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 2gm6-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-4.0-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/2gm6-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-4.0-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 22:23:05 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/2gm6-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-4.0-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 216 and 0 Target number of residues in the AU: 216 Target solvent content: 0.6679 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: 2gm6-4.0-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: 92 Cell parameters: 57.001 57.001 216.648 90.000 90.000 90.000 Input sequence file: 2gm6-4.0-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 4.001 Wilson plot Bfac: 89.81 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3398 reflections ( 99.62 % complete ) and 0 restraints for refining 1850 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3719 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3547 (Rfree = 0.000) for 1850 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.03 Search for helices and strands: 0 residues in 0 chains, 1880 seeds are put forward Round 1: 101 peptides, 16 chains. Longest chain 12 peptides. Score 0.376 Round 2: 122 peptides, 13 chains. Longest chain 19 peptides. Score 0.531 Round 3: 131 peptides, 16 chains. Longest chain 16 peptides. Score 0.511 Round 4: 126 peptides, 13 chains. Longest chain 18 peptides. Score 0.547 Round 5: 132 peptides, 12 chains. Longest chain 24 peptides. Score 0.588 Taking the results from Round 5 Chains 12, Residues 120, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3398 reflections ( 99.62 % complete ) and 3163 restraints for refining 1502 atoms. 2663 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2719 (Rfree = 0.000) for 1502 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 2: After refmac, R = 0.2565 (Rfree = 0.000) for 1481 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.2467 (Rfree = 0.000) for 1473 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.2400 (Rfree = 0.000) for 1474 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.2377 (Rfree = 0.000) for 1471 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 2.98 Search for helices and strands: 0 residues in 0 chains, 1530 seeds are put forward Round 1: 133 peptides, 17 chains. Longest chain 17 peptides. Score 0.500 Round 2: 130 peptides, 13 chains. Longest chain 30 peptides. Score 0.563 Round 3: 139 peptides, 14 chains. Longest chain 21 peptides. Score 0.578 Round 4: 133 peptides, 12 chains. Longest chain 31 peptides. Score 0.592 Round 5: 138 peptides, 13 chains. Longest chain 23 peptides. Score 0.592 Taking the results from Round 5 Chains 14, Residues 125, Estimated correctness of the model 0.0 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 3398 reflections ( 99.62 % complete ) and 2978 restraints for refining 1506 atoms. 2331 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2698 (Rfree = 0.000) for 1506 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 7: After refmac, R = 0.2381 (Rfree = 0.000) for 1486 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 8: After refmac, R = 0.2253 (Rfree = 0.000) for 1472 atoms. Found 6 (7 requested) and removed 9 (3 requested) atoms. Cycle 9: After refmac, R = 0.2223 (Rfree = 0.000) for 1463 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 10: After refmac, R = 0.2576 (Rfree = 0.000) for 1459 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.81 2.96 Search for helices and strands: 0 residues in 0 chains, 1525 seeds are put forward Round 1: 116 peptides, 15 chains. Longest chain 17 peptides. Score 0.467 Round 2: 136 peptides, 16 chains. Longest chain 20 peptides. Score 0.531 Round 3: 135 peptides, 14 chains. Longest chain 21 peptides. Score 0.563 Round 4: 139 peptides, 14 chains. Longest chain 23 peptides. Score 0.578 Round 5: 143 peptides, 13 chains. Longest chain 35 peptides. Score 0.610 Taking the results from Round 5 Chains 15, Residues 130, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3398 reflections ( 99.62 % complete ) and 3068 restraints for refining 1503 atoms. 2485 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2556 (Rfree = 0.000) for 1503 atoms. Found 7 (7 requested) and removed 27 (3 requested) atoms. Cycle 12: After refmac, R = 0.2301 (Rfree = 0.000) for 1465 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 13: After refmac, R = 0.2389 (Rfree = 0.000) for 1456 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 14: After refmac, R = 0.2318 (Rfree = 0.000) for 1447 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.2284 (Rfree = 0.000) for 1440 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 2.93 Search for helices and strands: 0 residues in 0 chains, 1494 seeds are put forward Round 1: 130 peptides, 17 chains. Longest chain 18 peptides. Score 0.487 Round 2: 128 peptides, 12 chains. Longest chain 28 peptides. Score 0.573 Round 3: 133 peptides, 14 chains. Longest chain 22 peptides. Score 0.556 Round 4: 128 peptides, 13 chains. Longest chain 19 peptides. Score 0.555 Round 5: 135 peptides, 12 chains. Longest chain 24 peptides. Score 0.599 Taking the results from Round 5 Chains 13, Residues 123, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3398 reflections ( 99.62 % complete ) and 3018 restraints for refining 1502 atoms. 2436 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2527 (Rfree = 0.000) for 1502 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.2342 (Rfree = 0.000) for 1483 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 18: After refmac, R = 0.2243 (Rfree = 0.000) for 1474 atoms. Found 5 (7 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.2186 (Rfree = 0.000) for 1468 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2149 (Rfree = 0.000) for 1462 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.00 Search for helices and strands: 0 residues in 0 chains, 1508 seeds are put forward Round 1: 120 peptides, 15 chains. Longest chain 19 peptides. Score 0.484 Round 2: 137 peptides, 15 chains. Longest chain 22 peptides. Score 0.553 Round 3: 128 peptides, 14 chains. Longest chain 22 peptides. Score 0.536 Round 4: 128 peptides, 14 chains. Longest chain 22 peptides. Score 0.536 Round 5: 122 peptides, 12 chains. Longest chain 24 peptides. Score 0.550 Taking the results from Round 2 Chains 17, Residues 122, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3398 reflections ( 99.62 % complete ) and 3060 restraints for refining 1503 atoms. 