Sun 23 Dec 22:22:43 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 2od5-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od5-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od5-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.8-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/2od5-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.8-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 22:22:52 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/2od5-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.8-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 103 and 0 Target number of residues in the AU: 103 Target solvent content: 0.6510 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: 2od5-3.8-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: 180 Cell parameters: 64.428 64.428 133.292 90.000 90.000 120.000 Input sequence file: 2od5-3.8-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 3.800 Wilson plot Bfac: 78.72 1858 reflections ( 99.57 % complete ) and 0 restraints for refining 1028 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3844 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4067 (Rfree = 0.000) for 1028 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.15 Search for helices and strands: 0 residues in 0 chains, 1038 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 10 peptides. Score 0.275 Round 2: 55 peptides, 8 chains. Longest chain 15 peptides. Score 0.436 Round 3: 64 peptides, 9 chains. Longest chain 15 peptides. Score 0.479 Round 4: 64 peptides, 7 chains. Longest chain 20 peptides. Score 0.560 Round 5: 56 peptides, 5 chains. Longest chain 20 peptides. Score 0.573 Taking the results from Round 5 Chains 5, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.57 % complete ) and 1929 restraints for refining 823 atoms. 1730 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.4145 (Rfree = 0.000) for 823 atoms. Found 4 (4 requested) and removed 13 (2 requested) atoms. Cycle 2: After refmac, R = 0.3637 (Rfree = 0.000) for 796 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 3: After refmac, R = 0.3677 (Rfree = 0.000) for 775 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.3629 (Rfree = 0.000) for 762 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 5: After refmac, R = 0.3531 (Rfree = 0.000) for 749 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.04 Search for helices and strands: 0 residues in 0 chains, 775 seeds are put forward Round 1: 60 peptides, 8 chains. Longest chain 17 peptides. Score 0.484 Round 2: 66 peptides, 5 chains. Longest chain 26 peptides. Score 0.649 Round 3: 61 peptides, 6 chains. Longest chain 26 peptides. Score 0.574 Round 4: 56 peptides, 6 chains. Longest chain 23 peptides. Score 0.532 Round 5: 64 peptides, 6 chains. Longest chain 36 peptides. Score 0.598 Taking the results from Round 2 Chains 7, Residues 61, Estimated correctness of the model 20.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.57 % complete ) and 1578 restraints for refining 778 atoms. 1286 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3530 (Rfree = 0.000) for 778 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 7: After refmac, R = 0.3562 (Rfree = 0.000) for 765 atoms. Found 4 (4 requested) and removed 16 (2 requested) atoms. Cycle 8: After refmac, R = 0.3357 (Rfree = 0.000) for 735 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 9: After refmac, R = 0.3523 (Rfree = 0.000) for 725 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 10: After refmac, R = 0.3275 (Rfree = 0.000) for 712 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.07 Search for helices and strands: 0 residues in 0 chains, 736 seeds are put forward Round 1: 63 peptides, 7 chains. Longest chain 19 peptides. Score 0.551 Round 2: 62 peptides, 5 chains. Longest chain 30 peptides. Score 0.620 Round 3: 58 peptides, 5 chains. Longest chain 34 peptides. Score 0.589 Round 4: 53 peptides, 7 chains. Longest chain 19 peptides. Score 0.461 Round 5: 49 peptides, 6 chains. Longest chain 14 peptides. Score 0.467 Taking the results from Round 2 Chains 7, Residues 57, Estimated correctness of the model 8.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.57 % complete ) and 1537 restraints for refining 736 atoms. 1290 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3537 (Rfree = 0.000) for 736 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 12: After refmac, R = 0.3692 (Rfree = 0.000) for 719 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 13: After refmac, R = 0.3658 (Rfree = 0.000) for 710 atoms. Found 3 (3 requested) and removed 12 (1 requested) atoms. Cycle 14: After refmac, R = 0.3374 (Rfree = 0.000) for 698 atoms. Found 2 (3 requested) and removed 6 (1 requested) atoms. Cycle 15: After refmac, R = 0.3380 (Rfree = 0.000) for 691 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.10 Search for helices and strands: 0 residues in 0 chains, 739 seeds are put forward Round 1: 61 peptides, 7 chains. Longest chain 20 peptides. Score 0.534 Round 2: 63 peptides, 5 chains. Longest chain 19 peptides. Score 0.627 Round 3: 66 peptides, 8 chains. Longest chain 16 peptides. Score 0.537 Round 4: 54 peptides, 6 chains. Longest chain 15 peptides. Score 0.514 Round 5: 52 peptides, 9 chains. Longest chain 9 peptides. Score 0.359 Taking the results from Round 2 Chains 5, Residues 58, Estimated correctness of the model 11.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.57 % complete ) and 1565 restraints for refining 725 atoms. 1338 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3970 (Rfree = 0.000) for 725 atoms. Found 3 (3 requested) and removed 19 (1 requested) atoms. Cycle 17: After refmac, R = 0.3402 (Rfree = 0.000) for 708 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 18: After refmac, R = 0.3321 (Rfree = 0.000) for 701 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 19: After refmac, R = 0.3099 (Rfree = 0.000) for 695 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. Cycle 20: After refmac, R = 0.3075 (Rfree = 0.000) for 693 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.09 Search for helices and strands: 0 residues in 0 chains, 728 seeds are put forward Round 1: 54 peptides, 6 chains. Longest chain 13 peptides. Score 0.514 Round 2: 65 peptides, 6 chains. Longest chain 21 peptides. Score 0.606 Round 3: 59 peptides, 7 chains. Longest chain 17 peptides. Score 0.517 Round 4: 62 peptides, 4 chains. Longest chain 22 peptides. Score 0.657 Round 5: 65 peptides, 5 chains. Longest chain 23 peptides. Score 0.642 Taking the results from Round 4 Chains 4, Residues 58, Estimated correctness of the model 23.