Mon 24 Dec 00:17:32 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 2opl-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-3.4-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/2opl-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-3.4-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 00:17:37 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/2opl-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-3.4-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 253 and 0 Target number of residues in the AU: 253 Target solvent content: 0.6333 Checking the provided sequence file Detected sequence length: 187 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 374 Adjusted target solvent content: 0.46 Input MTZ file: 2opl-3.4-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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2992 target number of atoms Had to go as low as 0.70 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: 62.588 3.400 Wilson plot Bfac: 67.67 5475 reflections ( 99.44 % complete ) and 0 restraints for refining 3298 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3227 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2647 (Rfree = 0.000) for 3298 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.45 Search for helices and strands: 0 residues in 0 chains, 3339 seeds are put forward NCS extension: 0 residues added, 3339 seeds are put forward Round 1: 184 peptides, 29 chains. Longest chain 15 peptides. Score 0.477 Round 2: 198 peptides, 25 chains. Longest chain 21 peptides. Score 0.590 Round 3: 224 peptides, 29 chains. Longest chain 16 peptides. Score 0.616 Round 4: 237 peptides, 26 chains. Longest chain 21 peptides. Score 0.690 Round 5: 250 peptides, 26 chains. Longest chain 18 peptides. Score 0.722 Taking the results from Round 5 Chains 28, Residues 224, Estimated correctness of the model 63.4 % 4 chains (37 residues) have been docked in sequence Building loops using Loopy2018 28 chains (224 residues) following loop building 4 chains (37 residues) in sequence following loop building ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5447 restraints for refining 2720 atoms. 4453 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2447 (Rfree = 0.000) for 2720 atoms. Found 17 (20 requested) and removed 17 (10 requested) atoms. Cycle 2: After refmac, R = 0.2247 (Rfree = 0.000) for 2692 atoms. Found 9 (20 requested) and removed 13 (10 requested) atoms. Cycle 3: After refmac, R = 0.2175 (Rfree = 0.000) for 2671 atoms. Found 5 (19 requested) and removed 12 (10 requested) atoms. Cycle 4: After refmac, R = 0.2231 (Rfree = 0.000) for 2659 atoms. Found 6 (19 requested) and removed 11 (10 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2184 (Rfree = 0.000) for 2647 atoms. Found 9 (18 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.48 Search for helices and strands: 0 residues in 0 chains, 2735 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2749 seeds are put forward Round 1: 223 peptides, 31 chains. Longest chain 17 peptides. Score 0.585 Round 2: 249 peptides, 28 chains. Longest chain 22 peptides. Score 0.697 Round 3: 253 peptides, 30 chains. Longest chain 21 peptides. Score 0.684 Round 4: 241 peptides, 28 chains. Longest chain 19 peptides. Score 0.677 Round 5: 251 peptides, 25 chains. Longest chain 28 peptides. Score 0.735 Taking the results from Round 5 Chains 30, Residues 226, Estimated correctness of the model 66.4 % 3 chains (31 residues) have been docked in sequence Building loops using Loopy2018 30 chains (226 residues) following loop building 3 chains (31 residues) in sequence following loop building ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5768 restraints for refining 2719 atoms. 4790 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2481 (Rfree = 0.000) for 2719 atoms. Found 17 (18 requested) and removed 16 (10 requested) atoms. Cycle 7: After refmac, R = 0.2247 (Rfree = 0.000) for 2709 atoms. Found 3 (18 requested) and removed 11 (10 requested) atoms. Cycle 8: After refmac, R = 0.2181 (Rfree = 0.000) for 2696 atoms. Found 7 (17 requested) and removed 11 (10 requested) atoms. Cycle 9: After refmac, R = 0.2102 (Rfree = 0.000) for 2687 atoms. Found 7 (17 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2151 (Rfree = 0.000) for 2680 atoms. Found 9 (16 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.46 Search for helices and strands: 