null Sun 23 Dec 22:22:56 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 2gm6-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.8-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/2gm6-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.8-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 22:23:05 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/2gm6-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.8-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 222 and 0 Target number of residues in the AU: 222 Target solvent content: 0.6586 Checking the provided sequence file Detected sequence length: 208 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 208 Adjusted target solvent content: 0.68 Input MTZ file: 2gm6-3.8-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: 92 Cell parameters: 57.001 57.001 216.648 90.000 90.000 90.000 Input sequence file: 2gm6-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1664 target number of atoms Had to go as low as 1.05 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 Loops will be built when appropriate and at the last cycle Resolution range: 55.125 3.800 Wilson plot Bfac: 83.67 3934 reflections ( 99.67 % complete ) and 0 restraints for refining 1861 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3668 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2627 (Rfree = 0.000) for 1861 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 2.81 Search for helices and strands: 0 residues in 0 chains, 1898 seeds are put forward Round 1: 128 peptides, 19 chains. Longest chain 13 peptides. Score 0.439 Round 2: 139 peptides, 15 chains. Longest chain 20 peptides. Score 0.561 Round 3: 151 peptides, 14 chains. Longest chain 25 peptides. Score 0.620 Round 4: 153 peptides, 11 chains. Longest chain 28 peptides. Score 0.674 Round 5: 161 peptides, 11 chains. Longest chain 31 peptides. Score 0.697 Taking the results from Round 5 Chains 13, Residues 150, Estimated correctness of the model 39.2 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3934 reflections ( 99.67 % complete ) and 3107 restraints for refining 1534 atoms. 2462 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2801 (Rfree = 0.000) for 1534 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 2: After refmac, R = 0.2654 (Rfree = 0.000) for 1516 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.2557 (Rfree = 0.000) for 1505 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. Cycle 4: After refmac, R = 0.2436 (Rfree = 0.000) for 1495 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2399 (Rfree = 0.000) for 1487 atoms. Found 2 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 2.84 Search for helices and strands: 0 residues in 0 chains, 1534 seeds are put forward Round 1: 134 peptides, 14 chains. Longest chain 18 peptides. Score 0.560 Round 2: 139 peptides, 11 chains. Longest chain 25 peptides. Score 0.630 Round 3: 148 peptides, 13 chains. Longest chain 39 peptides. Score 0.627 Round 4: 148 peptides, 15 chains. Longest chain 24 peptides. Score 0.594 Round 5: 153 peptides, 13 chains. Longest chain 23 peptides. Score 0.643 Taking the results from Round 5 Chains 15, Residues 140, Estimated correctness of the model 17.9 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3934 reflections ( 99.67 % complete ) and 3260 restraints for refining 1505 atoms. 2686 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2782 (Rfree = 0.000) for 1505 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 7: After refmac, R = 0.2542 (Rfree = 0.000) for 1501 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2597 (Rfree = 0.000) for 1491 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.2534 (Rfree = 0.000) for 1484 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2427 (Rfree = 0.000) for 1482 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 2.82 Search for helices and strands: 0 residues in 0 chains, 1523 seeds are put forward Round 1: 132 peptides, 15 chains. Longest chain 17 peptides. Score 0.533 Round 2: 143 peptides, 15 chains. Longest chain 29 peptides. Score 0.575 Round 3: 129 peptides, 13 chains. Longest chain 17 peptides. Score 0.559 Round 4: 141 peptides, 12 chains. Longest chain 35 peptides. Score 0.620 Round 5: 143 peptides, 12 chains. Longest chain 22 peptides. Score 0.626 Taking the results from Round 5 Chains 12, Residues 131, Estimated correctness of the model 10.6 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3934 reflections ( 99.67 % complete ) and 3154 restraints for refining 1505 atoms. 2606 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2793 (Rfree = 0.000) for 1505 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 12: After refmac, R = 0.2462 (Rfree = 0.000) for 1504 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2348 (Rfree = 0.000) for 1496 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.2437 (Rfree = 0.000) for 1485 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 15: After refmac, R = 0.2531 (Rfree = 0.000) for 1470 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 2.78 Search for helices and strands: 0 residues in 0 chains, 1519 seeds are put forward Round 1: 125 peptides, 19 chains. Longest chain 13 peptides. Score 0.426 Round 2: 141 peptides, 15 chains. Longest chain 14 peptides. Score 0.568 Round 3: 145 peptides, 14 chains. Longest chain 21 peptides. Score 0.600 Round 4: 148 peptides, 15 chains. Longest chain 19 peptides. Score 0.594 Round 5: 150 peptides, 13 chains. Longest chain 44 peptides. Score 0.633 Taking the results from Round 5 Chains 15, Residues 137, Estimated correctness of the model 13.6 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3934 reflections ( 99.67 % complete ) and 3153 restraints for refining 1505 atoms. 2576 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2664 (Rfree = 0.000) for 1505 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 17: After refmac, R = 0.2551 (Rfree = 0.000) for 1490 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.2467 (Rfree = 0.000) for 1486 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 19: After refmac, R = 0.2309 (Rfree = 0.000) for 1483 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2189 (Rfree = 0.000) for 1478 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 2.86 Search for helices and strands: 0 residues in 0 chains, 1523 seeds are put forward Round 1: 130 peptides, 17 chains. Longest chain 24 peptides. Score 0.487 Round 2: 127 peptides, 13 chains. Longest chain 31 peptides. Score 0.551 Round 3: 134 peptides, 16 chains. Longest chain 26 peptides. Score 0.523 Round 4: 138 peptides, 12 chains. Longest chain 37 peptides. Score 0.609 Round 5: 134 peptides, 14 chains. Longest chain 21 peptides. Score 0.560 Taking the results from Round 4 Chains 13, Residues 126, Estimated correctness of the model 3.