null Mon 24 Dec 00:08:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ozj-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ozj-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ozj-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-mrncs ############### 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 00:09:01 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-mrncs/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-mrncs.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-mrncs.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 2015 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3290 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3708 (Rfree = 0.000) for 2015 atoms. Found 12 (12 requested) and removed 54 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 4.22 Search for helices and strands: 0 residues in 0 chains, 1993 seeds are put forward NCS extension: 0 residues added, 1993 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.255 Round 2: 101 peptides, 17 chains. Longest chain 14 peptides. Score 0.433 Round 3: 111 peptides, 16 chains. Longest chain 16 peptides. Score 0.529 Round 4: 112 peptides, 16 chains. Longest chain 13 peptides. Score 0.536 Round 5: 106 peptides, 16 chains. Longest chain 13 peptides. Score 0.497 Taking the results from Round 4 Chains 16, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3937 restraints for refining 1654 atoms. 3569 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3181 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 2: After refmac, R = 0.3008 (Rfree = 0.000) for 1603 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.3348 (Rfree = 0.000) for 1572 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 4: After refmac, R = 0.3100 (Rfree = 0.000) for 1537 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.2950 (Rfree = 0.000) for 1525 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.99 Search for helices and strands: 0 residues in 0 chains, 1578 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1596 seeds are put forward Round 1: 90 peptides, 17 chains. Longest chain 10 peptides. Score 0.352 Round 2: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.455 Round 3: 110 peptides, 18 chains. Longest chain 14 peptides. Score 0.466 Round 4: 119 peptides, 18 chains. Longest chain 17 peptides. Score 0.525 Round 5: 107 peptides, 19 chains. Longest chain 14 peptides. Score 0.415 Taking the results from Round 4 Chains 18, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3338 restraints for refining 1486 atoms. 2952 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3053 (Rfree = 0.000) for 1486 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 7: After refmac, R = 0.2983 (Rfree = 0.000) for 1471 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 8: After refmac, R = 0.3049 (Rfree = 0.000) for 1457 atoms. Found 8 (9 requested) and removed 16 (4 requested) atoms. Cycle 9: After refmac, R = 0.2912 (Rfree = 0.000) for 1432 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.3710 (Rfree = 0.000) for 1426 atoms. Found 8 (9 requested) and removed 35 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 1495 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 1523 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.311 Round 2: 91 peptides, 17 chains. Longest chain 12 peptides. Score 0.359 Round 3: 95 peptides, 16 chains. Longest chain 12 peptides. Score 0.421 Round 4: 102 peptides, 15 chains. Longest chain 13 peptides. Score 0.500 Round 5: 103 peptides, 17 chains. Longest chain 10 peptides. Score 0.448 Taking the results from Round 4 Chains 15, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3392 restraints for refining 1490 atoms. 3059 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3238 (Rfree = 0.000) for 1490 atoms. Found 7 (9 requested) and removed 23 (4 requested) atoms. Cycle 12: After refmac, R = 0.3048 (Rfree = 0.000) for 1453 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 13: After refmac, R = 0.3423 (Rfree = 0.000) for 1435 atoms. Found 9 (9 requested) and removed 34 (4 requested) atoms. Cycle 14: After refmac, R = 0.3126 (Rfree = 0.000) for 1396 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.3854 (Rfree = 0.000) for 1389 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.99 Search for helices and strands: 0 residues in 0 chains, 1437 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 1444 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.331 Round 2: 76 peptides, 11 chains. Longest chain 14 peptides. Score 0.443 Round 3: 78 peptides, 11 chains. Longest chain 16 peptides. Score 0.458 Round 4: 74 peptides, 12 chains. Longest chain 9 peptides. Score 0.395 Round 5: 78 peptides, 13 chains. Longest chain 9 peptides. Score 0.392 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 ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3031 restraints for refining 1372 atoms. 2774 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3275 (Rfree = 0.000) for 1372 atoms. Found 8 (8 requested) and removed 23 (4 requested) atoms. Cycle 17: After refmac, R = 0.2760 (Rfree = 0.000) for 1347 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 18: After refmac, R = 0.3339 (Rfree = 0.000) for 1337 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 19: After refmac, R = 0.3120 (Rfree = 0.000) for 1325 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2970 (Rfree = 0.000) for 1313 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 1358 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1384 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 10 peptides. Score 0.236 Round 2: 70 peptides, 13 chains. Longest chain 11 peptides. Score 0.328 Round 3: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.381 Round 4: 79 peptides, 14 chains. Longest chain 11 peptides. Score 0.366 Round 5: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.350 Taking the results from Round 3 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2795 restraints for refining 1297 atoms. 