Sun 23 Dec 22:23:10 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 1vpz-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-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/1vpz-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-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 22:23:20 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/1vpz-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-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 83 and 0 Target number of residues in the AU: 83 Target solvent content: 0.6718 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-3.8-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: 20 Cell parameters: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1168 target number of atoms Had to go as low as 0.55 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 3.801 Wilson plot Bfac: 92.10 1438 reflections ( 97.49 % complete ) and 0 restraints for refining 1290 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3684 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3492 (Rfree = 0.000) for 1290 atoms. Found 1 (7 requested) and removed 84 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 4.02 Search for helices and strands: 0 residues in 0 chains, 1223 seeds are put forward NCS extension: 0 residues added, 1223 seeds are put forward Round 1: 9 peptides, 2 chains. Longest chain 5 peptides. Score 0.196 Round 2: 23 peptides, 5 chains. Longest chain 6 peptides. Score 0.220 Round 3: 29 peptides, 6 chains. Longest chain 6 peptides. Score 0.248 Round 4: 36 peptides, 7 chains. Longest chain 7 peptides. Score 0.287 Round 5: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.297 Taking the results from Round 5 Chains 8, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1438 reflections ( 97.49 % complete ) and 2407 restraints for refining 965 atoms. 2283 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3557 (Rfree = 0.000) for 965 atoms. Found 2 (5 requested) and removed 39 (2 requested) atoms. Cycle 2: After refmac, R = 0.3351 (Rfree = 0.000) for 917 atoms. Found 0 (5 requested) and removed 23 (2 requested) atoms. Cycle 3: After refmac, R = 0.3270 (Rfree = 0.000) for 892 atoms. Found 1 (4 requested) and removed 14 (2 requested) atoms. Cycle 4: After refmac, R = 0.3556 (Rfree = 0.000) for 874 atoms. Found 2 (4 requested) and removed 19 (2 requested) atoms. Cycle 5: After refmac, R = 0.3540 (Rfree = 0.000) for 853 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.83 Search for helices and strands: 0 residues in 0 chains, 875 seeds are put forward NCS extension: 0 residues added, 875 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.227 Round 2: 43 peptides, 7 chains. Longest chain 11 peptides. Score 0.379 Round 3: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.382 Round 4: 49 peptides, 9 chains. Longest chain 10 peptides. Score 0.345 Round 5: 53 peptides, 9 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 5 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1438 reflections ( 97.49 % complete ) and 1754 restraints for refining 781 atoms. 1587 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3583 (Rfree = 0.000) for 781 atoms. Found 2 (4 requested) and removed 66 (2 requested) atoms. Cycle 7: After refmac, R = 0.3337 (Rfree = 0.000) for 716 atoms. Found 3 (3 requested) and removed 21 (1 requested) atoms. Cycle 8: After refmac, R = 0.3397 (Rfree = 0.000) for 698 atoms. Found 3 (3 requested) and removed 9 (1 requested) atoms. Cycle 9: After refmac, R = 0.3226 (Rfree = 0.000) for 691 atoms. Found 1 (3 requested) and removed 11 (1 requested) atoms. Cycle 10: After refmac, R = 0.3429 (Rfree = 0.000) for 680 atoms. Found 2 (3 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 4.01 Search for helices and strands: 0 residues in 0 chains, 691 seeds are put forward NCS extension: 0 residues added, 691 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.225 Round 2: 40 peptides, 8 chains. Longest chain 8 peptides. Score 0.284 Round 3: 43 peptides, 8 chains. Longest chain 11 peptides. Score 0.324 Round 4: 45 peptides, 9 chains. Longest chain 8 peptides. Score 0.294 Round 5: 40 peptides, 8 chains. Longest chain 6 peptides. Score 0.284 Taking the results from Round 3 Chains 8, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1438 reflections ( 97.49 % complete ) and 1885 restraints for refining 792 atoms. 