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3934 reflections ( 99.67 % complete ) and 3190 restraints for refining 1504 atoms. 2674 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2545 (Rfree = 0.000) for 1504 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 22: After refmac, R = 0.2369 (Rfree = 0.000) for 1493 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 23: After refmac, R = 0.2277 (Rfree = 0.000) for 1488 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2294 (Rfree = 0.000) for 1482 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2225 (Rfree = 0.000) for 1482 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 2.86 Search for helices and strands: 0 residues in 0 chains, 1526 seeds are put forward Round 1: 140 peptides, 17 chains. Longest chain 16 peptides. Score 0.528 Round 2: 148 peptides, 15 chains. Longest chain 33 peptides. Score 0.594 Round 3: 140 peptides, 15 chains. Longest chain 20 peptides. Score 0.564 Round 4: 151 peptides, 14 chains. Longest chain 28 peptides. Score 0.620 Round 5: 146 peptides, 13 chains. Longest chain 20 peptides. Score 0.620 Taking the results from Round 5 Chains 13, Residues 133, Estimated correctness of the model 8.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3934 reflections ( 99.67 % complete ) and 3273 restraints for refining 1505 atoms. 2733 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2726 (Rfree = 0.000) for 1505 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2605 (Rfree = 0.000) for 1500 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.2526 (Rfree = 0.000) for 1489 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.2470 (Rfree = 0.000) for 1472 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.2439 (Rfree = 0.000) for 1469 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 2.87 Search for helices and strands: 0 residues in 0 chains, 1512 seeds are put forward Round 1: 133 peptides, 17 chains. Longest chain 13 peptides. Score 0.500 Round 2: 144 peptides, 18 chains. Longest chain 12 peptides. Score 0.526 Round 3: 142 peptides, 14 chains. Longest chain 20 peptides. Score 0.589 Round 4: 145 peptides, 17 chains. Longest chain 19 peptides. Score 0.548 Round 5: 152 peptides, 17 chains. Longest chain 26 peptides. Score 0.574 Taking the results from Round 3 Chains 16, Residues 128, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3934 reflections ( 99.67 % complete ) and 3165 restraints for refining 1505 atoms. 2603 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2701 (Rfree = 0.000) for 1505 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 32: After refmac, R = 0.2419 (Rfree = 0.000) for 1487 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 33: After refmac, R = 0.2477 (Rfree = 0.000) for 1480 atoms. Found 5 (8 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.2362 (Rfree = 0.000) for 1471 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 35: After refmac, R = 0.2393 (Rfree = 0.000) for 1462 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 2.86 Search for helices and strands: 0 residues in 0 chains, 1515 seeds are put forward Round 1: 121 peptides, 18 chains. Longest chain 12 peptides. Score 0.428 Round 2: 134 peptides, 17 chains. Longest chain 16 peptides. Score 0.504 Round 3: 138 peptides, 13 chains. Longest chain 25 peptides. Score 0.592 Round 4: 130 peptides, 14 chains. Longest chain 19 peptides. Score 0.544 Round 5: 125 peptides, 13 chains. Longest chain 18 peptides. Score 0.543 Taking the results from Round 3 Chains 14, Residues 125, Estimated correctness of the model 0.0 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 3934 reflections ( 99.67 % complete ) and 2873 restraints for refining 1505 atoms. 2221 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2625 (Rfree = 0.000) for 1505 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 37: After refmac, R = 0.2461 (Rfree = 0.000) for 1496 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2402 (Rfree = 0.000) for 1497 atoms. Found 6 (8 requested) and removed 13 (4 requested) atoms. Cycle 39: After refmac, R = 0.2212 (Rfree = 0.000) for 1484 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.2182 (Rfree = 0.000) for 1477 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 2.87 Search for helices and strands: 0 residues in 0 chains, 1529 seeds are put forward Round 1: 125 peptides, 18 chains. Longest chain 13 peptides. Score 0.446 Round 2: 129 peptides, 13 chains. Longest chain 21 peptides. Score 0.559 Round 3: 128 peptides, 13 chains. Longest chain 17 peptides. Score 0.555 Round 4: 131 peptides, 12 chains. Longest chain 24 peptides. Score 0.584 Round 5: 122 peptides, 14 chains. Longest chain 19 peptides. Score 0.512 Taking the results from Round 4 Chains 13, Residues 119, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3934 reflections ( 99.67 % complete ) and 3353 restraints for refining 1505 atoms. 2848 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2738 (Rfree = 0.000) for 1505 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2615 (Rfree = 0.000) for 1494 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 43: After refmac, R = 0.2561 (Rfree = 0.000) for 1488 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.3034 (Rfree = 0.000) for 1488 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.2348 (Rfree = 0.000) for 1488 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 2.86 Search for helices and strands: 0 residues in 0 chains, 1523 seeds are put forward Round 1: 123 peptides, 16 chains. Longest chain 15 peptides. Score 0.477 Round 2: 124 peptides, 14 chains. Longest chain 25 peptides. Score 0.520 Round 3: 122 peptides, 12 chains. Longest chain 24 peptides. Score 0.550 Round 4: 131 peptides, 15 chains. Longest chain 25 peptides. Score 0.530 Round 5: 138 peptides, 13 chains. Longest chain 24 peptides. Score 0.592 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 125, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2gm6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3934 reflections ( 99.67 % complete ) and 3077 restraints for refining 1505 atoms. 2481 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2661 (Rfree = 0.000) for 1505 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2486 (Rfree = 0.000) for 1496 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2500 (Rfree = 0.000) for 1486 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2472 (Rfree = 0.000) for 1480 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:46 GMT 2018 Job finished. TimeTaking 33.84 Used memory is bytes: 6480592