Mon 24 Dec 07:44:41 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 2ozj-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.2-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/2ozj-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.2-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 07:44:46 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/2ozj-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.2-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 141 and 0 Target number of residues in the AU: 141 Target solvent content: 0.6453 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.43 Input MTZ file: 2ozj-3.2-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: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.60 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: 75.275 3.200 Wilson plot Bfac: 74.11 3785 reflections ( 99.45 % complete ) and 0 restraints for refining 2030 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3221 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2816 (Rfree = 0.000) for 2030 atoms. Found 5 (18 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 2033 seeds are put forward NCS extension: 0 residues added, 2033 seeds are put forward Round 1: 111 peptides, 20 chains. Longest chain 11 peptides. Score 0.413 Round 2: 152 peptides, 22 chains. Longest chain 16 peptides. Score 0.613 Round 3: 157 peptides, 19 chains. Longest chain 19 peptides. Score 0.699 Round 4: 158 peptides, 17 chains. Longest chain 24 peptides. Score 0.739 Round 5: 156 peptides, 18 chains. Longest chain 24 peptides. Score 0.714 Taking the results from Round 4 Chains 19, Residues 141, Estimated correctness of the model 73.0 % 2 chains (33 residues) have been docked in sequence Building loops using Loopy2018 19 chains (141 residues) following loop building 2 chains (33 residues) in sequence following loop building ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3341 restraints for refining 1665 atoms. 2678 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3177 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. Cycle 2: After refmac, R = 0.3090 (Rfree = 0.000) for 1618 atoms. Found 8 (14 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.2882 (Rfree = 0.000) for 1588 atoms. Found 11 (13 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2605 (Rfree = 0.000) for 1571 atoms. Found 4 (13 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2430 (Rfree = 0.000) for 1558 atoms. Found 7 (13 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 1579 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 1589 seeds are put forward Round 1: 137 peptides, 18 chains. Longest chain 24 peptides. Score 0.627 Round 2: 152 peptides, 17 chains. Longest chain 22 peptides. Score 0.716 Round 3: 154 peptides, 18 chains. Longest chain 29 peptides. Score 0.705 Round 4: 161 peptides, 16 chains. Longest chain 32 peptides. Score 0.766 Round 5: 157 peptides, 15 chains. Longest chain 27 peptides. Score 0.769 Taking the results from Round 5 Chains 16, Residues 142, Estimated correctness of the model 78.4 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3284 restraints for refining 1631 atoms. 2652 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3432 (Rfree = 0.000) for 1631 atoms. Found 13 (13 requested) and removed 26 (7 requested) atoms. Cycle 7: After refmac, R = 0.3071 (Rfree = 0.000) for 1601 atoms. Found 8 (12 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.3338 (Rfree = 0.000) for 1579 atoms. Found 12 (12 requested) and removed 21 (7 requested) atoms. Cycle 9: After refmac, R = 0.2953 (Rfree = 0.000) for 1555 atoms. Found 12 (12 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.3106 (Rfree = 0.000) for 1552 atoms. Found 11 (11 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 1591 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1609 seeds are put forward Round 1: 126 peptides, 20 chains. Longest chain 18 peptides. Score 0.514 Round 2: 139 peptides, 16 chains. Longest chain 21 peptides. Score 0.680 Round 3: 138 peptides, 18 chains. Longest chain 23 peptides. Score 0.632 Round 4: 130 peptides, 13 chains. Longest chain 29 peptides. Score 0.702 Round 5: 136 peptides, 13 chains. Longest chain 25 peptides. Score 0.727 Taking the results from Round 5 Chains 15, Residues 123, Estimated correctness of the model 70.7 % 2 chains (34 residues) have been docked in sequence Building loops using Loopy2018 15 chains (123 residues) following loop building 2 chains (34 residues) in sequence following loop building ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3368 restraints for refining 1665 atoms. 