Sun 23 Dec 22:22:59 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-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/1vpz-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-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 22:23:07 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-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 85 and 0 Target number of residues in the AU: 85 Target solvent content: 0.6639 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-3.6-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: 20 Cell parameters: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-3.6-parrot-hancs.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 3.601 Wilson plot Bfac: 86.64 1697 reflections ( 97.87 % complete ) and 0 restraints for refining 1290 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3613 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2843 (Rfree = 0.000) for 1290 atoms. Found 1 (8 requested) and removed 78 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 4.13 Search for helices and strands: 0 residues in 0 chains, 1216 seeds are put forward NCS extension: 0 residues added, 1216 seeds are put forward Round 1: 24 peptides, 6 chains. Longest chain 4 peptides. Score 0.167 Round 2: 34 peptides, 8 chains. Longest chain 5 peptides. Score 0.197 Round 3: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.196 Round 4: 39 peptides, 9 chains. Longest chain 5 peptides. Score 0.211 Round 5: 41 peptides, 9 chains. Longest chain 6 peptides. Score 0.239 Taking the results from Round 5 Chains 9, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 2671 restraints for refining 1035 atoms. 2552 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3191 (Rfree = 0.000) for 1035 atoms. Found 3 (6 requested) and removed 24 (3 requested) atoms. Cycle 2: After refmac, R = 0.3202 (Rfree = 0.000) for 1006 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.3204 (Rfree = 0.000) for 999 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.3189 (Rfree = 0.000) for 992 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.3183 (Rfree = 0.000) for 987 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.50 Search for helices and strands: 0 residues in 0 chains, 1009 seeds are put forward NCS extension: 0 residues added, 1009 seeds are put forward Round 1: 27 peptides, 6 chains. Longest chain 5 peptides. Score 0.217 Round 2: 32 peptides, 7 chains. Longest chain 6 peptides. Score 0.229 Round 3: 42 peptides, 9 chains. Longest chain 7 peptides. Score 0.253 Round 4: 48 peptides, 9 chains. Longest chain 10 peptides. Score 0.333 Round 5: 45 peptides, 8 chains. Longest chain 10 peptides. Score 0.349 Taking the results from Round 5 Chains 8, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 1964 restraints for refining 834 atoms. 1824 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3148 (Rfree = 0.000) for 834 atoms. Found 3 (5 requested) and removed 14 (2 requested) atoms. Cycle 7: After refmac, R = 0.3032 (Rfree = 0.000) for 820 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2982 (Rfree = 0.000) for 815 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.2942 (Rfree = 0.000) for 812 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2933 (Rfree = 0.000) for 809 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.85 3.17 Search for helices and strands: 0 residues in 0 chains, 821 seeds are put forward NCS extension: 0 residues added, 821 seeds are put forward Round 1: 38 peptides, 8 chains. Longest chain 7 peptides. Score 0.256 Round 2: 44 peptides, 8 chains. Longest chain 8 peptides. Score 0.337 Round 3: 44 peptides, 8 chains. Longest chain 8 peptides. Score 0.337 Round 4: 44 peptides, 7 chains. Longest chain 10 peptides. Score 0.392 Round 5: 46 peptides, 7 chains. Longest chain 10 peptides. Score 0.416 Taking the results from Round 5 Chains 7, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 1863 restraints for refining 816 atoms. 1714 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3241 (Rfree = 0.000) for 816 atoms. Found 3 (5 requested) and removed 43 (2 requested) atoms. Cycle 12: After refmac, R = 0.3120 (Rfree = 0.000) for 774 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 13: After refmac, R = 0.3042 (Rfree = 0.000) for 765 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 14: After refmac, R = 0.3013 (Rfree = 0.000) for 762 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 15: After refmac, R = 0.2985 (Rfree = 0.000) for 758 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.89 Search for helices and strands: 0 residues in 0 chains, 776 seeds are put forward NCS extension: 0 residues added, 776 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.224 Round 2: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.345 Round 3: 52 peptides, 9 chains. Longest chain 11 peptides. Score 0.382 Round 4: 50 peptides, 9 chains. Longest chain 12 peptides. Score 0.358 Round 5: 54 peptides, 8 chains. Longest chain 12 peptides. Score 0.457 Taking the results from Round 5 Chains 8, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 1755 restraints for refining 788 atoms. 1579 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3327 (Rfree = 0.000) for 788 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 17: After refmac, R = 0.3120 (Rfree = 0.000) for 777 atoms. Found 1 (4 requested) and removed 7 (2 requested) atoms. Cycle 18: After refmac, R = 0.3052 (Rfree = 0.000) for 770 atoms. Found 3 (4 requested) and removed 18 (2 requested) atoms. Cycle 19: After refmac, R = 0.3004 (Rfree = 0.000) for 755 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2985 (Rfree = 0.000) for 754 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.86 Search for helices and strands: 0 residues in 0 chains, 778 seeds are put forward NCS extension: 0 residues added, 778 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 7 peptides. Score 0.227 Round 2: 48 peptides, 9 chains. Longest chain 9 peptides. Score 0.333 Round 3: 48 peptides, 9 chains. Longest chain 9 peptides. Score 0.333 Round 4: 42 peptides, 7 chains. Longest chain 9 peptides. Score 0.367 Round 5: 38 peptides, 8 chains. Longest chain 7 peptides. Score 0.256 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 ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 1874 restraints for refining 815 atoms. 