null Mon 24 Dec 00:12:38 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vpz-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.2-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:12:43 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.2-parrot-mrncs/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 91 and 0 Target number of residues in the AU: 91 Target solvent content: 0.6402 Checking the provided sequence file Detected sequence length: 73 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 146 Adjusted target solvent content: 0.42 Input MTZ file: 1vpz-3.2-parrot-mrncs.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: 20 Cell parameters: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1168 target number of atoms Had to go as low as 0.50 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 24.580 3.200 Wilson plot Bfac: 71.57 2402 reflections ( 98.40 % complete ) and 0 restraints for refining 1297 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3552 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3598 (Rfree = 0.000) for 1297 atoms. Found 8 (11 requested) and removed 20 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.89 Search for helices and strands: 0 residues in 0 chains, 1292 seeds are put forward NCS extension: 0 residues added, 1292 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 7 peptides. Score 0.229 Round 2: 45 peptides, 7 chains. Longest chain 9 peptides. Score 0.404 Round 3: 51 peptides, 10 chains. Longest chain 7 peptides. Score 0.317 Round 4: 62 peptides, 10 chains. Longest chain 11 peptides. Score 0.448 Round 5: 68 peptides, 11 chains. Longest chain 14 peptides. Score 0.466 Taking the results from Round 5 Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 2208 restraints for refining 952 atoms. 1991 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3387 (Rfree = 0.000) for 952 atoms. Found 4 (8 requested) and removed 22 (4 requested) atoms. Cycle 2: After refmac, R = 0.3340 (Rfree = 0.000) for 916 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.3587 (Rfree = 0.000) for 906 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 4: After refmac, R = 0.3167 (Rfree = 0.000) for 888 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 5: After refmac, R = 0.3404 (Rfree = 0.000) for 885 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.77 Search for helices and strands: 0 residues in 0 chains, 933 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 958 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.224 Round 2: 59 peptides, 11 chains. Longest chain 11 peptides. Score 0.364 Round 3: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.373 Round 4: 72 peptides, 13 chains. Longest chain 13 peptides. Score 0.416 Round 5: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.379 Taking the results from Round 4 Chains 13, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1918 restraints for refining 876 atoms. 1695 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3509 (Rfree = 0.000) for 876 atoms. Found 7 (7 requested) and removed 76 (3 requested) atoms. Cycle 7: After refmac, R = 0.3585 (Rfree = 0.000) for 804 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.3795 (Rfree = 0.000) for 792 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.3442 (Rfree = 0.000) for 785 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.3797 (Rfree = 0.000) for 779 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.47 Search for helices and strands: 0 residues in 0 chains, 823 seeds are put forward NCS extension: 0 residues added, 823 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 7 peptides. Score 0.248 Round 2: 54 peptides, 10 chains. Longest chain 11 peptides. Score 0.355 Round 3: 60 peptides, 11 chains. Longest chain 9 peptides. Score 0.376 Round 4: 68 peptides, 12 chains. Longest chain 12 peptides. Score 0.419 Round 5: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.402 Taking the results from Round 4 Chains 12, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1843 restraints for refining 837 atoms. 1631 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3527 (Rfree = 0.000) for 837 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.3374 (Rfree = 0.000) for 827 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.3439 (Rfree = 0.000) for 821 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 14: After refmac, R = 0.3388 (Rfree = 0.000) for 818 atoms. Found 5 (7 requested) and removed 8 (3 requested) atoms. Cycle 15: After refmac, R = 0.3372 (Rfree = 0.000) for 812 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.56 Search for helices and strands: 0 residues in 0 chains, 850 seeds are put forward NCS extension: 0 residues added, 850 seeds are put forward Round 1: 43 peptides, 9 chains. Longest chain 6 peptides. Score 0.267 Round 2: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.314 Round 3: 55 peptides, 9 chains. Longest chain 12 peptides. Score 0.418 Round 4: 53 peptides, 8 chains. Longest chain 15 peptides. Score 0.446 Round 5: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.536 Taking the results from Round 5 Chains 9, Residues 57, Estimated correctness of the model 22.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1648 restraints for refining 825 atoms. 1429 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3533 (Rfree = 0.000) for 825 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 17: After refmac, R = 0.3807 (Rfree = 0.000) for 819 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 18: After refmac, R = 0.3420 (Rfree = 0.000) for 812 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.3355 (Rfree = 0.000) for 811 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.3295 (Rfree = 0.000) for 813 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.76 5.30 Search for helices and strands: 0 residues in 0 chains, 828 seeds are put forward NCS extension: 6 residues added (1 deleted due to clashes), 834 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.289 Round 2: 48 peptides, 8 chains. Longest chain 9 peptides. Score 0.387 Round 3: 51 peptides, 7 chains. Longest chain 10 peptides. Score 0.473 Round 4: 51 peptides, 8 chains. Longest chain 11 peptides. Score 0.423 Round 5: 41 peptides, 7 chains. Longest chain 9 peptides. Score 0.354 Taking the results from Round 3 Chains 7, Residues 44, Estimated correctness of the model 2.