null Tue 25 Dec 19:27:57 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 1vlo-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-3.2-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/1vlo-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-3.2-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 ============================================================ Tue 25 Dec 19:28:07 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/1vlo-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-3.2-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 264 and 0 Target number of residues in the AU: 264 Target solvent content: 0.5946 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 381 Adjusted target solvent content: 0.41 Input MTZ file: 1vlo-3.2-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: 19 Cell parameters: 46.529 64.578 117.291 90.000 90.000 90.000 Input sequence file: 1vlo-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3048 target number of atoms Had to go as low as 0.60 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: 43.415 3.200 Wilson plot Bfac: 49.92 6096 reflections ( 97.86 % complete ) and 0 restraints for refining 3389 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3287 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2896 (Rfree = 0.000) for 3389 atoms. Found 30 (30 requested) and removed 69 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.95 3.33 Search for helices and strands: 0 residues in 0 chains, 3397 seeds are put forward Round 1: 156 peptides, 32 chains. Longest chain 12 peptides. Score 0.309 Round 2: 193 peptides, 31 chains. Longest chain 26 peptides. Score 0.491 Round 3: 206 peptides, 36 chains. Longest chain 13 peptides. Score 0.458 Round 4: 211 peptides, 34 chains. Longest chain 12 peptides. Score 0.511 Round 5: 224 peptides, 37 chains. Longest chain 13 peptides. Score 0.512 Taking the results from Round 5 Chains 37, Residues 187, Estimated correctness of the model 15.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6096 reflections ( 97.86 % complete ) and 6278 restraints for refining 2781 atoms. 5567 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2425 (Rfree = 0.000) for 2781 atoms. Found 17 (24 requested) and removed 21 (12 requested) atoms. Cycle 2: After refmac, R = 0.2327 (Rfree = 0.000) for 2758 atoms. Found 9 (24 requested) and removed 19 (12 requested) atoms. Cycle 3: After refmac, R = 0.2274 (Rfree = 0.000) for 2739 atoms. Found 17 (24 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.2216 (Rfree = 0.000) for 2735 atoms. Found 11 (24 requested) and removed 16 (12 requested) atoms. Cycle 5: After refmac, R = 0.2143 (Rfree = 0.000) for 2724 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.95 3.33 Search for helices and strands: 0 residues in 0 chains, 2818 seeds are put forward Round 1: 179 peptides, 34 chains. Longest chain 12 peptides. Score 0.378 Round 2: 202 peptides, 32 chains. Longest chain 16 peptides. Score 0.510 Round 3: 214 peptides, 32 chains. Longest chain 17 peptides. Score 0.554 Round 4: 210 peptides, 31 chains. Longest chain 18 peptides. Score 0.556 Round 5: 221 peptides, 28 chains. Longest chain 14 peptides. Score 0.636 Taking the results from Round 5 Chains 28, Residues 193, Estimated correctness of the model 50.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6096 reflections ( 97.86 % complete ) and 6243 restraints for refining 2782 atoms. 5499 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2347 (Rfree = 0.000) for 2782 atoms. Found 18 (24 requested) and removed 24 (12 requested) atoms. Cycle 7: After refmac, R = 0.2159 (Rfree = 0.000) for 2767 atoms. Found 6 (24 requested) and removed 18 (12 requested) atoms. Cycle 8: After refmac, R = 0.2165 (Rfree = 0.000) for 2751 atoms. Found 6 (24 requested) and removed 14 (12 requested) atoms. Cycle 9: After refmac, R = 0.2068 (Rfree = 0.000) for 2739 atoms. Found 10 (24 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.2051 (Rfree = 0.000) for 2733 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.94 3.32 Search for helices and strands: 0 residues in 0 chains, 2810 seeds are put forward Round 1: 190 peptides, 30 chains. Longest chain 15 peptides. Score 0.497 Round 2: 209 peptides, 28 chains. Longest chain 16 peptides. Score 0.598 Round 3: 225 peptides, 31 chains. Longest chain 24 peptides. Score 0.607 Round 4: 217 peptides, 28 chains. Longest chain 26 peptides. Score 0.624 Round 5: 223 peptides, 28 chains. Longest chain 17 peptides. Score 0.643 Taking the results from Round 5 Chains 30, Residues 195, Estimated correctness of the model 52.1 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 6096 reflections ( 97.86 % complete ) and 5741 restraints for refining 2782 atoms. 