Sun 23 Dec 22:23:02 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-3.4-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 22:23:11 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-3.4-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 257 and 0 Target number of residues in the AU: 257 Target solvent content: 0.6053 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-3.4-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-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3048 target number of atoms Had to go as low as 0.65 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 3.400 Wilson plot Bfac: 54.55 5096 reflections ( 97.70 % complete ) and 0 restraints for refining 3396 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3323 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2738 (Rfree = 0.000) for 3396 atoms. Found 25 (25 requested) and removed 58 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 3429 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 9 peptides. Score 0.321 Round 2: 168 peptides, 31 chains. Longest chain 11 peptides. Score 0.385 Round 3: 186 peptides, 29 chains. Longest chain 12 peptides. Score 0.498 Round 4: 182 peptides, 28 chains. Longest chain 20 peptides. Score 0.499 Round 5: 200 peptides, 28 chains. Longest chain 20 peptides. Score 0.567 Taking the results from Round 5 Chains 28, Residues 172, Estimated correctness of the model 17.5 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 5096 reflections ( 97.70 % complete ) and 5977 restraints for refining 2772 atoms. 5173 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2216 (Rfree = 0.000) for 2772 atoms. Found 18 (20 requested) and removed 16 (10 requested) atoms. Cycle 2: After refmac, R = 0.2026 (Rfree = 0.000) for 2752 atoms. Found 9 (20 requested) and removed 16 (10 requested) atoms. Cycle 3: After refmac, R = 0.1986 (Rfree = 0.000) for 2736 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 4: After refmac, R = 0.1945 (Rfree = 0.000) for 2729 atoms. Found 3 (20 requested) and removed 12 (10 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1915 (Rfree = 0.000) for 2719 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 2797 seeds are put forward Round 1: 172 peptides, 30 chains. Longest chain 17 peptides. Score 0.422 Round 2: 190 peptides, 26 chains. Longest chain 19 peptides. Score 0.563 Round 3: 188 peptides, 27 chains. Longest chain 20 peptides. Score 0.539 Round 4: 196 peptides, 26 chains. Longest chain 20 peptides. Score 0.584 Round 5: 198 peptides, 29 chains. Longest chain 15 peptides. Score 0.544 Taking the results from Round 4 Chains 27, Residues 170, Estimated correctness of the model 23.4 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 5096 reflections ( 97.70 % complete ) and 5951 restraints for refining 2772 atoms. 5166 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2186 (Rfree = 0.000) for 2772 atoms. Found 16 (20 requested) and removed 22 (10 requested) atoms. Cycle 7: After refmac, R = 0.2041 (Rfree = 0.000) for 2748 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. Cycle 8: After refmac, R = 0.1949 (Rfree = 0.000) for 2724 atoms. Found 5 (20 requested) and removed 15 (10 requested) atoms. Cycle 9: After refmac, R = 0.1837 (Rfree = 0.000) for 2701 atoms. Found 4 (20 requested) and removed 14 (10 requested) atoms. Cycle 10: After refmac, R = 0.1779 (Rfree = 0.000) for 2686 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 2759 seeds are put forward Round 1: 175 peptides, 30 chains. Longest chain 11 peptides. Score 0.435 Round 2: 185 peptides, 25 chains. Longest chain 17 peptides. Score 0.561 Round 3: 180 peptides, 28 chains. Longest chain 15 peptides. Score 0.491 Round 4: 186 peptides, 25 chains. Longest chain 25 peptides. Score 0.564 Round 5: 178 peptides, 27 chains. Longest chain 19 peptides. Score 0.501 Taking the results from Round 4 Chains 27, Residues 161, Estimated correctness of the model 16.5 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5096 reflections ( 97.70 % complete ) and 6121 restraints for refining 2767 atoms. 