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1865 restraints for refining 848 atoms. 1696 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3685 (Rfree = 0.000) for 848 atoms. Found 7 (7 requested) and removed 22 (3 requested) atoms. Cycle 22: After refmac, R = 0.3560 (Rfree = 0.000) for 825 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 23: After refmac, R = 0.3531 (Rfree = 0.000) for 822 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.3665 (Rfree = 0.000) for 819 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 25: After refmac, R = 0.3609 (Rfree = 0.000) for 816 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.36 4.85 Search for helices and strands: 0 residues in 0 chains, 836 seeds are put forward NCS extension: 0 residues added, 836 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 8 peptides. Score 0.242 Round 2: 42 peptides, 6 chains. Longest chain 15 peptides. Score 0.422 Round 3: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.333 Round 4: 43 peptides, 7 chains. Longest chain 13 peptides. Score 0.379 Round 5: 38 peptides, 6 chains. Longest chain 13 peptides. Score 0.373 Taking the results from Round 2 Chains 6, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1704 restraints for refining 798 atoms. 1566 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3589 (Rfree = 0.000) for 798 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.3480 (Rfree = 0.000) for 793 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 28: After refmac, R = 0.3402 (Rfree = 0.000) for 789 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.3788 (Rfree = 0.000) for 786 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.3329 (Rfree = 0.000) for 788 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.53 Search for helices and strands: 0 residues in 0 chains, 816 seeds are put forward NCS extension: 0 residues added, 816 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 6 peptides. Score 0.239 Round 2: 48 peptides, 10 chains. Longest chain 6 peptides. Score 0.278 Round 3: 43 peptides, 9 chains. Longest chain 8 peptides. Score 0.267 Round 4: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.253 Round 5: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.302 Taking the results from Round 5 Chains 11, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1503 restraints for refining 759 atoms. 1342 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3073 (Rfree = 0.000) for 759 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.3270 (Rfree = 0.000) for 756 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 33: After refmac, R = 0.3142 (Rfree = 0.000) for 749 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.3532 (Rfree = 0.000) for 747 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2994 (Rfree = 0.000) for 747 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.64 Search for helices and strands: 0 residues in 0 chains, 773 seeds are put forward NCS extension: 0 residues added, 773 seeds are put forward Round 1: 30 peptides, 7 chains. Longest chain 5 peptides. Score 0.199 Round 2: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.239 Round 3: 44 peptides, 9 chains. Longest chain 9 peptides. Score 0.280 Round 4: 42 peptides, 7 chains. Longest chain 9 peptides. Score 0.367 Round 5: 36 peptides, 7 chains. Longest chain 6 peptides. Score 0.287 Taking the results from Round 4 Chains 7, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1495 restraints for refining 734 atoms. 1362 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3273 (Rfree = 0.000) for 734 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 37: After refmac, R = 0.3533 (Rfree = 0.000) for 728 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.3310 (Rfree = 0.000) for 722 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.3208 (Rfree = 0.000) for 720 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.3340 (Rfree = 0.000) for 721 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.70 Search for helices and strands: 0 residues in 0 chains, 741 seeds are put forward NCS extension: 0 residues added, 741 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 8 peptides. Score 0.270 Round 2: 53 peptides, 11 chains. Longest chain 9 peptides. Score 0.289 Round 3: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.302 Round 4: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.314 Round 5: 56 peptides, 11 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 5 Chains 11, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2402 reflections ( 98.40 % complete ) and 1455 restraints for refining 727 atoms. 1286 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3185 (Rfree = 0.000) for 727 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.2997 (Rfree = 0.000) for 726 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.2974 (Rfree = 0.000) for 724 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.3232 (Rfree = 0.000) for 720 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.3197 (Rfree = 0.000) for 719 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.55 Search for helices and strands: 0 residues in 0 chains, 744 seeds are put forward NCS extension: 0 residues added, 744 seeds are put forward Round 1: 41 peptides, 10 chains. Longest chain 5 peptides. Score 0.181 Round 2: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.210 Round 3: 41 peptides, 8 chains. Longest chain 6 peptides. Score 0.297 Round 4: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.297 Round 5: 51 peptides, 8 chains. Longest chain 9 peptides. Score 0.423 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 43, 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 1vpz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2402 reflections ( 98.40 % complete ) and 1567 restraints for refining 765 atoms. 1403 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3121 (Rfree = 0.000) for 765 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3518 (Rfree = 0.000) for 760 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3200 (Rfree = 0.000) for 755 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3268 (Rfree = 0.000) for 751 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:33:13 GMT 2018 Job finished. TimeTaking 20.58 Used memory is bytes: 2655312