null Mon 24 Dec 07:34:25 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-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 07:34:29 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-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 138 and 0 Target number of residues in the AU: 138 Target solvent content: 0.6528 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 79.88 2686 reflections ( 99.26 % complete ) and 0 restraints for refining 2010 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3324 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3494 (Rfree = 0.000) for 2010 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 2023 seeds are put forward NCS extension: 0 residues added, 2023 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 10 peptides. Score 0.316 Round 2: 118 peptides, 17 chains. Longest chain 14 peptides. Score 0.545 Round 3: 117 peptides, 18 chains. Longest chain 13 peptides. Score 0.512 Round 4: 126 peptides, 18 chains. Longest chain 24 peptides. Score 0.567 Round 5: 128 peptides, 19 chains. Longest chain 21 peptides. Score 0.553 Taking the results from Round 4 Chains 18, Residues 108, Estimated correctness of the model 1.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3810 restraints for refining 1653 atoms. 3396 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3310 (Rfree = 0.000) for 1653 atoms. Found 5 (10 requested) and removed 21 (5 requested) atoms. Cycle 2: After refmac, R = 0.3107 (Rfree = 0.000) for 1591 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 3: After refmac, R = 0.3106 (Rfree = 0.000) for 1547 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 4: After refmac, R = 0.2880 (Rfree = 0.000) for 1521 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 5: After refmac, R = 0.2785 (Rfree = 0.000) for 1502 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.88 Search for helices and strands: 0 residues in 0 chains, 1558 seeds are put forward NCS extension: 47 residues added (1 deleted due to clashes), 1605 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.364 Round 2: 122 peptides, 19 chains. Longest chain 16 peptides. Score 0.516 Round 3: 123 peptides, 16 chains. Longest chain 13 peptides. Score 0.600 Round 4: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.484 Round 5: 115 peptides, 16 chains. Longest chain 21 peptides. Score 0.554 Taking the results from Round 3 Chains 16, Residues 107, Estimated correctness of the model 14.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3369 restraints for refining 1533 atoms. 2957 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3131 (Rfree = 0.000) for 1533 atoms. Found 7 (9 requested) and removed 25 (4 requested) atoms. Cycle 7: After refmac, R = 0.2970 (Rfree = 0.000) for 1492 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 8: After refmac, R = 0.2842 (Rfree = 0.000) for 1471 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 9: After refmac, R = 0.2632 (Rfree = 0.000) for 1461 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 10: After refmac, R = 0.3337 (Rfree = 0.000) for 1449 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 1520 seeds are put forward NCS extension: 0 residues added, 1520 seeds are put forward Round 1: 93 peptides, 18 chains. Longest chain 10 peptides. Score 0.342 Round 2: 102 peptides, 17 chains. Longest chain 13 peptides. Score 0.441 Round 3: 102 peptides, 16 chains. Longest chain 17 peptides. Score 0.471 Round 4: 107 peptides, 16 chains. Longest chain 18 peptides. Score 0.504 Round 5: 105 peptides, 15 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 5 Chains 15, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3608 restraints for refining 1569 atoms. 3263 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3054 (Rfree = 0.000) for 1569 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 12: After refmac, R = 0.3084 (Rfree = 0.000) for 1541 atoms. Found 10 (10 requested) and removed 33 (5 requested) atoms. Cycle 13: After refmac, R = 0.3328 (Rfree = 0.000) for 1505 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 14: After refmac, R = 0.2938 (Rfree = 0.000) for 1483 atoms. Found 9 (9 requested) and removed 32 (4 requested) atoms. Cycle 15: After refmac, R = 0.2967 (Rfree = 0.000) for 1451 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.86 Search for helices and strands: 0 residues in 0 chains, 1535 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 1561 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.256 Round 2: 90 peptides, 13 chains. Longest chain 20 peptides. Score 0.479 Round 3: 98 peptides, 16 chains. Longest chain 12 peptides. Score 0.443 Round 4: 97 peptides, 14 chains. Longest chain 14 peptides. Score 0.496 Round 5: 89 peptides, 15 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 4 Chains 14, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3271 restraints for refining 1443 atoms. 2953 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2996 (Rfree = 0.000) for 1443 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 17: After refmac, R = 0.2814 (Rfree = 0.000) for 1433 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.3042 (Rfree = 0.000) for 1429 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 19: After refmac, R = 0.2762 (Rfree = 0.000) for 1403 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 20: After refmac, R = 0.3063 (Rfree = 0.000) for 1398 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 1441 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 1462 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 6 peptides. Score 0.237 Round 2: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.394 Round 3: 92 peptides, 14 chains. Longest chain 13 peptides. Score 0.462 Round 4: 93 peptides, 15 chains. Longest chain 11 peptides. Score 0.438 Round 5: 99 peptides, 15 chains. Longest chain 13 peptides. Score 0.480 Taking the results from Round 5 Chains 15, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3128 restraints for refining 1427 atoms. 