Sun 23 Dec 22:23:08 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-4.0-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 22:23:18 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-4.0-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 142 and 0 Target number of residues in the AU: 142 Target solvent content: 0.6509 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1792 target number of atoms Had to go as low as 0.75 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 4.000 Wilson plot Bfac: 78.61 1938 reflections ( 99.69 % complete ) and 0 restraints for refining 1994 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3725 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3766 (Rfree = 0.000) for 1994 atoms. Found 9 (9 requested) and removed 43 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.89 Search for helices and strands: 0 residues in 0 chains, 1994 seeds are put forward NCS extension: 0 residues added, 1994 seeds are put forward Round 1: 36 peptides, 9 chains. Longest chain 4 peptides. Score 0.167 Round 2: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.205 Round 3: 67 peptides, 14 chains. Longest chain 6 peptides. Score 0.265 Round 4: 74 peptides, 14 chains. Longest chain 10 peptides. Score 0.323 Round 5: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.301 Taking the results from Round 4 Chains 14, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1938 reflections ( 99.69 % complete ) and 4010 restraints for refining 1619 atoms. 3784 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3000 (Rfree = 0.000) for 1619 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 2: After refmac, R = 0.2417 (Rfree = 0.000) for 1587 atoms. Found 6 (7 requested) and removed 12 (3 requested) atoms. Cycle 3: After refmac, R = 0.2136 (Rfree = 0.000) for 1573 atoms. Found 2 (7 requested) and removed 10 (3 requested) atoms. Cycle 4: After refmac, R = 0.1811 (Rfree = 0.000) for 1562 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2069 (Rfree = 0.000) for 1558 atoms. Found 0 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.91 Search for helices and strands: 0 residues in 0 chains, 1590 seeds are put forward NCS extension: 0 residues added, 1590 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.274 Round 2: 80 peptides, 14 chains. Longest chain 9 peptides. Score 0.370 Round 3: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.385 Round 4: 74 peptides, 14 chains. Longest chain 8 peptides. Score 0.323 Round 5: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 5 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1938 reflections ( 99.69 % complete ) and 3897 restraints for refining 1590 atoms. 3646 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1970 (Rfree = 0.000) for 1590 atoms. Found 0 (7 requested) and removed 15 (3 requested) atoms. Cycle 7: After refmac, R = 0.1880 (Rfree = 0.000) for 1565 atoms. Found 1 (7 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.3529 (Rfree = 0.000) for 1552 atoms. Found 7 (7 requested) and removed 33 (3 requested) atoms. Cycle 9: After refmac, R = 0.2256 (Rfree = 0.000) for 1519 atoms. Found 4 (7 requested) and removed 12 (3 requested) atoms. Cycle 10: After refmac, R = 0.1914 (Rfree = 0.000) for 1508 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 1551 seeds are put forward NCS extension: 3 residues added (1 deleted due to clashes), 1554 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.292 Round 2: 72 peptides, 13 chains. Longest chain 8 peptides. Score 0.341 Round 3: 77 peptides, 12 chains. Longest chain 10 peptides. Score 0.413 Round 4: 79 peptides, 12 chains. Longest chain 10 peptides. Score 0.428 Round 5: 72 peptides, 11 chains. Longest chain 10 peptides. Score 0.409 Taking the results from Round 4 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1938 reflections ( 99.69 % complete ) and 3888 restraints for refining 1577 atoms. 3632 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2042 (Rfree = 0.000) for 1577 atoms. Found 2 (7 requested) and removed 15 (3 requested) atoms. Cycle 12: After refmac, R = 0.1938 (Rfree = 0.000) for 1557 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.1788 (Rfree = 0.000) for 1549 atoms. Found 0 (7 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.1625 (Rfree = 0.000) for 1541 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1693 (Rfree = 0.000) for 1535 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 3.90 Search for helices and strands: 0 residues in 0 chains, 1576 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 1581 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.276 Round 2: 73 peptides, 12 chains. Longest chain 11 peptides. Score 0.383 Round 3: 81 peptides, 11 chains. Longest chain 11 peptides. Score 0.474 Round 4: 80 peptides, 11 chains. Longest chain 15 peptides. Score 0.467 Round 5: 77 peptides, 13 chains. Longest chain 10 peptides. Score 0.380 Taking the results from Round 3 Chains 11, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1938 reflections ( 99.69 % complete ) and 3750 restraints for refining 1562 atoms. 3481 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1997 (Rfree = 0.000) for 1562 atoms. Found 2 (7 requested) and removed 10 (3 requested) atoms. Cycle 17: After refmac, R = 0.1840 (Rfree = 0.000) for 1546 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.1766 (Rfree = 0.000) for 1540 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.1825 (Rfree = 0.000) for 1533 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.1809 (Rfree = 0.000) for 1525 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.86 Search for helices and strands: 0 residues in 0 chains, 1576 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1589 seeds are put forward Round 1: 59 peptides, 14 chains. Longest chain 5 peptides. Score 0.195 Round 2: 71 peptides, 13 chains. Longest chain 12 peptides. Score 0.333 Round 3: 72 peptides, 12 chains. Longest chain 10 peptides. Score 0.376 Round 4: 73 peptides, 13 chains. Longest chain 9 peptides. Score 0.349 Round 5: 73 peptides, 11 chains. Longest chain 9 peptides. Score 0.417 Taking the results from Round 5 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1938 reflections ( 99.69 % complete ) and 3876 restraints for refining 1619 atoms. 