Sun 23 Dec 22:22:52 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-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/2nlv-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-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 22:23:00 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-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 152 and 0 Target number of residues in the AU: 152 Target solvent content: 0.6263 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-3.4-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: 4 Cell parameters: 46.793 37.359 63.476 90.000 97.240 90.000 Input sequence file: 2nlv-3.4-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 3.401 Wilson plot Bfac: 64.64 3120 reflections ( 99.81 % complete ) and 0 restraints for refining 1987 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3543 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3214 (Rfree = 0.000) for 1987 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.40 Search for helices and strands: 0 residues in 0 chains, 2012 seeds are put forward NCS extension: 0 residues added, 2012 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 7 peptides. Score 0.237 Round 2: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.324 Round 3: 90 peptides, 17 chains. Longest chain 9 peptides. Score 0.348 Round 4: 104 peptides, 17 chains. Longest chain 10 peptides. Score 0.449 Round 5: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 4 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3751 restraints for refining 1628 atoms. 3420 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3094 (Rfree = 0.000) for 1628 atoms. Found 7 (12 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.2753 (Rfree = 0.000) for 1604 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. Cycle 3: After refmac, R = 0.2646 (Rfree = 0.000) for 1592 atoms. Found 11 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2615 (Rfree = 0.000) for 1585 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2578 (Rfree = 0.000) for 1577 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 1637 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1649 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 9 peptides. Score 0.269 Round 2: 89 peptides, 18 chains. Longest chain 9 peptides. Score 0.308 Round 3: 92 peptides, 15 chains. Longest chain 10 peptides. Score 0.426 Round 4: 94 peptides, 16 chains. Longest chain 9 peptides. Score 0.410 Round 5: 98 peptides, 17 chains. Longest chain 10 peptides. Score 0.407 Taking the results from Round 3 Chains 15, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3545 restraints for refining 1570 atoms. 3252 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2320 (Rfree = 0.000) for 1570 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 7: After refmac, R = 0.2033 (Rfree = 0.000) for 1563 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.1946 (Rfree = 0.000) for 1556 atoms. Found 0 (11 requested) and removed 8 (5 requested) atoms. Cycle 9: After refmac, R = 0.2003 (Rfree = 0.000) for 1548 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.1894 (Rfree = 0.000) for 1545 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 1596 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1602 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.276 Round 2: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.393 Round 3: 106 peptides, 18 chains. Longest chain 13 peptides. Score 0.434 Round 4: 94 peptides, 16 chains. Longest chain 12 peptides. Score 0.410 Round 5: 100 peptides, 17 chains. Longest chain 13 peptides. Score 0.422 Taking the results from Round 3 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3509 restraints for refining 1629 atoms. 3119 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2083 (Rfree = 0.000) for 1629 atoms. Found 5 (12 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.2138 (Rfree = 0.000) for 1612 atoms. Found 6 (12 requested) and removed 14 (6 requested) atoms. Cycle 13: After refmac, R = 0.1901 (Rfree = 0.000) for 1602 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1820 (Rfree = 0.000) for 1595 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.1796 (Rfree = 0.000) for 1589 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.43 Search for helices and strands: 0 residues in 0 chains, 1634 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 1641 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 11 peptides. Score 0.287 Round 2: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.378 Round 3: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.380 Round 4: 92 peptides, 13 chains. Longest chain 14 peptides. Score 0.487 Round 5: 85 peptides, 13 chains. Longest chain 11 peptides. Score 0.439 Taking the results from Round 4 Chains 13, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3654 restraints for refining 1629 atoms. 3351 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2255 (Rfree = 0.000) for 1629 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 17: After refmac, R = 0.2477 (Rfree = 0.000) for 1628 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 18: After refmac, R = 0.2378 (Rfree = 0.000) for 1627 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2281 (Rfree = 0.000) for 1624 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 20: After refmac, R = 0.1823 (Rfree = 0.000) for 1616 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 1656 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 1667 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.286 Round 2: 97 peptides, 19 chains. Longest chain 10 peptides. Score 0.337 Round 3: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.353 Round 4: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.420 Round 5: 101 peptides, 17 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 5 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3627 restraints for refining 1628 atoms. 