4819 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2383 (Rfree = 0.000) for 2782 atoms. Found 16 (24 requested) and removed 22 (12 requested) atoms. Cycle 12: After refmac, R = 0.2284 (Rfree = 0.000) for 2767 atoms. Found 10 (24 requested) and removed 17 (12 requested) atoms. Cycle 13: After refmac, R = 0.2265 (Rfree = 0.000) for 2753 atoms. Found 9 (24 requested) and removed 17 (12 requested) atoms. Cycle 14: After refmac, R = 0.2156 (Rfree = 0.000) for 2743 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.2108 (Rfree = 0.000) for 2733 atoms. Found 6 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.94 3.32 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward Round 1: 201 peptides, 32 chains. Longest chain 28 peptides. Score 0.506 Round 2: 209 peptides, 28 chains. Longest chain 28 peptides. Score 0.598 Round 3: 204 peptides, 29 chains. Longest chain 27 peptides. Score 0.566 Round 4: 206 peptides, 28 chains. Longest chain 27 peptides. Score 0.588 Round 5: 208 peptides, 29 chains. Longest chain 21 peptides. Score 0.580 Taking the results from Round 2 Chains 29, Residues 181, Estimated correctness of the model 40.5 % 5 chains (26 residues) have been docked in sequence ------------------------------------------------------ 6096 reflections ( 97.86 % complete ) and 6185 restraints for refining 2782 atoms. 5427 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2181 (Rfree = 0.000) for 2782 atoms. Found 17 (24 requested) and removed 18 (12 requested) atoms. Cycle 17: After refmac, R = 0.2070 (Rfree = 0.000) for 2775 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.2027 (Rfree = 0.000) for 2763 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.1948 (Rfree = 0.000) for 2753 atoms. Found 10 (24 requested) and removed 15 (12 requested) atoms. Cycle 20: After refmac, R = 0.1864 (Rfree = 0.000) for 2747 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.91 3.28 Search for helices and strands: 0 residues in 0 chains, 2817 seeds are put forward Round 1: 172 peptides, 27 chains. Longest chain 20 peptides. Score 0.476 Round 2: 192 peptides, 31 chains. Longest chain 18 peptides. Score 0.487 Round 3: 205 peptides, 30 chains. Longest chain 21 peptides. Score 0.553 Round 4: 201 peptides, 27 chains. Longest chain 26 peptides. Score 0.586 Round 5: 210 peptides, 26 chains. Longest chain 28 peptides. Score 0.630 Taking the results from Round 5 Chains 29, Residues 184, Estimated correctness of the model 48.9 % 6 chains (50 residues) have been docked in sequence ------------------------------------------------------ 6096 reflections ( 97.86 % complete ) and 5681 restraints for refining 2782 atoms. 4796 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2142 (Rfree = 0.000) for 2782 atoms. Found 17 (24 requested) and removed 18 (12 requested) atoms. Cycle 22: After refmac, R = 0.1989 (Rfree = 0.000) for 2775 atoms. Found 7 (24 requested) and removed 14 (12 requested) atoms. Cycle 23: After refmac, R = 0.1921 (Rfree = 0.000) for 2764 atoms. Found 9 (24 requested) and removed 13 (12 requested) atoms. Cycle 24: After refmac, R = 0.1918 (Rfree = 0.000) for 2758 atoms. Found 12 (24 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.1838 (Rfree = 0.000) for 2756 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.96 3.34 Search for helices and strands: 0 residues in 0 chains, 2849 seeds are put forward Round 1: 166 peptides, 31 chains. Longest chain 13 peptides. Score 0.376 Round 2: 181 peptides, 29 chains. Longest chain 21 peptides. Score 0.478 Round 3: 184 peptides, 26 chains. Longest chain 21 peptides. Score 0.541 Round 4: 202 peptides, 29 chains. Longest chain 21 peptides. Score 0.558 Round 5: 198 peptides, 26 chains. Longest chain 21 peptides. Score 0.591 Taking the results from Round 5 Chains 28, Residues 172, Estimated correctness of the model 38.6 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 6096 reflections ( 97.86 % complete ) and 5829 restraints for refining 2782 atoms. 5013 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2093 (Rfree = 0.000) for 2782 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 27: After refmac, R = 0.1930 (Rfree = 0.000) for 2781 atoms. Found 10 (24 requested) and removed 15 (12 requested) atoms. Cycle 28: After refmac, R = 0.1866 (Rfree = 0.000) for 2771 atoms. Found 7 (24 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.1865 (Rfree = 0.000) for 2765 atoms. Found 3 (24 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.1845 (Rfree = 0.000) for 2756 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.95 3.33 Search for helices and strands: 0 residues in 0 chains, 2804 seeds are put forward Round 1: 166 peptides, 29 chains. Longest chain 21 peptides. Score 0.414 Round 2: 182 peptides, 31 chains. Longest chain 21 peptides. Score 0.446 Round 3: 187 peptides, 29 chains. Longest chain 20 peptides. Score 0.502 Round 4: 190 peptides, 27 chains. Longest chain 21 peptides. Score 0.547 Round 5: 180 peptides, 29 chains. Longest chain 19 peptides. Score 0.474 Taking the results from Round 4 Chains 27, Residues 163, Estimated correctness of the model 26.