Mon 24 Dec 07:38:56 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 2oc6-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oc6-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oc6-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-4.0-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/2oc6-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-4.0-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 07:39:01 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/2oc6-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-4.0-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 168 and 0 Target number of residues in the AU: 168 Target solvent content: 0.6724 Checking the provided sequence file Detected sequence length: 124 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 248 Adjusted target solvent content: 0.52 Input MTZ file: 2oc6-4.0-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: 3 Cell parameters: 48.794 46.883 64.576 90.000 110.073 90.000 Input sequence file: 2oc6-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.90 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: 60.653 4.001 Wilson plot Bfac: 94.12 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2411 reflections ( 99.55 % complete ) and 0 restraints for refining 2206 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3745 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3572 (Rfree = 0.000) for 2206 atoms. Found 6 (10 requested) and removed 94 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.87 3.77 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward NCS extension: 0 residues added, 2153 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.206 Round 2: 58 peptides, 10 chains. Longest chain 13 peptides. Score 0.311 Round 3: 78 peptides, 11 chains. Longest chain 15 peptides. Score 0.411 Round 4: 73 peptides, 10 chains. Longest chain 16 peptides. Score 0.409 Round 5: 72 peptides, 10 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 3 Chains 11, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4300 restraints for refining 1791 atoms. 4043 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3197 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 2: After refmac, R = 0.3311 (Rfree = 0.000) for 1758 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2964 (Rfree = 0.000) for 1732 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.3215 (Rfree = 0.000) for 1704 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 5: After refmac, R = 0.2777 (Rfree = 0.000) for 1687 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 1745 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 1769 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 11 peptides. Score 0.274 Round 2: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.416 Round 3: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.402 Round 4: 100 peptides, 16 chains. Longest chain 15 peptides. Score 0.408 Round 5: 95 peptides, 15 chains. Longest chain 15 peptides. Score 0.405 Taking the results from Round 2 Chains 15, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 3408 restraints for refining 1579 atoms. 3095 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2895 (Rfree = 0.000) for 1579 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.2573 (Rfree = 0.000) for 1559 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.2406 (Rfree = 0.000) for 1546 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2494 (Rfree = 0.000) for 1538 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 10: After refmac, R = 0.2068 (Rfree = 0.000) for 1533 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 1613 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1619 seeds are put forward Round 1: 82 peptides, 16 chains. Longest chain 11 peptides. Score 0.296 Round 2: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.406 Round 3: 103 peptides, 16 chains. Longest chain 14 peptides. Score 0.425 Round 4: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.439 Round 5: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.439 Taking the results from Round 5 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 3556 restraints for refining 1637 atoms. 3227 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2636 (Rfree = 0.000) for 1637 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 12: After refmac, R = 0.2487 (Rfree = 0.000) for 1615 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.2352 (Rfree = 0.000) for 1600 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.2419 (Rfree = 0.000) for 1596 atoms. Found 6 (7 requested) and removed 10 (3 requested) atoms. Cycle 15: After refmac, R = 0.2009 (Rfree = 0.000) for 1590 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 1645 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1666 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 11 peptides. Score 0.279 Round 2: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.318 Round 3: 99 peptides, 17 chains. Longest chain 12 peptides. Score 0.376 Round 4: 98 peptides, 15 chains. Longest chain 14 peptides. Score 0.422 Round 5: 103 peptides, 17 chains. Longest chain 13 peptides. Score 0.400 Taking the results from Round 4 Chains 15, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 3763 restraints for refining 1700 atoms. 3446 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3051 (Rfree = 0.000) for 1700 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 17: After refmac, R = 0.2119 (Rfree = 0.000) for 1691 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. Cycle 18: After refmac, R = 0.1891 (Rfree = 0.000) for 1679 atoms. Found 2 (7 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.1572 (Rfree = 0.000) for 1669 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.1591 (Rfree = 0.000) for 1667 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 1710 seeds are put forward NCS extension: 0 residues added, 1710 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 11 peptides. Score 0.290 Round 2: 102 peptides, 18 chains. Longest chain 15 peptides. Score 0.368 Round 3: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.358 Round 4: 100 peptides, 17 chains. Longest chain 17 peptides. Score 0.382 Round 5: 102 peptides, 19 chains. Longest chain 11 peptides. Score 0.342 Taking the results from Round 4 Chains 17, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4071 restraints for refining 1791 atoms. 