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.57 % complete ) and 1646 restraints for refining 771 atoms. 1418 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3629 (Rfree = 0.000) for 771 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 22: After refmac, R = 0.3318 (Rfree = 0.000) for 757 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 23: After refmac, R = 0.3290 (Rfree = 0.000) for 750 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.2837 (Rfree = 0.000) for 749 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 25: After refmac, R = 0.3105 (Rfree = 0.000) for 744 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, 777 seeds are put forward Round 1: 60 peptides, 8 chains. Longest chain 12 peptides. Score 0.484 Round 2: 50 peptides, 6 chains. Longest chain 14 peptides. Score 0.477 Round 3: 58 peptides, 6 chains. Longest chain 17 peptides. Score 0.549 Round 4: 58 peptides, 7 chains. Longest chain 16 peptides. Score 0.508 Round 5: 62 peptides, 8 chains. Longest chain 13 peptides. Score 0.502 Taking the results from Round 3 Chains 6, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.57 % complete ) and 1703 restraints for refining 766 atoms. 1501 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3496 (Rfree = 0.000) for 766 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 27: After refmac, R = 0.3347 (Rfree = 0.000) for 753 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 28: After refmac, R = 0.3187 (Rfree = 0.000) for 744 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 29: After refmac, R = 0.3333 (Rfree = 0.000) for 738 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 30: After refmac, R = 0.3061 (Rfree = 0.000) for 730 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 764 seeds are put forward Round 1: 49 peptides, 8 chains. Longest chain 10 peptides. Score 0.374 Round 2: 52 peptides, 7 chains. Longest chain 12 peptides. Score 0.451 Round 3: 57 peptides, 6 chains. Longest chain 21 peptides. Score 0.541 Round 4: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.387 Round 5: 64 peptides, 8 chains. Longest chain 12 peptides. Score 0.520 Taking the results from Round 3 Chains 6, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.57 % complete ) and 1732 restraints for refining 775 atoms. 1534 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3341 (Rfree = 0.000) for 775 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 32: After refmac, R = 0.3373 (Rfree = 0.000) for 760 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 33: After refmac, R = 0.3624 (Rfree = 0.000) for 748 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.3243 (Rfree = 0.000) for 743 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 35: After refmac, R = 0.3439 (Rfree = 0.000) for 736 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.09 Search for helices and strands: 0 residues in 0 chains, 781 seeds are put forward Round 1: 50 peptides, 9 chains. Longest chain 10 peptides. Score 0.337 Round 2: 46 peptides, 7 chains. Longest chain 13 peptides. Score 0.390 Round 3: 59 peptides, 6 chains. Longest chain 16 peptides. Score 0.558 Round 4: 58 peptides, 7 chains. Longest chain 17 peptides. Score 0.508 Round 5: 54 peptides, 7 chains. Longest chain 13 peptides. Score 0.471 Taking the results from Round 3 Chains 6, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.57 % complete ) and 1634 restraints for refining 739 atoms. 1428 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3663 (Rfree = 0.000) for 739 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 37: After refmac, R = 0.3829 (Rfree = 0.000) for 726 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 38: After refmac, R = 0.3281 (Rfree = 0.000) for 717 atoms. Found 3 (3 requested) and removed 9 (1 requested) atoms. Cycle 39: After refmac, R = 0.3468 (Rfree = 0.000) for 706 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 40: After refmac, R = 0.3231 (Rfree = 0.000) for 704 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.10 Search for helices and strands: 0 residues in 0 chains, 744 seeds are put forward Round 1: 50 peptides, 6 chains. Longest chain 14 peptides. Score 0.477 Round 2: 60 peptides, 7 chains. Longest chain 19 peptides. Score 0.525 Round 3: 57 peptides, 7 chains. Longest chain 13 peptides. Score 0.499 Round 4: 57 peptides, 8 chains. Longest chain 19 peptides. Score 0.455 Round 5: 62 peptides, 7 chains. Longest chain 19 peptides. Score 0.543 Taking the results from Round 5 Chains 7, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.57 % complete ) and 1668 restraints for refining 749 atoms. 1455 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3685 (Rfree = 0.000) for 749 atoms. Found 4 (4 requested) and removed 13 (2 requested) atoms. Cycle 42: After refmac, R = 0.3500 (Rfree = 0.000) for 735 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 43: After refmac, R = 0.3230 (Rfree = 0.000) for 719 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 44: After refmac, R = 0.3253 (Rfree = 0.000) for 713 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 45: After refmac, R = 0.3103 (Rfree = 0.000) for 707 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.01 Search for helices and strands: 0 residues in 0 chains, 748 seeds are put forward Round 1: 51 peptides, 8 chains. Longest chain 10 peptides. Score 0.395 Round 2: 52 peptides, 8 chains. Longest chain 10 peptides. Score 0.406 Round 3: 55 peptides, 7 chains. Longest chain 11 peptides. Score 0.480 Round 4: 59 peptides, 8 chains. Longest chain 14 peptides. Score 0.474 Round 5: 57 peptides, 8 chains. Longest chain 13 peptides. Score 0.455 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 48, 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. 1858 reflections ( 99.57 % complete ) and 1561 restraints for refining 720 atoms. 1376 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3443 (Rfree = 0.000) for 720 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.3334 (Rfree = 0.000) for 712 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.3315 (Rfree = 0.000) for 708 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.3358 (Rfree = 0.000) for 705 atoms. TimeTaking 23.75