Sun 23 Dec 22:22:59 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 2nyh-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-4.0-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/2nyh-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-4.0-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 22:23:09 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/2nyh-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-4.0-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 178 and 0 Target number of residues in the AU: 178 Target solvent content: 0.6532 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 234 Adjusted target solvent content: 0.54 Input MTZ file: 2nyh-4.0-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: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.85 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: 55.335 4.000 Wilson plot Bfac: 79.66 2464 reflections ( 97.66 % complete ) and 0 restraints for refining 2063 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3622 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3504 (Rfree = 0.000) for 2063 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.86 3.66 Search for helices and strands: 0 residues in 0 chains, 2086 seeds are put forward NCS extension: 0 residues added, 2086 seeds are put forward Round 1: 48 peptides, 11 chains. Longest chain 6 peptides. Score 0.201 Round 2: 56 peptides, 12 chains. Longest chain 8 peptides. Score 0.232 Round 3: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.295 Round 4: 76 peptides, 15 chains. Longest chain 7 peptides. Score 0.284 Round 5: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.314 Taking the results from Round 5 Chains 17, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 4095 restraints for refining 1686 atoms. 3824 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3505 (Rfree = 0.000) for 1686 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 2: After refmac, R = 0.3310 (Rfree = 0.000) for 1645 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 3: After refmac, R = 0.3389 (Rfree = 0.000) for 1630 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 4: After refmac, R = 0.3338 (Rfree = 0.000) for 1607 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 5: After refmac, R = 0.3052 (Rfree = 0.000) for 1585 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 1624 seeds are put forward NCS extension: 0 residues added, 1624 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 11 peptides. Score 0.267 Round 2: 102 peptides, 21 chains. Longest chain 9 peptides. Score 0.288 Round 3: 110 peptides, 19 chains. Longest chain 12 peptides. Score 0.390 Round 4: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.384 Round 5: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 5 Chains 20, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3633 restraints for refining 1620 atoms. 3273 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3032 (Rfree = 0.000) for 1620 atoms. Found 6 (7 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.2995 (Rfree = 0.000) for 1583 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 8: After refmac, R = 0.3080 (Rfree = 0.000) for 1555 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. Cycle 9: After refmac, R = 0.2797 (Rfree = 0.000) for 1523 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 10: After refmac, R = 0.2832 (Rfree = 0.000) for 1508 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.63 Search for helices and strands: 0 residues in 0 chains, 1564 seeds are put forward NCS extension: 0 residues added, 1564 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 8 peptides. Score 0.265 Round 2: 106 peptides, 18 chains. Longest chain 14 peptides. Score 0.392 Round 3: 107 peptides, 18 chains. Longest chain 11 peptides. Score 0.398 Round 4: 112 peptides, 17 chains. Longest chain 17 peptides. Score 0.451 Round 5: 115 peptides, 17 chains. Longest chain 17 peptides. Score 0.467 Taking the results from Round 5 Chains 17, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3596 restraints for refining 1596 atoms. 3221 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2899 (Rfree = 0.000) for 1596 atoms. Found 5 (7 requested) and removed 16 (3 requested) atoms. Cycle 12: After refmac, R = 0.3002 (Rfree = 0.000) for 1569 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 13: After refmac, R = 0.2801 (Rfree = 0.000) for 1545 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2978 (Rfree = 0.000) for 1536 atoms. Found 7 (7 requested) and removed 24 (3 requested) atoms. Cycle 15: After refmac, R = 0.2750 (Rfree = 0.000) for 1504 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 1531 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1550 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.286 Round 2: 101 peptides, 15 chains. Longest chain 13 peptides. Score 0.439 Round 3: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.345 Round 4: 100 peptides, 17 chains. Longest chain 10 peptides. Score 0.382 Round 5: 102 peptides, 18 chains. Longest chain 10 peptides. Score 0.368 Taking the results from Round 2 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3437 restraints for refining 1563 atoms. 3108 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3164 (Rfree = 0.000) for 1563 atoms. Found 7 (7 requested) and removed 23 (3 requested) atoms. Cycle 17: After refmac, R = 0.2769 (Rfree = 0.000) for 1530 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 18: After refmac, R = 0.2970 (Rfree = 0.000) for 1516 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 19: After refmac, R = 0.2744 (Rfree = 0.000) for 1500 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 20: After refmac, R = 0.2974 (Rfree = 0.000) for 1489 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.58 Search for helices and strands: 0 residues in 0 chains, 1510 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1530 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.259 Round 2: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.366 Round 3: 99 peptides, 17 chains. Longest chain 12 peptides. Score 0.376 Round 4: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.378 Round 5: 106 peptides, 17 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 5 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3658 restraints for refining 1643 atoms. 