1753 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3394 (Rfree = 0.000) for 792 atoms. Found 4 (4 requested) and removed 40 (2 requested) atoms. Cycle 12: After refmac, R = 0.3263 (Rfree = 0.000) for 756 atoms. Found 3 (4 requested) and removed 10 (2 requested) atoms. Cycle 13: After refmac, R = 0.3371 (Rfree = 0.000) for 748 atoms. Found 3 (4 requested) and removed 7 (2 requested) atoms. Cycle 14: After refmac, R = 0.3150 (Rfree = 0.000) for 740 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.3006 (Rfree = 0.000) for 736 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.44 Search for helices and strands: 0 residues in 0 chains, 757 seeds are put forward NCS extension: 0 residues added, 757 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.239 Round 2: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.253 Round 3: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.289 Round 4: 51 peptides, 9 chains. Longest chain 15 peptides. Score 0.370 Round 5: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.304 Taking the results from Round 4 Chains 9, Residues 42, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1438 reflections ( 97.49 % complete ) and 1814 restraints for refining 804 atoms. 1655 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3374 (Rfree = 0.000) for 804 atoms. Found 3 (4 requested) and removed 63 (2 requested) atoms. Cycle 17: After refmac, R = 0.3301 (Rfree = 0.000) for 743 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 18: After refmac, R = 0.3324 (Rfree = 0.000) for 737 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. Cycle 19: After refmac, R = 0.3269 (Rfree = 0.000) for 732 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.3255 (Rfree = 0.000) for 731 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.89 Search for helices and strands: 0 residues in 0 chains, 733 seeds are put forward NCS extension: 0 residues added, 733 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.238 Round 2: 28 peptides, 6 chains. Longest chain 6 peptides. Score 0.232 Round 3: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.259 Round 4: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.265 Round 5: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.315 Taking the results from Round 5 Chains 7, Residues 31, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1438 reflections ( 97.49 % complete ) and 2020 restraints for refining 845 atoms. 1903 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3668 (Rfree = 0.000) for 845 atoms. Found 4 (4 requested) and removed 18 (2 requested) atoms. Cycle 22: After refmac, R = 0.3300 (Rfree = 0.000) for 829 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.3376 (Rfree = 0.000) for 825 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 24: After refmac, R = 0.3247 (Rfree = 0.000) for 821 atoms. Found 1 (4 requested) and removed 7 (2 requested) atoms. Cycle 25: After refmac, R = 0.3212 (Rfree = 0.000) for 814 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. WARNING: The data used for computing density maps have negative Wilson B factor WARNING: Is the model/space group correct? ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.64 1.83 Search for helices and strands: 0 residues in 0 chains, 832 seeds are put forward NCS extension: 0 residues added, 832 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 7 peptides. Score 0.253 Round 2: 52 peptides, 10 chains. Longest chain 7 peptides. Score 0.330 Round 3: 47 peptides, 10 chains. Longest chain 6 peptides. Score 0.265 Round 4: 44 peptides, 8 chains. Longest chain 8 peptides. Score 0.337 Round 5: 47 peptides, 8 chains. Longest chain 9 peptides. Score 0.374 Taking the results from Round 5 Chains 8, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1438 reflections ( 97.49 % complete ) and 2025 restraints for refining 871 atoms. 1877 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3705 (Rfree = 0.000) for 871 atoms. Found 4 (4 requested) and removed 22 (2 requested) atoms. Cycle 27: After refmac, R = 0.3644 (Rfree = 0.000) for 853 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 28: After refmac, R = 0.3604 (Rfree = 0.000) for 855 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.3517 (Rfree = 0.000) for 855 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 30: After refmac, R = 0.3480 (Rfree = 0.000) for 851 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.76 3.07 Search for helices and strands: 0 residues in 0 chains, 858 seeds are put forward NCS extension: 0 residues added, 858 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 5 peptides. Score 0.212 Round 2: 41 peptides, 9 chains. Longest chain 6 peptides. Score 0.239 Round 3: 38 peptides, 8 chains. Longest chain 7 peptides. Score 0.256 Round 4: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.280 Round 5: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.333 Taking the results from Round 5 Chains 9, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1438 reflections ( 97.49 % complete ) and 2091 restraints for refining 889 atoms. 