2761 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2990 (Rfree = 0.000) for 1665 atoms. Found 9 (11 requested) and removed 22 (7 requested) atoms. Cycle 12: After refmac, R = 0.3364 (Rfree = 0.000) for 1645 atoms. Found 11 (11 requested) and removed 19 (7 requested) atoms. Cycle 13: After refmac, R = 0.3085 (Rfree = 0.000) for 1626 atoms. Found 11 (11 requested) and removed 7 (7 requested) atoms. Cycle 14: After refmac, R = 0.2756 (Rfree = 0.000) for 1615 atoms. Found 9 (10 requested) and removed 15 (7 requested) atoms. Cycle 15: After refmac, R = 0.2983 (Rfree = 0.000) for 1596 atoms. Found 10 (10 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.73 Search for helices and strands: 0 residues in 0 chains, 1633 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1653 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 9 peptides. Score 0.396 Round 2: 119 peptides, 17 chains. Longest chain 13 peptides. Score 0.551 Round 3: 146 peptides, 21 chains. Longest chain 13 peptides. Score 0.605 Round 4: 140 peptides, 21 chains. Longest chain 18 peptides. Score 0.572 Round 5: 141 peptides, 18 chains. Longest chain 19 peptides. Score 0.647 Taking the results from Round 5 Chains 18, Residues 123, Estimated correctness of the model 53.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3739 restraints for refining 1664 atoms. 3265 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3386 (Rfree = 0.000) for 1664 atoms. Found 10 (10 requested) and removed 23 (7 requested) atoms. Cycle 17: After refmac, R = 0.3210 (Rfree = 0.000) for 1642 atoms. Found 10 (10 requested) and removed 10 (7 requested) atoms. Cycle 18: After refmac, R = 0.3132 (Rfree = 0.000) for 1640 atoms. Found 10 (10 requested) and removed 13 (7 requested) atoms. Cycle 19: After refmac, R = 0.2503 (Rfree = 0.000) for 1632 atoms. Found 7 (10 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.3025 (Rfree = 0.000) for 1631 atoms. Found 10 (10 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.65 Search for helices and strands: 0 residues in 0 chains, 1681 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 1704 seeds are put forward Round 1: 95 peptides, 19 chains. Longest chain 8 peptides. Score 0.325 Round 2: 122 peptides, 16 chains. Longest chain 20 peptides. Score 0.594 Round 3: 120 peptides, 16 chains. Longest chain 22 peptides. Score 0.583 Round 4: 126 peptides, 18 chains. Longest chain 14 peptides. Score 0.567 Round 5: 123 peptides, 17 chains. Longest chain 15 peptides. Score 0.575 Taking the results from Round 2 Chains 16, Residues 106, Estimated correctness of the model 39.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3673 restraints for refining 1628 atoms. 3265 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2798 (Rfree = 0.000) for 1628 atoms. Found 10 (10 requested) and removed 12 (7 requested) atoms. Cycle 22: After refmac, R = 0.2436 (Rfree = 0.000) for 1622 atoms. Found 6 (10 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.2777 (Rfree = 0.000) for 1615 atoms. Found 10 (10 requested) and removed 10 (7 requested) atoms. Cycle 24: After refmac, R = 0.2915 (Rfree = 0.000) for 1610 atoms. Found 10 (10 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.2630 (Rfree = 0.000) for 1605 atoms. Found 9 (10 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.76 Search for helices and strands: 0 residues in 0 chains, 1655 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1673 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.299 Round 2: 90 peptides, 15 chains. Longest chain 10 peptides. Score 0.416 Round 3: 106 peptides, 15 chains. Longest chain 13 peptides. Score 0.526 Round 4: 104 peptides, 14 chains. Longest chain 13 peptides. Score 0.541 Round 5: 108 peptides, 15 chains. Longest chain 15 peptides. Score 0.538 Taking the results from Round 4 Chains 14, Residues 90, Estimated correctness of the model 24.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3576 restraints for refining 1584 atoms. 3230 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3364 (Rfree = 0.000) for 1584 atoms. Found 10 (10 requested) and removed 23 (7 requested) atoms. Cycle 27: After refmac, R = 0.2880 (Rfree = 0.000) for 1560 atoms. Found 10 (10 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.2582 (Rfree = 0.000) for 1556 atoms. Found 2 (10 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.3097 (Rfree = 0.000) for 1541 atoms. Found 9 (9 requested) and removed 12 (6 requested) atoms. Cycle 30: After refmac, R = 0.3594 (Rfree = 0.000) for 1533 atoms. Found 9 (9 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.80 Search for helices and strands: 0 residues in 0 chains, 1591 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 1605 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 9 peptides. Score 0.278 Round 2: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.358 Round 3: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.358 Round 4: 75 peptides, 12 chains. Longest chain 13 peptides. Score 0.402 Round 5: 78 peptides, 12 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 5 Chains 12, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 3451 restraints for refining 1552 atoms. 