5448 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1955 (Rfree = 0.000) for 2767 atoms. Found 10 (20 requested) and removed 19 (10 requested) atoms. Cycle 12: After refmac, R = 0.1755 (Rfree = 0.000) for 2751 atoms. Found 6 (20 requested) and removed 14 (10 requested) atoms. Cycle 13: After refmac, R = 0.1659 (Rfree = 0.000) for 2736 atoms. Found 1 (20 requested) and removed 11 (10 requested) atoms. Cycle 14: After refmac, R = 0.1603 (Rfree = 0.000) for 2725 atoms. Found 1 (20 requested) and removed 11 (10 requested) atoms. Cycle 15: After refmac, R = 0.1545 (Rfree = 0.000) for 2714 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 2792 seeds are put forward Round 1: 164 peptides, 28 chains. Longest chain 15 peptides. Score 0.424 Round 2: 208 peptides, 31 chains. Longest chain 19 peptides. Score 0.548 Round 3: 210 peptides, 31 chains. Longest chain 20 peptides. Score 0.556 Round 4: 210 peptides, 29 chains. Longest chain 18 peptides. Score 0.586 Round 5: 221 peptides, 31 chains. Longest chain 18 peptides. Score 0.594 Taking the results from Round 5 Chains 32, Residues 190, Estimated correctness of the model 26.7 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5096 reflections ( 97.70 % complete ) and 6011 restraints for refining 2772 atoms. 5212 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1969 (Rfree = 0.000) for 2772 atoms. Found 9 (20 requested) and removed 17 (10 requested) atoms. Cycle 17: After refmac, R = 0.1793 (Rfree = 0.000) for 2758 atoms. Found 8 (20 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.1661 (Rfree = 0.000) for 2748 atoms. Found 1 (20 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.1626 (Rfree = 0.000) for 2734 atoms. Found 2 (20 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.1593 (Rfree = 0.000) for 2724 atoms. Found 3 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.52 Search for helices and strands: 0 residues in 0 chains, 2822 seeds are put forward Round 1: 161 peptides, 27 chains. Longest chain 13 peptides. Score 0.430 Round 2: 177 peptides, 23 chains. Longest chain 18 peptides. Score 0.564 Round 3: 182 peptides, 26 chains. Longest chain 18 peptides. Score 0.533 Round 4: 175 peptides, 26 chains. Longest chain 15 peptides. Score 0.506 Round 5: 173 peptides, 23 chains. Longest chain 18 peptides. Score 0.550 Taking the results from Round 2 Chains 24, Residues 154, Estimated correctness of the model 16.5 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5096 reflections ( 97.70 % complete ) and 6130 restraints for refining 2772 atoms. 5476 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1772 (Rfree = 0.000) for 2772 atoms. Found 11 (20 requested) and removed 14 (10 requested) atoms. Cycle 22: After refmac, R = 0.1640 (Rfree = 0.000) for 2765 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.1652 (Rfree = 0.000) for 2759 atoms. Found 1 (20 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.1639 (Rfree = 0.000) for 2742 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.1700 (Rfree = 0.000) for 2734 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.54 Search for helices and strands: 0 residues in 0 chains, 2800 seeds are put forward Round 1: 157 peptides, 31 chains. Longest chain 12 peptides. Score 0.334 Round 2: 164 peptides, 28 chains. Longest chain 12 peptides. Score 0.424 Round 3: 169 peptides, 27 chains. Longest chain 15 peptides. Score 0.464 Round 4: 174 peptides, 28 chains. Longest chain 15 peptides. Score 0.467 Round 5: 180 peptides, 29 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 5 Chains 31, Residues 151, Estimated correctness of the model 0.0 % 6 chains (40 residues) have been docked in sequence ------------------------------------------------------ 5096 reflections ( 97.70 % complete ) and 5890 restraints for refining 2771 atoms. 5208 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2025 (Rfree = 0.000) for 2771 atoms. Found 14 (20 requested) and removed 15 (10 requested) atoms. Cycle 27: After refmac, R = 0.1752 (Rfree = 0.000) for 2759 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. Cycle 28: After refmac, R = 0.1675 (Rfree = 0.000) for 2751 atoms. Found 4 (20 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.1661 (Rfree = 0.000) for 2738 atoms. Found 2 (20 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1488 (Rfree = 0.000) for 2725 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.53 Search for helices and strands: 0 residues in 0 chains, 2790 seeds are put forward Round 1: 148 peptides, 28 chains. Longest chain 15 peptides. Score 0.351 Round 2: 166 peptides, 28 chains. Longest chain 15 peptides. Score 0.433 Round 3: 167 peptides, 26 chains. Longest chain 15 peptides. Score 0.474 Round 4: 162 peptides, 24 chains. Longest chain 15 peptides. Score 0.489 Round 5: 164 peptides, 21 chains. Longest chain 23 peptides. Score 0.550 Taking the results from Round 5 Chains 23, Residues 143, Estimated correctness of the model 11.5 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 5096 reflections ( 97.70 % complete ) and 6120 restraints for refining 2772 atoms. 