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6096 reflections ( 97.86 % complete ) and 6253 restraints for refining 2781 atoms. 5607 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2087 (Rfree = 0.000) for 2781 atoms. Found 16 (24 requested) and removed 16 (12 requested) atoms. Cycle 32: After refmac, R = 0.1960 (Rfree = 0.000) for 2778 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. Cycle 33: After refmac, R = 0.1983 (Rfree = 0.000) for 2771 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.1959 (Rfree = 0.000) for 2764 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1935 (Rfree = 0.000) for 2759 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.94 3.32 Search for helices and strands: 0 residues in 0 chains, 2813 seeds are put forward Round 1: 155 peptides, 31 chains. Longest chain 12 peptides. Score 0.325 Round 2: 159 peptides, 27 chains. Longest chain 15 peptides. Score 0.421 Round 3: 164 peptides, 25 chains. Longest chain 17 peptides. Score 0.479 Round 4: 182 peptides, 28 chains. Longest chain 17 peptides. Score 0.499 Round 5: 174 peptides, 27 chains. Longest chain 15 peptides. Score 0.485 Taking the results from Round 4 Chains 29, Residues 154, Estimated correctness of the model 11.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 6096 reflections ( 97.86 % complete ) and 5952 restraints for refining 2781 atoms. 5251 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2166 (Rfree = 0.000) for 2781 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 37: After refmac, R = 0.2053 (Rfree = 0.000) for 2784 atoms. Found 13 (25 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.1969 (Rfree = 0.000) for 2780 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.1919 (Rfree = 0.000) for 2774 atoms. Found 9 (24 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.1859 (Rfree = 0.000) for 2770 atoms. Found 10 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.95 3.33 Search for helices and strands: 0 residues in 0 chains, 2826 seeds are put forward Round 1: 137 peptides, 26 chains. Longest chain 11 peptides. Score 0.339 Round 2: 157 peptides, 26 chains. Longest chain 11 peptides. Score 0.431 Round 3: 167 peptides, 28 chains. Longest chain 15 peptides. Score 0.437 Round 4: 150 peptides, 25 chains. Longest chain 15 peptides. Score 0.419 Round 5: 167 peptides, 26 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 5 Chains 27, Residues 141, Estimated correctness of the model 2.7 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6096 reflections ( 97.86 % complete ) and 6016 restraints for refining 2782 atoms. 5375 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2025 (Rfree = 0.000) for 2782 atoms. Found 18 (24 requested) and removed 14 (12 requested) atoms. Cycle 42: After refmac, R = 0.1953 (Rfree = 0.000) for 2780 atoms. Found 12 (25 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.1897 (Rfree = 0.000) for 2776 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 44: After refmac, R = 0.1817 (Rfree = 0.000) for 2769 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.1778 (Rfree = 0.000) for 2759 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.94 3.32 Search for helices and strands: 0 residues in 0 chains, 2804 seeds are put forward Round 1: 150 peptides, 29 chains. Longest chain 11 peptides. Score 0.341 Round 2: 151 peptides, 24 chains. Longest chain 13 peptides. Score 0.443 Round 3: 170 peptides, 27 chains. Longest chain 12 peptides. Score 0.468 Round 4: 154 peptides, 24 chains. Longest chain 14 peptides. Score 0.456 Round 5: 159 peptides, 26 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 143, Estimated correctness of the model 0.7 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vlo-3_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (143 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6096 reflections ( 97.86 % complete ) and 6311 restraints for refining 2782 atoms. 5752 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1929 (Rfree = 0.000) for 2782 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1827 (Rfree = 0.000) for 2767 atoms. Found 0 (24 requested) and removed 5 (12 requested) atoms. Cycle 48: After refmac, R = 0.1785 (Rfree = 0.000) for 2761 atoms. Found 0 (24 requested) and removed 3 (12 requested) atoms. Cycle 49: After refmac, R = 0.1713 (Rfree = 0.000) for 2757 atoms. Found 0 (24 requested) and removed 2 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:19:05 GMT 2018 Job finished. TimeTaking 51.13 Used memory is bytes: 14695568