1741 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3164 (Rfree = 0.000) for 815 atoms. Found 4 (5 requested) and removed 59 (2 requested) atoms. Cycle 22: After refmac, R = 0.3044 (Rfree = 0.000) for 756 atoms. Found 3 (4 requested) and removed 25 (2 requested) atoms. Cycle 23: After refmac, R = 0.3130 (Rfree = 0.000) for 734 atoms. Found 4 (4 requested) and removed 22 (2 requested) atoms. Cycle 24: After refmac, R = 0.2990 (Rfree = 0.000) for 713 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 25: After refmac, R = 0.2953 (Rfree = 0.000) for 709 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.80 Search for helices and strands: 0 residues in 0 chains, 729 seeds are put forward NCS extension: 0 residues added, 729 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 7 peptides. Score 0.209 Round 2: 52 peptides, 12 chains. Longest chain 5 peptides. Score 0.221 Round 3: 52 peptides, 12 chains. Longest chain 5 peptides. Score 0.221 Round 4: 43 peptides, 9 chains. Longest chain 9 peptides. Score 0.267 Round 5: 43 peptides, 8 chains. Longest chain 10 peptides. Score 0.324 Taking the results from Round 5 Chains 8, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 1651 restraints for refining 756 atoms. 1519 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3330 (Rfree = 0.000) for 756 atoms. Found 1 (4 requested) and removed 38 (2 requested) atoms. Cycle 27: After refmac, R = 0.3241 (Rfree = 0.000) for 719 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 28: After refmac, R = 0.3163 (Rfree = 0.000) for 717 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 29: After refmac, R = 0.3176 (Rfree = 0.000) for 712 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.3179 (Rfree = 0.000) for 710 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.80 3.12 Search for helices and strands: 0 residues in 0 chains, 720 seeds are put forward NCS extension: 0 residues added, 720 seeds are put forward Round 1: 45 peptides, 9 chains. Longest chain 8 peptides. Score 0.294 Round 2: 44 peptides, 8 chains. Longest chain 6 peptides. Score 0.337 Round 3: 46 peptides, 8 chains. Longest chain 8 peptides. Score 0.362 Round 4: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.280 Round 5: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.297 Taking the results from Round 3 Chains 8, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 1751 restraints for refining 775 atoms. 1607 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3264 (Rfree = 0.000) for 775 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 32: After refmac, R = 0.3126 (Rfree = 0.000) for 770 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.3080 (Rfree = 0.000) for 768 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.3061 (Rfree = 0.000) for 765 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.3033 (Rfree = 0.000) for 765 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.30 2.56 Search for helices and strands: 0 residues in 0 chains, 782 seeds are put forward NCS extension: 0 residues added, 782 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.224 Round 2: 50 peptides, 9 chains. Longest chain 12 peptides. Score 0.358 Round 3: 49 peptides, 10 chains. Longest chain 6 peptides. Score 0.291 Round 4: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.310 Round 5: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.273 Taking the results from Round 2 Chains 9, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 1820 restraints for refining 802 atoms. 1665 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3226 (Rfree = 0.000) for 802 atoms. Found 2 (5 requested) and removed 10 (2 requested) atoms. Cycle 37: After refmac, R = 0.3099 (Rfree = 0.000) for 794 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.3032 (Rfree = 0.000) for 794 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.3030 (Rfree = 0.000) for 792 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.3004 (Rfree = 0.000) for 793 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.72 Search for helices and strands: 0 residues in 0 chains, 819 seeds are put forward NCS extension: 0 residues added, 819 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.280 Round 2: 44 peptides, 9 chains. Longest chain 8 peptides. Score 0.280 Round 3: 45 peptides, 9 chains. Longest chain 7 peptides. Score 0.294 Round 4: 37 peptides, 6 chains. Longest chain 9 peptides. Score 0.360 Round 5: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.337 Taking the results from Round 4 Chains 6, Residues 31, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1697 reflections ( 97.87 % complete ) and 1947 restraints for refining 837 atoms. 1829 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3259 (Rfree = 0.000) for 837 atoms. Found 2 (5 requested) and removed 32 (2 requested) atoms. Cycle 42: After refmac, R = 0.3130 (Rfree = 0.000) for 807 atoms. Found 2 (5 requested) and removed 11 (2 requested) atoms. Cycle 43: After refmac, R = 0.3120 (Rfree = 0.000) for 798 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. Cycle 44: After refmac, R = 0.2999 (Rfree = 0.000) for 793 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 45: After refmac, R = 0.2952 (Rfree = 0.000) for 788 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.87 Search for helices and strands: 0 residues in 0 chains, 805 seeds are put forward NCS extension: 0 residues added, 805 seeds are put forward Round 1: 27 peptides, 6 chains. Longest chain 7 peptides. Score 0.217 Round 2: 39 peptides, 8 chains. Longest chain 8 peptides. Score 0.270 Round 3: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.256 Round 4: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.196 Round 5: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 37, 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. 1697 reflections ( 97.87 % complete ) and 1880 restraints for refining 837 atoms. 1741 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3162 (Rfree = 0.000) for 837 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3038 (Rfree = 0.000) for 833 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2977 (Rfree = 0.000) for 828 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2931 (Rfree = 0.000) for 826 atoms. TimeTaking 21.48