null Sun 23 Dec 22:23:02 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 2pg4-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.2-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/2pg4-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.2-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 22:23:12 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/2pg4-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.2-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 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.6364 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 190 Adjusted target solvent content: 0.54 Input MTZ file: 2pg4-3.2-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: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.70 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: 77.669 3.201 Wilson plot Bfac: 68.80 4027 reflections ( 99.65 % complete ) and 0 restraints for refining 1687 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3724 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3505 (Rfree = 0.000) for 1687 atoms. Found 8 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 1717 seeds are put forward NCS extension: 0 residues added, 1717 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 10 peptides. Score 0.313 Round 2: 103 peptides, 14 chains. Longest chain 21 peptides. Score 0.527 Round 3: 105 peptides, 12 chains. Longest chain 23 peptides. Score 0.593 Round 4: 115 peptides, 13 chains. Longest chain 25 peptides. Score 0.622 Round 5: 116 peptides, 12 chains. Longest chain 25 peptides. Score 0.650 Taking the results from Round 5 Chains 12, Residues 104, Estimated correctness of the model 53.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3062 restraints for refining 1387 atoms. 2658 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3172 (Rfree = 0.000) for 1387 atoms. Found 3 (12 requested) and removed 11 (6 requested) atoms. Cycle 2: After refmac, R = 0.3141 (Rfree = 0.000) for 1363 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.2870 (Rfree = 0.000) for 1347 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.2792 (Rfree = 0.000) for 1337 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2891 (Rfree = 0.000) for 1329 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 1391 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 1402 seeds are put forward Round 1: 100 peptides, 13 chains. Longest chain 23 peptides. Score 0.537 Round 2: 100 peptides, 14 chains. Longest chain 17 peptides. Score 0.509 Round 3: 111 peptides, 11 chains. Longest chain 26 peptides. Score 0.649 Round 4: 107 peptides, 10 chains. Longest chain 30 peptides. Score 0.652 Round 5: 110 peptides, 13 chains. Longest chain 17 peptides. Score 0.595 Taking the results from Round 4 Chains 11, Residues 97, Estimated correctness of the model 54.3 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 2804 restraints for refining 1387 atoms. 2311 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3097 (Rfree = 0.000) for 1387 atoms. Found 6 (12 requested) and removed 20 (6 requested) atoms. Cycle 7: After refmac, R = 0.3070 (Rfree = 0.000) for 1368 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2903 (Rfree = 0.000) for 1358 atoms. Found 0 (12 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.2864 (Rfree = 0.000) for 1346 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2909 (Rfree = 0.000) for 1342 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 1388 seeds are put forward NCS extension: 58 residues added (3 deleted due to clashes), 1446 seeds are put forward Round 1: 107 peptides, 14 chains. Longest chain 18 peptides. Score 0.552 Round 2: 119 peptides, 14 chains. Longest chain 24 peptides. Score 0.618 Round 3: 113 peptides, 11 chains. Longest chain 31 peptides. Score 0.658 Round 4: 104 peptides, 9 chains. Longest chain 32 peptides. Score 0.661 Round 5: 111 peptides, 13 chains. Longest chain 22 peptides. Score 0.600 Taking the results from Round 4 Chains 9, Residues 95, Estimated correctness of the model 56.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3081 restraints for refining 1387 atoms. 2710 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3226 (Rfree = 0.000) for 1387 atoms. Found 9 (12 requested) and removed 15 (6 requested) atoms. Cycle 12: After refmac, R = 0.3024 (Rfree = 0.000) for 1379 atoms. Found 2 (12 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.3094 (Rfree = 0.000) for 1371 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. Cycle 14: After refmac, R = 0.2770 (Rfree = 0.000) for 1363 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.3077 (Rfree = 0.000) for 1356 atoms. Found 9 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 1422 seeds are put forward NCS extension: 51 residues added (3 deleted due to clashes), 1473 seeds are put forward Round 1: 87 peptides, 11 chains. Longest chain 18 peptides. Score 0.512 Round 2: 105 peptides, 13 chains. Longest chain 23 peptides. Score 0.566 Round 3: 102 peptides, 14 chains. Longest chain 18 peptides. Score 0.521 Round 4: 107 peptides, 14 chains. Longest chain 19 peptides. Score 0.552 Round 5: 108 peptides, 13 chains. Longest chain 22 peptides. Score 0.584 Taking the results from Round 5 Chains 13, Residues 95, Estimated correctness of the model 36.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3111 restraints for refining 1387 atoms. 2744 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3022 (Rfree = 0.000) for 1387 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 17: After refmac, R = 0.2935 (Rfree = 0.000) for 1381 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2677 (Rfree = 0.000) for 1373 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.2673 (Rfree = 0.000) for 1362 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.2744 (Rfree = 0.000) for 1356 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 1402 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 1431 seeds are put forward Round 1: 97 peptides, 16 chains. Longest chain 18 peptides. Score 0.430 Round 2: 104 peptides, 15 chains. Longest chain 14 peptides. Score 0.506 Round 3: 107 peptides, 15 chains. Longest chain 22 peptides. Score 0.525 Round 4: 107 peptides, 13 chains. Longest chain 16 peptides. Score 0.578 Round 5: 107 peptides, 17 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 4 Chains 13, Residues 94, Estimated correctness of the model 34.