3319 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3015 (Rfree = 0.000) for 1643 atoms. Found 7 (7 requested) and removed 22 (3 requested) atoms. Cycle 22: After refmac, R = 0.3340 (Rfree = 0.000) for 1609 atoms. Found 7 (7 requested) and removed 37 (3 requested) atoms. Cycle 23: After refmac, R = 0.2866 (Rfree = 0.000) for 1558 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 24: After refmac, R = 0.2847 (Rfree = 0.000) for 1544 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 25: After refmac, R = 0.2830 (Rfree = 0.000) for 1534 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.59 Search for helices and strands: 0 residues in 0 chains, 1582 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1600 seeds are put forward Round 1: 83 peptides, 18 chains. Longest chain 8 peptides. Score 0.246 Round 2: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.356 Round 3: 101 peptides, 15 chains. Longest chain 13 peptides. Score 0.439 Round 4: 91 peptides, 14 chains. Longest chain 13 peptides. Score 0.407 Round 5: 96 peptides, 14 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 3 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3600 restraints for refining 1583 atoms. 3271 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3391 (Rfree = 0.000) for 1583 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 27: After refmac, R = 0.3123 (Rfree = 0.000) for 1560 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 28: After refmac, R = 0.3082 (Rfree = 0.000) for 1534 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2586 (Rfree = 0.000) for 1515 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2749 (Rfree = 0.000) for 1508 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 1527 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1541 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.298 Round 2: 94 peptides, 15 chains. Longest chain 13 peptides. Score 0.399 Round 3: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.336 Round 4: 89 peptides, 16 chains. Longest chain 8 peptides. Score 0.341 Round 5: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.360 Taking the results from Round 2 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3479 restraints for refining 1544 atoms. 3178 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3254 (Rfree = 0.000) for 1544 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.3075 (Rfree = 0.000) for 1525 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 33: After refmac, R = 0.2844 (Rfree = 0.000) for 1496 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.2743 (Rfree = 0.000) for 1490 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 35: After refmac, R = 0.2760 (Rfree = 0.000) for 1483 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 1510 seeds are put forward NCS extension: 0 residues added, 1510 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 6 peptides. Score 0.223 Round 2: 80 peptides, 16 chains. Longest chain 9 peptides. Score 0.282 Round 3: 89 peptides, 17 chains. Longest chain 13 peptides. Score 0.314 Round 4: 84 peptides, 15 chains. Longest chain 11 peptides. Score 0.337 Round 5: 88 peptides, 16 chains. Longest chain 9 peptides. Score 0.335 Taking the results from Round 4 Chains 15, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3548 restraints for refining 1559 atoms. 3287 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3054 (Rfree = 0.000) for 1559 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 37: After refmac, R = 0.3047 (Rfree = 0.000) for 1537 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 38: After refmac, R = 0.3156 (Rfree = 0.000) for 1522 atoms. Found 7 (7 requested) and removed 23 (3 requested) atoms. Cycle 39: After refmac, R = 0.2897 (Rfree = 0.000) for 1492 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 40: After refmac, R = 0.2819 (Rfree = 0.000) for 1488 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 1535 seeds are put forward NCS extension: 0 residues added, 1535 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.249 Round 2: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.286 Round 3: 79 peptides, 14 chains. Longest chain 14 peptides. Score 0.333 Round 4: 81 peptides, 16 chains. Longest chain 12 peptides. Score 0.289 Round 5: 78 peptides, 12 chains. Longest chain 16 peptides. Score 0.383 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 ------------------------------------------------------ 2464 reflections ( 97.66 % complete ) and 3478 restraints for refining 1543 atoms. 3226 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3066 (Rfree = 0.000) for 1543 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 42: After refmac, R = 0.3056 (Rfree = 0.000) for 1521 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 43: After refmac, R = 0.2762 (Rfree = 0.000) for 1499 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2976 (Rfree = 0.000) for 1491 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 45: After refmac, R = 0.2653 (Rfree = 0.000) for 1474 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 1502 seeds are put forward NCS extension: 0 residues added, 1502 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.241 Round 2: 64 peptides, 11 chains. Longest chain 13 peptides. Score 0.321 Round 3: 66 peptides, 11 chains. Longest chain 13 peptides. Score 0.335 Round 4: 65 peptides, 10 chains. Longest chain 13 peptides. Score 0.358 Round 5: 65 peptides, 11 chains. Longest chain 13 peptides. Score 0.328 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 55, 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 2nyh-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2464 reflections ( 97.66 % complete ) and 3468 restraints for refining 1529 atoms. 3258 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2884 (Rfree = 0.000) for 1529 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3020 (Rfree = 0.000) for 1519 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3040 (Rfree = 0.000) for 1506 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2815 (Rfree = 0.000) for 1494 atoms. TimeTaking 28.92