null Sun 23 Dec 22:22:49 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 1vmg-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.6-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/1vmg-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.6-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 22:22:59 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/1vmg-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.6-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 99 and 0 Target number of residues in the AU: 99 Target solvent content: 0.6486 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 95 Adjusted target solvent content: 0.66 Input MTZ file: 1vmg-3.6-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: 98 Cell parameters: 79.748 79.748 95.906 90.000 90.000 90.000 Input sequence file: 1vmg-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 760 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 Loops will be built when appropriate and at the last cycle Resolution range: 61.319 3.600 Wilson plot Bfac: 76.99 1953 reflections ( 99.59 % complete ) and 0 restraints for refining 837 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3398 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2653 (Rfree = 0.000) for 837 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.78 3.03 Search for helices and strands: 0 residues in 0 chains, 872 seeds are put forward Round 1: 46 peptides, 8 chains. Longest chain 11 peptides. Score 0.347 Round 2: 52 peptides, 5 chains. Longest chain 14 peptides. Score 0.551 Round 3: 49 peptides, 4 chains. Longest chain 15 peptides. Score 0.568 Round 4: 55 peptides, 3 chains. Longest chain 26 peptides. Score 0.658 Round 5: 56 peptides, 4 chains. Longest chain 18 peptides. Score 0.626 Taking the results from Round 4 Chains 3, Residues 52, Estimated correctness of the model 35.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1953 reflections ( 99.59 % complete ) and 1493 restraints for refining 692 atoms. 1288 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2809 (Rfree = 0.000) for 692 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 2: After refmac, R = 0.2617 (Rfree = 0.000) for 678 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 3: After refmac, R = 0.2632 (Rfree = 0.000) for 669 atoms. Found 4 (4 requested) and removed 27 (2 requested) atoms. Cycle 4: After refmac, R = 0.2589 (Rfree = 0.000) for 640 atoms. Found 3 (4 requested) and removed 10 (2 requested) atoms. Cycle 5: After refmac, R = 0.2511 (Rfree = 0.000) for 625 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 2.97 Search for helices and strands: 0 residues in 0 chains, 670 seeds are put forward Round 1: 49 peptides, 8 chains. Longest chain 8 peptides. Score 0.381 Round 2: 52 peptides, 6 chains. Longest chain 13 peptides. Score 0.506 Round 3: 49 peptides, 6 chains. Longest chain 14 peptides. Score 0.477 Round 4: 47 peptides, 5 chains. Longest chain 13 peptides. Score 0.504 Round 5: 52 peptides, 7 chains. Longest chain 10 peptides. Score 0.461 Taking the results from Round 2 Chains 6, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1953 reflections ( 99.59 % complete ) and 1505 restraints for refining 654 atoms. 1327 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2608 (Rfree = 0.000) for 654 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 7: After refmac, R = 0.2428 (Rfree = 0.000) for 651 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.2305 (Rfree = 0.000) for 649 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 9: After refmac, R = 0.2298 (Rfree = 0.000) for 645 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2687 (Rfree = 0.000) for 647 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 2.99 Search for helices and strands: 0 residues in 0 chains, 669 seeds are put forward Round 1: 46 peptides, 7 chains. Longest chain 10 peptides. Score 0.397 Round 2: 52 peptides, 6 chains. Longest chain 20 peptides. Score 0.506 Round 3: 55 peptides, 6 chains. Longest chain 16 peptides. Score 0.534 Round 4: 58 peptides, 6 chains. Longest chain 15 peptides. Score 0.561 Round 5: 62 peptides, 7 chains. Longest chain 16 peptides. Score 0.555 Taking the results from Round 4 Chains 6, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1953 reflections ( 99.59 % complete ) and 1526 restraints for refining 689 atoms. 1324 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2725 (Rfree = 0.000) for 689 atoms. Found 4 (4 requested) and removed 20 (2 requested) atoms. Cycle 12: After refmac, R = 0.3077 (Rfree = 0.000) for 668 atoms. Found 4 (4 requested) and removed 21 (2 requested) atoms. Cycle 13: After refmac, R = 0.2470 (Rfree = 0.000) for 641 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 14: After refmac, R = 0.2390 (Rfree = 0.000) for 632 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.2376 (Rfree = 0.000) for 626 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 2.79 Search for helices and strands: 0 residues in 0 chains, 669 seeds are put forward Round 1: 47 peptides, 8 chains. Longest chain 8 peptides. Score 0.359 Round 2: 54 peptides, 6 chains. Longest chain 16 peptides. Score 0.525 Round 3: 53 peptides, 8 chains. Longest chain 10 peptides. Score 0.424 Round 4: 50 peptides, 7 chains. Longest chain 10 peptides. Score 0.440 Round 5: 54 peptides, 8 chains. Longest chain 10 peptides. Score 0.435 Taking the results from Round 2 Chains 6, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1953 reflections ( 99.59 % complete ) and 1303 restraints for refining 624 atoms. 1117 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2659 (Rfree = 0.000) for 624 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 17: After refmac, R = 0.2528 (Rfree = 0.000) for 611 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 18: After refmac, R = 0.2533 (Rfree = 0.000) for 608 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 19: After refmac, R = 0.3132 (Rfree = 0.000) for 604 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 20: After refmac, R = 0.2731 (Rfree = 0.000) for 596 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.02 Search for helices and strands: 0 residues in 0 chains, 645 seeds are put forward Round 1: 48 peptides, 8 chains. Longest chain 10 peptides. Score 0.370 Round 2: 55 peptides, 8 chains. Longest chain 14 peptides. Score 0.445 Round 3: 51 peptides, 5 chains. Longest chain 21 peptides. Score 0.542 Round 4: 51 peptides, 6 chains. Longest chain 24 peptides. Score 0.497 Round 5: 54 peptides, 5 chains. Longest chain 31 peptides. Score 0.568 Taking the results from Round 5 Chains 5, Residues 49, Estimated correctness of the model 1.7 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 1953 reflections ( 99.59 % complete ) and 1075 restraints for refining 680 atoms. 