3199 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3801 (Rfree = 0.000) for 1552 atoms. Found 9 (9 requested) and removed 22 (6 requested) atoms. Cycle 32: After refmac, R = 0.3279 (Rfree = 0.000) for 1527 atoms. Found 9 (9 requested) and removed 19 (6 requested) atoms. Cycle 33: After refmac, R = 0.2866 (Rfree = 0.000) for 1512 atoms. Found 9 (9 requested) and removed 11 (6 requested) atoms. Cycle 34: After refmac, R = 0.3627 (Rfree = 0.000) for 1509 atoms. Found 9 (9 requested) and removed 22 (6 requested) atoms. Cycle 35: After refmac, R = 0.3262 (Rfree = 0.000) for 1491 atoms. Found 9 (9 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 4.15 Search for helices and strands: 0 residues in 0 chains, 1531 seeds are put forward NCS extension: 0 residues added, 1531 seeds are put forward Round 1: 49 peptides, 12 chains. Longest chain 5 peptides. Score 0.177 Round 2: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.320 Round 3: 62 peptides, 10 chains. Longest chain 11 peptides. Score 0.370 Round 4: 60 peptides, 10 chains. Longest chain 9 peptides. Score 0.354 Round 5: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.264 Taking the results from Round 3 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 2922 restraints for refining 1358 atoms. 2724 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3039 (Rfree = 0.000) for 1358 atoms. Found 8 (8 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.3285 (Rfree = 0.000) for 1352 atoms. Found 8 (8 requested) and removed 12 (6 requested) atoms. Cycle 38: After refmac, R = 0.2998 (Rfree = 0.000) for 1346 atoms. Found 8 (8 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.3338 (Rfree = 0.000) for 1340 atoms. Found 8 (8 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.3275 (Rfree = 0.000) for 1338 atoms. Found 8 (8 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 1372 seeds are put forward NCS extension: 0 residues added, 1372 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.266 Round 2: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.303 Round 3: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.345 Round 4: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.347 Round 5: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.392 Taking the results from Round 5 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3785 reflections ( 99.45 % complete ) and 2665 restraints for refining 1318 atoms. 2418 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3339 (Rfree = 0.000) for 1318 atoms. Found 8 (8 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.3318 (Rfree = 0.000) for 1311 atoms. Found 8 (8 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.3423 (Rfree = 0.000) for 1302 atoms. Found 8 (8 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.3878 (Rfree = 0.000) for 1298 atoms. Found 8 (8 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.3160 (Rfree = 0.000) for 1292 atoms. Found 8 (8 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.71 Search for helices and strands: 0 residues in 0 chains, 1339 seeds are put forward NCS extension: 0 residues added, 1339 seeds are put forward Round 1: 50 peptides, 12 chains. Longest chain 6 peptides. Score 0.187 Round 2: 59 peptides, 13 chains. Longest chain 6 peptides. Score 0.233 Round 3: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.282 Round 4: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.291 Round 5: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.264 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 46, 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 2ozj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3785 reflections ( 99.45 % complete ) and 2615 restraints for refining 1257 atoms. 2442 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3533 (Rfree = 0.000) for 1257 atoms. Found 0 (8 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3240 (Rfree = 0.000) for 1248 atoms. Found 0 (8 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.3537 (Rfree = 0.000) for 1237 atoms. Found 0 (8 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3337 (Rfree = 0.000) for 1226 atoms. TimeTaking 25.22