3308 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2127 (Rfree = 0.000) for 1628 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2280 (Rfree = 0.000) for 1623 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.1855 (Rfree = 0.000) for 1624 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1767 (Rfree = 0.000) for 1619 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1805 (Rfree = 0.000) for 1617 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 1654 seeds are put forward NCS extension: 0 residues added, 1654 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.245 Round 2: 94 peptides, 17 chains. Longest chain 13 peptides. Score 0.378 Round 3: 88 peptides, 15 chains. Longest chain 10 peptides. Score 0.397 Round 4: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.373 Round 5: 87 peptides, 14 chains. Longest chain 10 peptides. Score 0.422 Taking the results from Round 5 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3683 restraints for refining 1628 atoms. 3405 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2489 (Rfree = 0.000) for 1628 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 27: After refmac, R = 0.2440 (Rfree = 0.000) for 1625 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.1890 (Rfree = 0.000) for 1624 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1817 (Rfree = 0.000) for 1617 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1708 (Rfree = 0.000) for 1615 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 1647 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1656 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 7 peptides. Score 0.287 Round 2: 80 peptides, 15 chains. Longest chain 11 peptides. Score 0.337 Round 3: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.335 Round 4: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.373 Round 5: 83 peptides, 14 chains. Longest chain 11 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 ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3637 restraints for refining 1629 atoms. 3375 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2148 (Rfree = 0.000) for 1629 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 32: After refmac, R = 0.1888 (Rfree = 0.000) for 1626 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.1760 (Rfree = 0.000) for 1622 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1738 (Rfree = 0.000) for 1618 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1680 (Rfree = 0.000) for 1615 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.44 Search for helices and strands: 0 residues in 0 chains, 1664 seeds are put forward NCS extension: 10 residues added (1 deleted due to clashes), 1674 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 6 peptides. Score 0.220 Round 2: 73 peptides, 16 chains. Longest chain 7 peptides. Score 0.246 Round 3: 72 peptides, 14 chains. Longest chain 7 peptides. Score 0.307 Round 4: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.272 Round 5: 74 peptides, 14 chains. Longest chain 7 peptides. Score 0.323 Taking the results from Round 5 Chains 14, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3813 restraints for refining 1629 atoms. 3587 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2048 (Rfree = 0.000) for 1629 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.2051 (Rfree = 0.000) for 1628 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.1628 (Rfree = 0.000) for 1627 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.1625 (Rfree = 0.000) for 1625 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1555 (Rfree = 0.000) for 1624 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 1656 seeds are put forward NCS extension: 0 residues added, 1656 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.211 Round 2: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.255 Round 3: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.276 Round 4: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.292 Round 5: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 5 Chains 14, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3696 restraints for refining 1629 atoms. 3478 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1989 (Rfree = 0.000) for 1629 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.1942 (Rfree = 0.000) for 1635 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.1891 (Rfree = 0.000) for 1638 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1773 (Rfree = 0.000) for 1643 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1432 (Rfree = 0.000) for 1644 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 1686 seeds are put forward NCS extension: 0 residues added, 1686 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.255 Round 2: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.308 Round 3: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.352 Round 4: 83 peptides, 14 chains. Longest chain 12 peptides. Score 0.393 Round 5: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.295 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 69, 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. 3120 reflections ( 99.81 % complete ) and 3556 restraints for refining 1629 atoms. 3294 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1773 (Rfree = 0.000) for 1629 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1660 (Rfree = 0.000) for 1621 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1626 (Rfree = 0.000) for 1614 atoms. Found 0 (12 requested) and removed 2 (6 requested) atoms. Cycle 49: After refmac, R = 0.1617 (Rfree = 0.000) for 1612 atoms. Found 0 (12 requested) and removed 0 (6 requested) atoms. Writing output files ... TimeTaking 28.6