2516 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2589 (Rfree = 0.000) for 1503 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 22: After refmac, R = 0.2349 (Rfree = 0.000) for 1492 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 23: After refmac, R = 0.2237 (Rfree = 0.000) for 1485 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2167 (Rfree = 0.000) for 1482 atoms. Found 1 (7 requested) and removed 9 (3 requested) atoms. Cycle 25: After refmac, R = 0.2152 (Rfree = 0.000) for 1472 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.86 3.00 Search for helices and strands: 0 residues in 0 chains, 1516 seeds are put forward Round 1: 112 peptides, 18 chains. Longest chain 12 peptides. Score 0.386 Round 2: 121 peptides, 15 chains. Longest chain 18 peptides. Score 0.488 Round 3: 108 peptides, 13 chains. Longest chain 18 peptides. Score 0.473 Round 4: 124 peptides, 17 chains. Longest chain 23 peptides. Score 0.462 Round 5: 124 peptides, 14 chains. Longest chain 17 peptides. Score 0.520 Taking the results from Round 5 Chains 15, Residues 110, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3398 reflections ( 99.62 % complete ) and 3286 restraints for refining 1503 atoms. 2802 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2615 (Rfree = 0.000) for 1503 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 27: After refmac, R = 0.2411 (Rfree = 0.000) for 1491 atoms. Found 4 (7 requested) and removed 10 (3 requested) atoms. Cycle 28: After refmac, R = 0.2357 (Rfree = 0.000) for 1476 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 29: After refmac, R = 0.2334 (Rfree = 0.000) for 1468 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.2473 (Rfree = 0.000) for 1466 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 2.98 Search for helices and strands: 0 residues in 0 chains, 1515 seeds are put forward Round 1: 109 peptides, 15 chains. Longest chain 14 peptides. Score 0.436 Round 2: 115 peptides, 13 chains. Longest chain 23 peptides. Score 0.503 Round 3: 125 peptides, 15 chains. Longest chain 16 peptides. Score 0.505 Round 4: 122 peptides, 14 chains. Longest chain 17 peptides. Score 0.512 Round 5: 137 peptides, 18 chains. Longest chain 24 peptides. Score 0.498 Taking the results from Round 4 Chains 15, Residues 108, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3398 reflections ( 99.62 % complete ) and 3324 restraints for refining 1503 atoms. 2869 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2641 (Rfree = 0.000) for 1503 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.2446 (Rfree = 0.000) for 1488 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.2311 (Rfree = 0.000) for 1473 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2397 (Rfree = 0.000) for 1469 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 35: After refmac, R = 0.2194 (Rfree = 0.000) for 1467 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 3.01 Search for helices and strands: 0 residues in 0 chains, 1528 seeds are put forward Round 1: 96 peptides, 16 chains. Longest chain 13 peptides. Score 0.351 Round 2: 103 peptides, 16 chains. Longest chain 9 peptides. Score 0.386 Round 3: 115 peptides, 16 chains. Longest chain 14 peptides. Score 0.442 Round 4: 114 peptides, 14 chains. Longest chain 14 peptides. Score 0.479 Round 5: 124 peptides, 14 chains. Longest chain 20 peptides. Score 0.520 Taking the results from Round 5 Chains 14, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3398 reflections ( 99.62 % complete ) and 3460 restraints for refining 1501 atoms. 3034 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2527 (Rfree = 0.000) for 1501 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.2285 (Rfree = 0.000) for 1498 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.2215 (Rfree = 0.000) for 1492 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.2208 (Rfree = 0.000) for 1488 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.2290 (Rfree = 0.000) for 1485 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.88 3.02 Search for helices and strands: 0 residues in 0 chains, 1539 seeds are put forward Round 1: 99 peptides, 18 chains. Longest chain 11 peptides. Score 0.321 Round 2: 113 peptides, 15 chains. Longest chain 20 peptides. Score 0.454 Round 3: 122 peptides, 18 chains. Longest chain 14 peptides. Score 0.433 Round 4: 120 peptides, 16 chains. Longest chain 14 peptides. Score 0.464 Round 5: 123 peptides, 16 chains. Longest chain 19 peptides. Score 0.477 Taking the results from Round 5 Chains 18, Residues 107, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3398 reflections ( 99.62 % complete ) and 3356 restraints for refining 1503 atoms. 2908 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2526 (Rfree = 0.000) for 1503 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.2464 (Rfree = 0.000) for 1492 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2509 (Rfree = 0.000) for 1491 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 44: After refmac, R = 0.2444 (Rfree = 0.000) for 1478 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 45: After refmac, R = 0.2349 (Rfree = 0.000) for 1469 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 2.98 Search for helices and strands: 0 residues in 0 chains, 1536 seeds are put forward Round 1: 112 peptides, 22 chains. Longest chain 8 peptides. Score 0.299 Round 2: 125 peptides, 17 chains. Longest chain 14 peptides. Score 0.466 Round 3: 119 peptides, 14 chains. Longest chain 17 peptides. Score 0.500 Round 4: 125 peptides, 17 chains. Longest chain 19 peptides. Score 0.466 Round 5: 122 peptides, 17 chains. Longest chain 14 peptides. Score 0.453 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 105, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 2gm6-4_warpNtrace.pdb as input Building loops using Loopy2018 16 chains (105 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3398 reflections ( 99.62 % complete ) and 3258 restraints for refining 1503 atoms. 2781 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2597 (Rfree = 0.000) for 1503 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2439 (Rfree = 0.000) for 1481 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2354 (Rfree = 0.000) for 1475 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2243 (Rfree = 0.000) for 1471 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:55:40 GMT 2018 Job finished. TimeTaking 32.73 Used memory is bytes: 14306600