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3124 restraints for refining 1387 atoms. 2761 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2994 (Rfree = 0.000) for 1387 atoms. Found 8 (12 requested) and removed 15 (6 requested) atoms. Cycle 22: After refmac, R = 0.3091 (Rfree = 0.000) for 1378 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2945 (Rfree = 0.000) for 1381 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.2841 (Rfree = 0.000) for 1370 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2950 (Rfree = 0.000) for 1365 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 1424 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1446 seeds are put forward Round 1: 88 peptides, 14 chains. Longest chain 15 peptides. Score 0.428 Round 2: 113 peptides, 15 chains. Longest chain 24 peptides. Score 0.560 Round 3: 101 peptides, 16 chains. Longest chain 16 peptides. Score 0.457 Round 4: 105 peptides, 14 chains. Longest chain 18 peptides. Score 0.540 Round 5: 108 peptides, 17 chains. Longest chain 15 peptides. Score 0.475 Taking the results from Round 2 Chains 15, Residues 98, Estimated correctness of the model 29.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3035 restraints for refining 1383 atoms. 2658 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2869 (Rfree = 0.000) for 1383 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.2783 (Rfree = 0.000) for 1377 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2870 (Rfree = 0.000) for 1368 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2992 (Rfree = 0.000) for 1364 atoms. Found 5 (12 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.3217 (Rfree = 0.000) for 1356 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 1421 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1434 seeds are put forward Round 1: 90 peptides, 13 chains. Longest chain 17 peptides. Score 0.472 Round 2: 102 peptides, 17 chains. Longest chain 13 peptides. Score 0.435 Round 3: 100 peptides, 13 chains. Longest chain 16 peptides. Score 0.537 Round 4: 90 peptides, 14 chains. Longest chain 13 peptides. Score 0.442 Round 5: 98 peptides, 15 chains. Longest chain 18 peptides. Score 0.467 Taking the results from Round 3 Chains 13, Residues 87, Estimated correctness of the model 22.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3019 restraints for refining 1387 atoms. 2684 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2919 (Rfree = 0.000) for 1387 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.2882 (Rfree = 0.000) for 1375 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.2845 (Rfree = 0.000) for 1366 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.3236 (Rfree = 0.000) for 1357 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.2661 (Rfree = 0.000) for 1349 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 1398 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1420 seeds are put forward Round 1: 70 peptides, 12 chains. Longest chain 15 peptides. Score 0.359 Round 2: 87 peptides, 13 chains. Longest chain 16 peptides. Score 0.452 Round 3: 81 peptides, 12 chains. Longest chain 13 peptides. Score 0.441 Round 4: 80 peptides, 10 chains. Longest chain 16 peptides. Score 0.497 Round 5: 85 peptides, 13 chains. Longest chain 10 peptides. Score 0.438 Taking the results from Round 4 Chains 10, Residues 70, Estimated correctness of the model 10.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 3044 restraints for refining 1387 atoms. 2774 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2895 (Rfree = 0.000) for 1387 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.2902 (Rfree = 0.000) for 1384 atoms. Found 5 (12 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.2765 (Rfree = 0.000) for 1376 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.2745 (Rfree = 0.000) for 1372 atoms. Found 9 (12 requested) and removed 18 (6 requested) atoms. Cycle 40: After refmac, R = 0.2765 (Rfree = 0.000) for 1362 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 1399 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1417 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.315 Round 2: 86 peptides, 14 chains. Longest chain 14 peptides. Score 0.414 Round 3: 87 peptides, 14 chains. Longest chain 14 peptides. Score 0.421 Round 4: 86 peptides, 12 chains. Longest chain 14 peptides. Score 0.476 Round 5: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.374 Taking the results from Round 4 Chains 12, Residues 74, Estimated correctness of the model 3.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4027 reflections ( 99.65 % complete ) and 2983 restraints for refining 1386 atoms. 2699 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2664 (Rfree = 0.000) for 1386 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2646 (Rfree = 0.000) for 1385 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 43: After refmac, R = 0.2651 (Rfree = 0.000) for 1381 atoms. Found 11 (12 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.2710 (Rfree = 0.000) for 1382 atoms. Found 5 (12 requested) and removed 17 (6 requested) atoms. Cycle 45: After refmac, R = 0.2624 (Rfree = 0.000) for 1366 atoms. Found 11 (12 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward NCS extension: 0 residues added, 1408 seeds are put forward Round 1: 65 peptides, 11 chains. Longest chain 14 peptides. Score 0.355 Round 2: 63 peptides, 9 chains. Longest chain 15 peptides. Score 0.409 Round 3: 69 peptides, 10 chains. Longest chain 16 peptides. Score 0.420 Round 4: 75 peptides, 10 chains. Longest chain 16 peptides. Score 0.463 Round 5: 66 peptides, 11 chains. Longest chain 15 peptides. Score 0.362 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 65, 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 2pg4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4027 reflections ( 99.65 % complete ) and 2952 restraints for refining 1383 atoms. 2702 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2801 (Rfree = 0.000) for 1383 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2939 (Rfree = 0.000) for 1375 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.3349 (Rfree = 0.000) for 1368 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2631 (Rfree = 0.000) for 1360 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:45 GMT 2018 Job finished. TimeTaking 30.71 Used memory is bytes: 18266480