 1636 atoms. 3505 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2142 (Rfree = 0.000) for 1636 atoms. Found 10 (14 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.2165 (Rfree = 0.000) for 1636 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 43: After refmac, R = 0.2085 (Rfree = 0.000) for 1632 atoms. Found 7 (14 requested) and removed 10 (7 requested) atoms. Cycle 44: After refmac, R = 0.2112 (Rfree = 0.000) for 1629 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.2040 (Rfree = 0.000) for 1629 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.28 Search for helices and strands: 0 residues in 0 chains, 1660 seeds are put forward NCS extension: 0 residues added, 1660 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 8 peptides. Score 0.262 Round 2: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.327 Round 3: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.311 Round 4: 86 peptides, 15 chains. Longest chain 12 peptides. Score 0.383 Round 5: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.343 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 71, 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 2nlv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3736 reflections ( 99.84 % complete ) and 3656 restraints for refining 1614 atoms. 3387 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2552 (Rfree = 0.000) for 1614 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2076 (Rfree = 0.000) for 1601 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1923 (Rfree = 0.000) for 1594 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1743 (Rfree = 0.000) for 1586 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 29.42