5475 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1845 (Rfree = 0.000) for 2772 atoms. Found 10 (20 requested) and removed 16 (10 requested) atoms. Cycle 32: After refmac, R = 0.1752 (Rfree = 0.000) for 2756 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.1749 (Rfree = 0.000) for 2751 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.1709 (Rfree = 0.000) for 2745 atoms. Found 15 (20 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1664 (Rfree = 0.000) for 2748 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.56 Search for helices and strands: 0 residues in 0 chains, 2828 seeds are put forward Round 1: 122 peptides, 23 chains. Longest chain 13 peptides. Score 0.328 Round 2: 147 peptides, 22 chains. Longest chain 15 peptides. Score 0.464 Round 3: 141 peptides, 19 chains. Longest chain 16 peptides. Score 0.495 Round 4: 151 peptides, 19 chains. Longest chain 19 peptides. Score 0.535 Round 5: 155 peptides, 19 chains. Longest chain 20 peptides. Score 0.550 Taking the results from Round 5 Chains 19, Residues 136, Estimated correctness of the model 11.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5096 reflections ( 97.70 % complete ) and 6565 restraints for refining 2772 atoms. 6040 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1733 (Rfree = 0.000) for 2772 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 37: After refmac, R = 0.1618 (Rfree = 0.000) for 2775 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 38: After refmac, R = 0.1589 (Rfree = 0.000) for 2770 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1593 (Rfree = 0.000) for 2767 atoms. Found 1 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1591 (Rfree = 0.000) for 2758 atoms. Found 1 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.54 Search for helices and strands: 0 residues in 0 chains, 2821 seeds are put forward Round 1: 129 peptides, 24 chains. Longest chain 18 peptides. Score 0.342 Round 2: 139 peptides, 27 chains. Longest chain 11 peptides. Score 0.328 Round 3: 149 peptides, 26 chains. Longest chain 14 peptides. Score 0.395 Round 4: 160 peptides, 26 chains. Longest chain 16 peptides. Score 0.444 Round 5: 143 peptides, 25 chains. Longest chain 10 peptides. Score 0.388 Taking the results from Round 4 Chains 26, Residues 134, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5096 reflections ( 97.70 % complete ) and 6399 restraints for refining 2772 atoms. 5873 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1790 (Rfree = 0.000) for 2772 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. Cycle 42: After refmac, R = 0.1657 (Rfree = 0.000) for 2764 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.1679 (Rfree = 0.000) for 2760 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.1655 (Rfree = 0.000) for 2757 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1628 (Rfree = 0.000) for 2751 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 3.52 Search for helices and strands: 0 residues in 0 chains, 2821 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 7 peptides. Score 0.266 Round 2: 120 peptides, 23 chains. Longest chain 7 peptides. Score 0.318 Round 3: 119 peptides, 22 chains. Longest chain 9 peptides. Score 0.335 Round 4: 117 peptides, 21 chains. Longest chain 10 peptides. Score 0.346 Round 5: 102 peptides, 17 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 85, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 1vlo-3_warpNtrace.pdb as input Building loops using Loopy2018 17 chains (85 residues) following loop building 3 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5096 reflections ( 97.70 % complete ) and 6590 restraints for refining 2772 atoms. 6232 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1692 (Rfree = 0.000) for 2772 atoms. Found 0 (20 requested) and removed 8 (10 requested) atoms. Cycle 47: After refmac, R = 0.1607 (Rfree = 0.000) for 2761 atoms. Found 0 (20 requested) and removed 2 (10 requested) atoms. Cycle 48: After refmac, R = 0.1663 (Rfree = 0.000) for 2757 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1645 (Rfree = 0.000) for 2745 atoms. TimeTaking 47.58