null Sun 23 Dec 22:23:08 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 2od5-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od5-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od5-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.6-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/2od5-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.6-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 22:23:18 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/2od5-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.6-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 106 and 0 Target number of residues in the AU: 106 Target solvent content: 0.6408 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 116 Adjusted target solvent content: 0.61 Input MTZ file: 2od5-3.6-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: 180 Cell parameters: 64.428 64.428 133.292 90.000 90.000 120.000 Input sequence file: 2od5-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 928 target number of atoms Had to go as low as 0.90 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: 55.796 3.600 Wilson plot Bfac: 71.74 2168 reflections ( 99.63 % complete ) and 0 restraints for refining 1022 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3876 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3921 (Rfree = 0.000) for 1022 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 1040 seeds are put forward Round 1: 48 peptides, 7 chains. Longest chain 14 peptides. Score 0.411 Round 2: 56 peptides, 6 chains. Longest chain 18 peptides. Score 0.532 Round 3: 53 peptides, 6 chains. Longest chain 17 peptides. Score 0.505 Round 4: 58 peptides, 6 chains. Longest chain 24 peptides. Score 0.549 Round 5: 64 peptides, 5 chains. Longest chain 35 peptides. Score 0.635 Taking the results from Round 5 Chains 5, Residues 59, Estimated correctness of the model 27.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2168 reflections ( 99.63 % complete ) and 1829 restraints for refining 839 atoms. 1598 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3155 (Rfree = 0.000) for 839 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 2: After refmac, R = 0.3403 (Rfree = 0.000) for 797 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 3: After refmac, R = 0.3505 (Rfree = 0.000) for 776 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 4: After refmac, R = 0.3388 (Rfree = 0.000) for 763 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.3226 (Rfree = 0.000) for 756 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 2.96 Search for helices and strands: 0 residues in 0 chains, 805 seeds are put forward Round 1: 59 peptides, 7 chains. Longest chain 16 peptides. Score 0.517 Round 2: 66 peptides, 6 chains. Longest chain 19 peptides. Score 0.613 Round 3: 65 peptides, 5 chains. Longest chain 26 peptides. Score 0.642 Round 4: 64 peptides, 5 chains. Longest chain 26 peptides. Score 0.635 Round 5: 60 peptides, 5 chains. Longest chain 24 peptides. Score 0.605 Taking the results from Round 3 Chains 5, Residues 60, Estimated correctness of the model 30.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2168 reflections ( 99.63 % complete ) and 1579 restraints for refining 739 atoms. 1344 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3401 (Rfree = 0.000) for 739 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 7: After refmac, R = 0.3332 (Rfree = 0.000) for 728 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 8: After refmac, R = 0.3519 (Rfree = 0.000) for 724 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.3534 (Rfree = 0.000) for 721 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.3409 (Rfree = 0.000) for 715 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 2.95 Search for helices and strands: 0 residues in 0 chains, 753 seeds are put forward Round 1: 60 peptides, 8 chains. Longest chain 14 peptides. Score 0.484 Round 2: 66 peptides, 8 chains. Longest chain 14 peptides. Score 0.537 Round 3: 62 peptides, 7 chains. Longest chain 19 peptides. Score 0.543 Round 4: 65 peptides, 6 chains. Longest chain 19 peptides. Score 0.606 Round 5: 67 peptides, 7 chains. Longest chain 17 peptides. Score 0.584 Taking the results from Round 4 Chains 6, Residues 59, Estimated correctness of the model 17.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2168 reflections ( 99.63 % complete ) and 1745 restraints for refining 785 atoms. 1515 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3393 (Rfree = 0.000) for 785 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 12: After refmac, R = 0.3508 (Rfree = 0.000) for 776 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 13: After refmac, R = 0.3167 (Rfree = 0.000) for 774 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.3200 (Rfree = 0.000) for 770 atoms. Found 3 (4 requested) and removed 7 (2 requested) atoms. Cycle 15: After refmac, R = 0.3643 (Rfree = 0.000) for 765 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 2.94 Search for helices and strands: 0 residues in 0 chains, 798 seeds are put forward Round 1: 62 peptides, 8 chains. Longest chain 15 peptides. Score 0.502 Round 2: 56 peptides, 7 chains. Longest chain 16 peptides. Score 0.489 Round 3: 56 peptides, 7 chains. Longest chain 15 peptides. Score 0.489 Round 4: 57 peptides, 7 chains. Longest chain 19 peptides. Score 0.499 Round 5: 61 peptides, 7 chains. Longest chain 13 peptides. Score 0.534 Taking the results from Round 5 Chains 7, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2168 reflections ( 99.63 % complete ) and 1821 restraints for refining 792 atoms. 1612 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3469 (Rfree = 0.000) for 792 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 17: After refmac, R = 0.3745 (Rfree = 0.000) for 779 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 18: After refmac, R = 0.3436 (Rfree = 0.000) for 769 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 19: After refmac, R = 0.3060 (Rfree = 0.000) for 761 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.3034 (Rfree = 0.000) for 762 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 807 seeds are put forward Round 1: 54 peptides, 6 chains. Longest chain 18 peptides. Score 0.514 Round 2: 54 peptides, 7 chains. Longest chain 17 peptides. Score 0.471 Round 3: 55 peptides, 7 chains. Longest chain 12 peptides. Score 0.480 Round 4: 52 peptides, 7 chains. Longest chain 11 peptides. Score 0.451 Round 5: 53 peptides, 7 chains. Longest chain 11 peptides. Score 0.461 Taking the results from Round 1 Chains 6, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2168 reflections ( 99.63 % complete ) and 1741 restraints for refining 773 atoms. 