730 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3161 (Rfree = 0.000) for 680 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 22: After refmac, R = 0.2858 (Rfree = 0.000) for 670 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 23: After refmac, R = 0.2765 (Rfree = 0.000) for 670 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 24: After refmac, R = 0.2584 (Rfree = 0.000) for 660 atoms. Found 3 (4 requested) and removed 8 (2 requested) atoms. Cycle 25: After refmac, R = 0.2613 (Rfree = 0.000) for 650 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.06 3.26 Search for helices and strands: 0 residues in 0 chains, 693 seeds are put forward Round 1: 52 peptides, 9 chains. Longest chain 9 peptides. Score 0.366 Round 2: 49 peptides, 7 chains. Longest chain 14 peptides. Score 0.430 Round 3: 52 peptides, 9 chains. Longest chain 8 peptides. Score 0.366 Round 4: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.426 Round 5: 59 peptides, 9 chains. Longest chain 12 peptides. Score 0.440 Taking the results from Round 5 Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1953 reflections ( 99.59 % complete ) and 1522 restraints for refining 688 atoms. 1331 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3353 (Rfree = 0.000) for 688 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 27: After refmac, R = 0.2886 (Rfree = 0.000) for 684 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.2680 (Rfree = 0.000) for 677 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.2602 (Rfree = 0.000) for 669 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2475 (Rfree = 0.000) for 669 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.00 Search for helices and strands: 0 residues in 0 chains, 702 seeds are put forward Round 1: 41 peptides, 7 chains. Longest chain 12 peptides. Score 0.340 Round 2: 43 peptides, 5 chains. Longest chain 13 peptides. Score 0.465 Round 3: 43 peptides, 6 chains. Longest chain 14 peptides. Score 0.415 Round 4: 44 peptides, 5 chains. Longest chain 14 peptides. Score 0.475 Round 5: 41 peptides, 6 chains. Longest chain 13 peptides. Score 0.392 Taking the results from Round 4 Chains 5, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1953 reflections ( 99.59 % complete ) and 1555 restraints for refining 679 atoms. 1404 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2894 (Rfree = 0.000) for 679 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 32: After refmac, R = 0.2599 (Rfree = 0.000) for 678 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.2474 (Rfree = 0.000) for 679 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.2379 (Rfree = 0.000) for 678 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2367 (Rfree = 0.000) for 678 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 2.97 Search for helices and strands: 0 residues in 0 chains, 701 seeds are put forward Round 1: 46 peptides, 8 chains. Longest chain 9 peptides. Score 0.347 Round 2: 54 peptides, 8 chains. Longest chain 9 peptides. Score 0.435 Round 3: 54 peptides, 8 chains. Longest chain 9 peptides. Score 0.435 Round 4: 47 peptides, 7 chains. Longest chain 10 peptides. Score 0.408 Round 5: 40 peptides, 6 chains. Longest chain 10 peptides. Score 0.381 Taking the results from Round 3 Chains 8, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1953 reflections ( 99.59 % complete ) and 1437 restraints for refining 664 atoms. 1261 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2602 (Rfree = 0.000) for 664 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 37: After refmac, R = 0.2638 (Rfree = 0.000) for 659 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 38: After refmac, R = 0.2515 (Rfree = 0.000) for 656 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.2536 (Rfree = 0.000) for 649 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2428 (Rfree = 0.000) for 648 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.02 Search for helices and strands: 0 residues in 0 chains, 679 seeds are put forward Round 1: 34 peptides, 6 chains. Longest chain 7 peptides. Score 0.309 Round 2: 45 peptides, 7 chains. Longest chain 11 peptides. Score 0.386 Round 3: 47 peptides, 6 chains. Longest chain 13 peptides. Score 0.457 Round 4: 45 peptides, 5 chains. Longest chain 14 peptides. Score 0.485 Round 5: 49 peptides, 5 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 5 Chains 5, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1953 reflections ( 99.59 % complete ) and 1450 restraints for refining 659 atoms. 1279 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2568 (Rfree = 0.000) for 659 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 42: After refmac, R = 0.2598 (Rfree = 0.000) for 657 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.2514 (Rfree = 0.000) for 653 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2447 (Rfree = 0.000) for 655 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2551 (Rfree = 0.000) for 653 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.08 Search for helices and strands: 0 residues in 0 chains, 696 seeds are put forward Round 1: 42 peptides, 8 chains. Longest chain 9 peptides. Score 0.300 Round 2: 38 peptides, 5 chains. Longest chain 11 peptides. Score 0.411 Round 3: 42 peptides, 6 chains. Longest chain 11 peptides. Score 0.404 Round 4: 45 peptides, 6 chains. Longest chain 17 peptides. Score 0.436 Round 5: 44 peptides, 6 chains. Longest chain 9 peptides. Score 0.425 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 39, 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 1vmg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1953 reflections ( 99.59 % complete ) and 1602 restraints for refining 689 atoms. 1452 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2398 (Rfree = 0.000) for 689 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2912 (Rfree = 0.000) for 687 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2278 (Rfree = 0.000) for 682 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2365 (Rfree = 0.000) for 676 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:24 GMT 2018 Job finished. TimeTaking 22.57 Used memory is bytes: 13342160