2541 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3207 (Rfree = 0.000) for 1297 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 22: After refmac, R = 0.3759 (Rfree = 0.000) for 1282 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 23: After refmac, R = 0.3333 (Rfree = 0.000) for 1259 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.3297 (Rfree = 0.000) for 1256 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 25: After refmac, R = 0.3180 (Rfree = 0.000) for 1250 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 1316 seeds are put forward NCS extension: 0 residues added, 1316 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.262 Round 2: 80 peptides, 15 chains. Longest chain 13 peptides. Score 0.340 Round 3: 71 peptides, 14 chains. Longest chain 7 peptides. Score 0.301 Round 4: 74 peptides, 13 chains. Longest chain 11 peptides. Score 0.361 Round 5: 69 peptides, 10 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 5 Chains 10, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2829 restraints for refining 1272 atoms. 2603 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3374 (Rfree = 0.000) for 1272 atoms. Found 5 (8 requested) and removed 22 (4 requested) atoms. Cycle 27: After refmac, R = 0.3888 (Rfree = 0.000) for 1250 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.3636 (Rfree = 0.000) for 1239 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 29: After refmac, R = 0.3327 (Rfree = 0.000) for 1225 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.3677 (Rfree = 0.000) for 1222 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 4.16 Search for helices and strands: 0 residues in 0 chains, 1262 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1278 seeds are put forward Round 1: 54 peptides, 13 chains. Longest chain 5 peptides. Score 0.186 Round 2: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.258 Round 3: 71 peptides, 13 chains. Longest chain 7 peptides. Score 0.336 Round 4: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.354 Round 5: 67 peptides, 11 chains. Longest chain 11 peptides. Score 0.375 Taking the results from Round 5 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2653 restraints for refining 1226 atoms. 2440 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3411 (Rfree = 0.000) for 1226 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 32: After refmac, R = 0.3415 (Rfree = 0.000) for 1209 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 33: After refmac, R = 0.3479 (Rfree = 0.000) for 1202 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.3692 (Rfree = 0.000) for 1195 atoms. Found 7 (7 requested) and removed 32 (3 requested) atoms. Cycle 35: After refmac, R = 0.3290 (Rfree = 0.000) for 1167 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 1190 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1201 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.208 Round 2: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.286 Round 3: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.274 Round 4: 74 peptides, 13 chains. Longest chain 13 peptides. Score 0.361 Round 5: 69 peptides, 14 chains. Longest chain 9 peptides. Score 0.284 Taking the results from Round 4 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2417 restraints for refining 1120 atoms. 2186 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3503 (Rfree = 0.000) for 1120 atoms. Found 6 (7 requested) and removed 9 (3 requested) atoms. Cycle 37: After refmac, R = 0.3284 (Rfree = 0.000) for 1110 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.3673 (Rfree = 0.000) for 1102 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.3256 (Rfree = 0.000) for 1099 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.3704 (Rfree = 0.000) for 1099 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 4.14 Search for helices and strands: 0 residues in 0 chains, 1140 seeds are put forward NCS extension: 0 residues added, 1140 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.198 Round 2: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.280 Round 3: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.303 Round 4: 51 peptides, 9 chains. Longest chain 9 peptides. Score 0.315 Round 5: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.349 Taking the results from Round 5 Chains 9, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2253 restraints for refining 1088 atoms. 2078 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3398 (Rfree = 0.000) for 1088 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.3357 (Rfree = 0.000) for 1085 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.3460 (Rfree = 0.000) for 1082 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 44: After refmac, R = 0.3148 (Rfree = 0.000) for 1070 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.3547 (Rfree = 0.000) for 1069 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 4.02 Search for helices and strands: 0 residues in 0 chains, 1079 seeds are put forward NCS extension: 0 residues added, 1079 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 6 peptides. Score 0.198 Round 2: 55 peptides, 11 chains. Longest chain 8 peptides. Score 0.273 Round 3: 54 peptides, 10 chains. Longest chain 10 peptides. Score 0.303 Round 4: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.325 Round 5: 68 peptides, 10 chains. Longest chain 14 peptides. Score 0.417 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 58, 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 2188 restraints for refining 1072 atoms. 1966 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3338 (Rfree = 0.000) for 1072 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3402 (Rfree = 0.000) for 1059 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2637 (Rfree = 0.000) for 1044 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2927 (Rfree = 0.000) for 1033 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:30:35 GMT 2018 Job finished. TimeTaking 21.64 Used memory is bytes: 13220736