1555 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3580 (Rfree = 0.000) for 773 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 22: After refmac, R = 0.3200 (Rfree = 0.000) for 768 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 23: After refmac, R = 0.3283 (Rfree = 0.000) for 762 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 24: After refmac, R = 0.2979 (Rfree = 0.000) for 753 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 25: After refmac, R = 0.2987 (Rfree = 0.000) for 745 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.02 Search for helices and strands: 0 residues in 0 chains, 791 seeds are put forward Round 1: 52 peptides, 7 chains. Longest chain 12 peptides. Score 0.451 Round 2: 53 peptides, 7 chains. Longest chain 13 peptides. Score 0.461 Round 3: 54 peptides, 8 chains. Longest chain 12 peptides. Score 0.426 Round 4: 52 peptides, 8 chains. Longest chain 13 peptides. Score 0.406 Round 5: 49 peptides, 7 chains. Longest chain 12 peptides. Score 0.421 Taking the results from Round 2 Chains 7, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2168 reflections ( 99.63 % complete ) and 1743 restraints for refining 749 atoms. 1566 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3544 (Rfree = 0.000) for 749 atoms. Found 4 (4 requested) and removed 18 (2 requested) atoms. Cycle 27: After refmac, R = 0.3340 (Rfree = 0.000) for 732 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 28: After refmac, R = 0.3304 (Rfree = 0.000) for 720 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 29: After refmac, R = 0.3065 (Rfree = 0.000) for 716 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 30: After refmac, R = 0.2954 (Rfree = 0.000) for 709 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 2.89 Search for helices and strands: 0 residues in 0 chains, 746 seeds are put forward Round 1: 51 peptides, 7 chains. Longest chain 11 peptides. Score 0.441 Round 2: 58 peptides, 8 chains. Longest chain 11 peptides. Score 0.465 Round 3: 55 peptides, 6 chains. Longest chain 13 peptides. Score 0.523 Round 4: 53 peptides, 6 chains. Longest chain 14 peptides. Score 0.505 Round 5: 58 peptides, 7 chains. Longest chain 14 peptides. Score 0.508 Taking the results from Round 3 Chains 6, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2168 reflections ( 99.63 % complete ) and 1652 restraints for refining 756 atoms. 1462 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3523 (Rfree = 0.000) for 756 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 32: After refmac, R = 0.2904 (Rfree = 0.000) for 752 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 33: After refmac, R = 0.3046 (Rfree = 0.000) for 745 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 34: After refmac, R = 0.2983 (Rfree = 0.000) for 738 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 35: After refmac, R = 0.2794 (Rfree = 0.000) for 728 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 2.85 Search for helices and strands: 0 residues in 0 chains, 763 seeds are put forward Round 1: 56 peptides, 6 chains. Longest chain 18 peptides. Score 0.532 Round 2: 51 peptides, 6 chains. Longest chain 12 peptides. Score 0.486 Round 3: 50 peptides, 6 chains. Longest chain 12 peptides. Score 0.477 Round 4: 56 peptides, 6 chains. Longest chain 17 peptides. Score 0.532 Round 5: 54 peptides, 5 chains. Longest chain 22 peptides. Score 0.556 Taking the results from Round 5 Chains 5, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2168 reflections ( 99.63 % complete ) and 1655 restraints for refining 751 atoms. 1464 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3534 (Rfree = 0.000) for 751 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 37: After refmac, R = 0.3208 (Rfree = 0.000) for 738 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 38: After refmac, R = 0.3220 (Rfree = 0.000) for 731 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 39: After refmac, R = 0.3210 (Rfree = 0.000) for 729 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 40: After refmac, R = 0.3300 (Rfree = 0.000) for 726 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 2.90 Search for helices and strands: 0 residues in 0 chains, 765 seeds are put forward Round 1: 51 peptides, 8 chains. Longest chain 12 peptides. Score 0.395 Round 2: 63 peptides, 7 chains. Longest chain 14 peptides. Score 0.551 Round 3: 67 peptides, 7 chains. Longest chain 18 peptides. Score 0.584 Round 4: 56 peptides, 5 chains. Longest chain 21 peptides. Score 0.573 Round 5: 61 peptides, 4 chains. Longest chain 30 peptides. Score 0.650 Taking the results from Round 5 Chains 4, Residues 57, Estimated correctness of the model 33.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2168 reflections ( 99.63 % complete ) and 1684 restraints for refining 789 atoms. 1460 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3777 (Rfree = 0.000) for 789 atoms. Found 5 (5 requested) and removed 110 (2 requested) atoms. Cycle 42: After refmac, R = 0.3172 (Rfree = 0.000) for 673 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.3277 (Rfree = 0.000) for 669 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 44: After refmac, R = 0.3269 (Rfree = 0.000) for 665 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 45: After refmac, R = 0.2914 (Rfree = 0.000) for 661 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 2.92 Search for helices and strands: 0 residues in 0 chains, 703 seeds are put forward Round 1: 47 peptides, 7 chains. Longest chain 11 peptides. Score 0.400 Round 2: 45 peptides, 5 chains. Longest chain 12 peptides. Score 0.475 Round 3: 50 peptides, 6 chains. Longest chain 13 peptides. Score 0.477 Round 4: 51 peptides, 6 chains. Longest chain 15 peptides. Score 0.486 Round 5: 54 peptides, 5 chains. Longest chain 17 peptides. Score 0.556 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 49, 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 2od5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2168 reflections ( 99.63 % complete ) and 1532 restraints for refining 704 atoms. 1341 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3423 (Rfree = 0.000) for 704 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3149 (Rfree = 0.000) for 700 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2822 (Rfree = 0.000) for 696 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2603 (Rfree = 0.000) for 693 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:00 GMT 2018 Job finished. TimeTaking 23.86 Used memory is bytes: 5885464