3639 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2007 (Rfree = 0.000) for 1619 atoms. Found 1 (7 requested) and removed 10 (3 requested) atoms. Cycle 22: After refmac, R = 0.1885 (Rfree = 0.000) for 1603 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.1794 (Rfree = 0.000) for 1597 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.1658 (Rfree = 0.000) for 1587 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1768 (Rfree = 0.000) for 1581 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.91 Search for helices and strands: 0 residues in 0 chains, 1610 seeds are put forward NCS extension: 0 residues added, 1610 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 8 peptides. Score 0.223 Round 2: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.224 Round 3: 62 peptides, 13 chains. Longest chain 6 peptides. Score 0.258 Round 4: 51 peptides, 9 chains. Longest chain 12 peptides. Score 0.313 Round 5: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.262 Taking the results from Round 4 Chains 9, Residues 42, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1938 reflections ( 99.69 % complete ) and 4117 restraints for refining 1619 atoms. 3958 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2156 (Rfree = 0.000) for 1619 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.1830 (Rfree = 0.000) for 1616 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.1963 (Rfree = 0.000) for 1611 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.1761 (Rfree = 0.000) for 1609 atoms. Found 0 (7 requested) and removed 11 (3 requested) atoms. Cycle 30: After refmac, R = 0.2048 (Rfree = 0.000) for 1597 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.90 Search for helices and strands: 0 residues in 0 chains, 1642 seeds are put forward NCS extension: 0 residues added, 1642 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 5 peptides. Score 0.197 Round 2: 51 peptides, 10 chains. Longest chain 10 peptides. Score 0.274 Round 3: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.227 Round 4: 44 peptides, 8 chains. Longest chain 11 peptides. Score 0.290 Round 5: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.292 Taking the results from Round 5 Chains 10, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1938 reflections ( 99.69 % complete ) and 4012 restraints for refining 1609 atoms. 3850 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2522 (Rfree = 0.000) for 1609 atoms. Found 2 (7 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.1825 (Rfree = 0.000) for 1589 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 33: After refmac, R = 0.2015 (Rfree = 0.000) for 1582 atoms. Found 4 (7 requested) and removed 9 (3 requested) atoms. Cycle 34: After refmac, R = 0.1882 (Rfree = 0.000) for 1576 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1931 (Rfree = 0.000) for 1574 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 1610 seeds are put forward NCS extension: 0 residues added, 1610 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 8 peptides. Score 0.216 Round 2: 48 peptides, 10 chains. Longest chain 9 peptides. Score 0.246 Round 3: 50 peptides, 10 chains. Longest chain 9 peptides. Score 0.265 Round 4: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.280 Round 5: 54 peptides, 8 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 5 Chains 8, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1938 reflections ( 99.69 % complete ) and 3932 restraints for refining 1567 atoms. 3756 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2066 (Rfree = 0.000) for 1567 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.1928 (Rfree = 0.000) for 1562 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.1843 (Rfree = 0.000) for 1555 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.1732 (Rfree = 0.000) for 1549 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1813 (Rfree = 0.000) for 1545 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.96 Search for helices and strands: 0 residues in 0 chains, 1575 seeds are put forward NCS extension: 0 residues added, 1575 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.262 Round 2: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.312 Round 3: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.351 Round 4: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.344 Round 5: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.323 Taking the results from Round 3 Chains 10, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1938 reflections ( 99.69 % complete ) and 3775 restraints for refining 1567 atoms. 3585 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1978 (Rfree = 0.000) for 1567 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.2197 (Rfree = 0.000) for 1557 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2127 (Rfree = 0.000) for 1552 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1776 (Rfree = 0.000) for 1550 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2134 (Rfree = 0.000) for 1546 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.95 Search for helices and strands: 0 residues in 0 chains, 1589 seeds are put forward NCS extension: 0 residues added, 1589 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 6 peptides. Score 0.196 Round 2: 64 peptides, 13 chains. Longest chain 9 peptides. Score 0.276 Round 3: 55 peptides, 11 chains. Longest chain 9 peptides. Score 0.271 Round 4: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.284 Round 5: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.297 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 47, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1938 reflections ( 99.69 % complete ) and 3824 restraints for refining 1565 atoms. 3647 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2495 (Rfree = 0.000) for 1565 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1780 (Rfree = 0.000) for 1556 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1874 (Rfree = 0.000) for 1552 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1848 (Rfree = 0.000) for 1547 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... TimeTaking 27.53