3756 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2952 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 22: After refmac, R = 0.2222 (Rfree = 0.000) for 1764 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.2557 (Rfree = 0.000) for 1753 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 24: After refmac, R = 0.2035 (Rfree = 0.000) for 1744 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2264 (Rfree = 0.000) for 1738 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 1780 seeds are put forward NCS extension: 0 residues added, 1780 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 9 peptides. Score 0.265 Round 2: 99 peptides, 18 chains. Longest chain 14 peptides. Score 0.350 Round 3: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.360 Round 4: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.388 Round 5: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 4 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4147 restraints for refining 1791 atoms. 3828 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2741 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 27: After refmac, R = 0.2433 (Rfree = 0.000) for 1774 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 28: After refmac, R = 0.2418 (Rfree = 0.000) for 1773 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.2282 (Rfree = 0.000) for 1768 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 30: After refmac, R = 0.2718 (Rfree = 0.000) for 1764 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward NCS extension: 0 residues added, 1830 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 5 peptides. Score 0.206 Round 2: 81 peptides, 17 chains. Longest chain 11 peptides. Score 0.260 Round 3: 79 peptides, 18 chains. Longest chain 6 peptides. Score 0.218 Round 4: 83 peptides, 19 chains. Longest chain 6 peptides. Score 0.217 Round 5: 90 peptides, 19 chains. Longest chain 7 peptides. Score 0.265 Taking the results from Round 5 Chains 19, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4181 restraints for refining 1789 atoms. 3916 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1860 (Rfree = 0.000) for 1789 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.1600 (Rfree = 0.000) for 1779 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.1893 (Rfree = 0.000) for 1774 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.1541 (Rfree = 0.000) for 1770 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.1572 (Rfree = 0.000) for 1767 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.69 Search for helices and strands: 0 residues in 0 chains, 1809 seeds are put forward NCS extension: 0 residues added, 1809 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 9 peptides. Score 0.260 Round 2: 84 peptides, 16 chains. Longest chain 11 peptides. Score 0.309 Round 3: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.371 Round 4: 89 peptides, 15 chains. Longest chain 12 peptides. Score 0.368 Round 5: 82 peptides, 15 chains. Longest chain 12 peptides. Score 0.324 Taking the results from Round 3 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4116 restraints for refining 1790 atoms. 3846 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1814 (Rfree = 0.000) for 1790 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.1567 (Rfree = 0.000) for 1788 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.1415 (Rfree = 0.000) for 1782 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.1333 (Rfree = 0.000) for 1782 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1277 (Rfree = 0.000) for 1779 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 1809 seeds are put forward NCS extension: 0 residues added, 1809 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 10 peptides. Score 0.281 Round 2: 91 peptides, 18 chains. Longest chain 10 peptides. Score 0.299 Round 3: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.356 Round 4: 98 peptides, 18 chains. Longest chain 10 peptides. Score 0.343 Round 5: 91 peptides, 17 chains. Longest chain 10 peptides. Score 0.326 Taking the results from Round 3 Chains 18, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4086 restraints for refining 1791 atoms. 3776 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1841 (Rfree = 0.000) for 1791 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 42: After refmac, R = 0.1511 (Rfree = 0.000) for 1783 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.1532 (Rfree = 0.000) for 1778 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.1431 (Rfree = 0.000) for 1769 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1499 (Rfree = 0.000) for 1766 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 1807 seeds are put forward NCS extension: 0 residues added, 1807 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 6 peptides. Score 0.223 Round 2: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.318 Round 3: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.309 Round 4: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.318 Round 5: 71 peptides, 11 chains. Longest chain 11 peptides. Score 0.368 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 60, 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 2oc6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2411 reflections ( 99.55 % complete ) and 4355 restraints for refining 1791 atoms. 4126 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2032 (Rfree = 0.000) for 1791 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1992 (Rfree = 0.000) for 1780 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1599 (Rfree = 0.000) for 1774 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1390 (Rfree = 0.000) for 1769 atoms. TimeTaking 24.88