2807 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3121 (Rfree = 0.000) for 1427 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 22: After refmac, R = 0.3274 (Rfree = 0.000) for 1410 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 23: After refmac, R = 0.3373 (Rfree = 0.000) for 1391 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 24: After refmac, R = 0.3148 (Rfree = 0.000) for 1365 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 25: After refmac, R = 0.2817 (Rfree = 0.000) for 1351 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.86 Search for helices and strands: 0 residues in 0 chains, 1424 seeds are put forward NCS extension: 0 residues added, 1424 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.228 Round 2: 64 peptides, 11 chains. Longest chain 8 peptides. Score 0.350 Round 3: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.280 Round 4: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.308 Round 5: 60 peptides, 10 chains. Longest chain 14 peptides. Score 0.354 Taking the results from Round 5 Chains 10, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3259 restraints for refining 1387 atoms. 3069 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3093 (Rfree = 0.000) for 1387 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 27: After refmac, R = 0.2945 (Rfree = 0.000) for 1370 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.2857 (Rfree = 0.000) for 1359 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.3351 (Rfree = 0.000) for 1355 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 30: After refmac, R = 0.2906 (Rfree = 0.000) for 1345 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 4.00 Search for helices and strands: 0 residues in 0 chains, 1368 seeds are put forward NCS extension: 0 residues added, 1368 seeds are put forward Round 1: 63 peptides, 15 chains. Longest chain 6 peptides. Score 0.195 Round 2: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.332 Round 3: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.338 Round 4: 80 peptides, 13 chains. Longest chain 16 peptides. Score 0.407 Round 5: 80 peptides, 14 chains. Longest chain 9 peptides. Score 0.374 Taking the results from Round 4 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2804 restraints for refining 1319 atoms. 2519 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3687 (Rfree = 0.000) for 1319 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 32: After refmac, R = 0.2982 (Rfree = 0.000) for 1300 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 33: After refmac, R = 0.2948 (Rfree = 0.000) for 1292 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 34: After refmac, R = 0.2938 (Rfree = 0.000) for 1286 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 35: After refmac, R = 0.3135 (Rfree = 0.000) for 1278 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 1318 seeds are put forward NCS extension: 0 residues added, 1318 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 8 peptides. Score 0.255 Round 2: 67 peptides, 10 chains. Longest chain 11 peptides. Score 0.410 Round 3: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.334 Round 4: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.342 Round 5: 67 peptides, 10 chains. Longest chain 10 peptides. Score 0.410 Taking the results from Round 5 Chains 10, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2722 restraints for refining 1276 atoms. 2504 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3335 (Rfree = 0.000) for 1276 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 37: After refmac, R = 0.3061 (Rfree = 0.000) for 1253 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.3141 (Rfree = 0.000) for 1243 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 39: After refmac, R = 0.3431 (Rfree = 0.000) for 1237 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 40: After refmac, R = 0.3060 (Rfree = 0.000) for 1222 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 4.01 Search for helices and strands: 0 residues in 0 chains, 1265 seeds are put forward NCS extension: 0 residues added, 1265 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 7 peptides. Score 0.223 Round 2: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.273 Round 3: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.332 Round 4: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.294 Round 5: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.303 Taking the results from Round 3 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2413 restraints for refining 1129 atoms. 2246 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3435 (Rfree = 0.000) for 1129 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 42: After refmac, R = 0.3509 (Rfree = 0.000) for 1118 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 43: After refmac, R = 0.3494 (Rfree = 0.000) for 1108 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 44: After refmac, R = 0.3422 (Rfree = 0.000) for 1102 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.3041 (Rfree = 0.000) for 1106 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 1138 seeds are put forward NCS extension: 0 residues added, 1138 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 6 peptides. Score 0.238 Round 2: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.276 Round 3: 63 peptides, 13 chains. Longest chain 6 peptides. Score 0.269 Round 4: 66 peptides, 13 chains. Longest chain 7 peptides. Score 0.295 Round 5: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.278 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 53, 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. 2686 reflections ( 99.26 % complete ) and 2354 restraints for refining 1112 atoms. 2155 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3538 (Rfree = 0.000) for 1112 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3241 (Rfree = 0.000) for 1102 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3937 (Rfree = 0.000) for 1094 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3434 (Rfree = 0.000) for 1089 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:57:24 GMT 2018 Job finished. TimeTaking 22.99 Used memory is bytes: 22011888