1944 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3773 (Rfree = 0.000) for 889 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 32: After refmac, R = 0.3582 (Rfree = 0.000) for 885 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.3491 (Rfree = 0.000) for 884 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.3439 (Rfree = 0.000) for 882 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.3393 (Rfree = 0.000) for 880 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.01 3.35 Search for helices and strands: 0 residues in 0 chains, 891 seeds are put forward NCS extension: 0 residues added, 891 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 7 peptides. Score 0.260 Round 2: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.347 Round 3: 63 peptides, 11 chains. Longest chain 11 peptides. Score 0.411 Round 4: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.339 Round 5: 55 peptides, 10 chains. Longest chain 8 peptides. Score 0.367 Taking the results from Round 3 Chains 11, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 1438 reflections ( 97.49 % complete ) and 2103 restraints for refining 923 atoms. 1906 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3939 (Rfree = 0.000) for 923 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 37: After refmac, R = 0.3798 (Rfree = 0.000) for 919 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 38: After refmac, R = 0.3637 (Rfree = 0.000) for 917 atoms. Found 3 (5 requested) and removed 32 (2 requested) atoms. Cycle 39: After refmac, R = 0.3677 (Rfree = 0.000) for 888 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 40: After refmac, R = 0.3669 (Rfree = 0.000) for 887 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.93 Search for helices and strands: 0 residues in 0 chains, 901 seeds are put forward NCS extension: 0 residues added, 901 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 6 peptides. Score 0.212 Round 2: 38 peptides, 8 chains. Longest chain 7 peptides. Score 0.256 Round 3: 43 peptides, 7 chains. Longest chain 9 peptides. Score 0.379 Round 4: 37 peptides, 7 chains. Longest chain 8 peptides. Score 0.301 Round 5: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.315 Taking the results from Round 3 Chains 7, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1438 reflections ( 97.49 % complete ) and 2115 restraints for refining 909 atoms. 1978 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3811 (Rfree = 0.000) for 909 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 42: After refmac, R = 0.3650 (Rfree = 0.000) for 904 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 43: After refmac, R = 0.3609 (Rfree = 0.000) for 903 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.3578 (Rfree = 0.000) for 902 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.3583 (Rfree = 0.000) for 900 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.82 3.14 Search for helices and strands: 0 residues in 0 chains, 927 seeds are put forward NCS extension: 0 residues added, 927 seeds are put forward Round 1: 25 peptides, 5 chains. Longest chain 7 peptides. Score 0.252 Round 2: 24 peptides, 5 chains. Longest chain 6 peptides. Score 0.236 Round 3: 27 peptides, 6 chains. Longest chain 6 peptides. Score 0.217 Round 4: 26 peptides, 5 chains. Longest chain 6 peptides. Score 0.268 Round 5: 23 peptides, 5 chains. Longest chain 5 peptides. Score 0.220 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 21, 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. 1438 reflections ( 97.49 % complete ) and 2296 restraints for refining 923 atoms. 2217 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3657 (Rfree = 0.000) for 923 atoms. Found 0 (5 requested) and removed 1 (2 requested) atoms. Cycle 47: After refmac, R = 0.3584 (Rfree = 0.000) for 922 atoms. Found 0 (5 requested) and removed 0 (2 requested) atoms. Cycle 48: After refmac, R = 0.3513 (Rfree = 0.000) for 922 atoms. Found 0 (5 requested) and removed 0 (2 requested) atoms. Cycle 49: After refmac, R = 0.3454 (Rfree = 0.000) for 922 atoms. Found 0 (5 requested) and removed 1 (2 requested) atoms. Writing output files ... TimeTaking 21.48