0 residues in 0 chains, 2767 seeds are put forward NCS extension: 8 residues added (11 deleted due to clashes), 2775 seeds are put forward Round 1: 216 peptides, 30 chains. Longest chain 20 peptides. Score 0.576 Round 2: 241 peptides, 30 chains. Longest chain 21 peptides. Score 0.652 Round 3: 246 peptides, 30 chains. Longest chain 21 peptides. Score 0.666 Round 4: 234 peptides, 29 chains. Longest chain 17 peptides. Score 0.645 Round 5: 214 peptides, 28 chains. Longest chain 18 peptides. Score 0.598 Taking the results from Round 3 Chains 34, Residues 216, Estimated correctness of the model 48.7 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5749 restraints for refining 2719 atoms. 4746 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2328 (Rfree = 0.000) for 2719 atoms. Found 16 (16 requested) and removed 18 (10 requested) atoms. Cycle 12: After refmac, R = 0.2132 (Rfree = 0.000) for 2703 atoms. Found 14 (16 requested) and removed 13 (10 requested) atoms. Cycle 13: After refmac, R = 0.2081 (Rfree = 0.000) for 2694 atoms. Found 11 (16 requested) and removed 12 (10 requested) atoms. Cycle 14: After refmac, R = 0.2017 (Rfree = 0.000) for 2690 atoms. Found 10 (16 requested) and removed 14 (10 requested) atoms. Cycle 15: After refmac, R = 0.1971 (Rfree = 0.000) for 2684 atoms. Found 8 (16 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.44 Search for helices and strands: 0 residues in 0 chains, 2775 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2786 seeds are put forward Round 1: 202 peptides, 31 chains. Longest chain 15 peptides. Score 0.512 Round 2: 226 peptides, 28 chains. Longest chain 22 peptides. Score 0.635 Round 3: 210 peptides, 24 chains. Longest chain 26 peptides. Score 0.641 Round 4: 243 peptides, 29 chains. Longest chain 21 peptides. Score 0.670 Round 5: 222 peptides, 27 chains. Longest chain 16 peptides. Score 0.637 Taking the results from Round 4 Chains 29, Residues 214, Estimated correctness of the model 49.8 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5895 restraints for refining 2720 atoms. 5011 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2147 (Rfree = 0.000) for 2720 atoms. Found 12 (16 requested) and removed 11 (10 requested) atoms. Cycle 17: After refmac, R = 0.1988 (Rfree = 0.000) for 2697 atoms. Found 16 (16 requested) and removed 12 (10 requested) atoms. Cycle 18: After refmac, R = 0.1968 (Rfree = 0.000) for 2697 atoms. Found 6 (16 requested) and removed 13 (10 requested) atoms. Cycle 19: After refmac, R = 0.1934 (Rfree = 0.000) for 2688 atoms. Found 7 (16 requested) and removed 13 (10 requested) atoms. Cycle 20: After refmac, R = 0.1975 (Rfree = 0.000) for 2675 atoms. Found 10 (16 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.48 Search for helices and strands: 0 residues in 0 chains, 2758 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2774 seeds are put forward Round 1: 222 peptides, 32 chains. Longest chain 23 peptides. Score 0.567 Round 2: 225 peptides, 28 chains. Longest chain 24 peptides. Score 0.632 Round 3: 227 peptides, 25 chains. Longest chain 26 peptides. Score 0.676 Round 4: 229 peptides, 24 chains. Longest chain 25 peptides. Score 0.693 Round 5: 228 peptides, 29 chains. Longest chain 22 peptides. Score 0.628 Taking the results from Round 4 Chains 28, Residues 205, Estimated correctness of the model 56.1 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5958 restraints for refining 2720 atoms. 5064 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2385 (Rfree = 0.000) for 2720 atoms. Found 16 (16 requested) and removed 18 (10 requested) atoms. Cycle 22: After refmac, R = 0.2162 (Rfree = 0.000) for 2711 atoms. Found 13 (16 requested) and removed 13 (10 requested) atoms. Cycle 23: After refmac, R = 0.2087 (Rfree = 0.000) for 2707 atoms. Found 13 (16 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.1958 (Rfree = 0.000) for 2706 atoms. Found 7 (16 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.1959 (Rfree = 0.000) for 2700 atoms. Found 5 (16 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.46 Search for helices and strands: 0 residues in 0 chains, 2790 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 2815 seeds are put forward Round 1: 168 peptides, 25 chains. Longest chain 26 peptides. Score 0.483 Round 2: 208 peptides, 27 chains. Longest chain 23 peptides. Score 0.593 Round 3: 222 peptides, 26 chains. Longest chain 24 peptides. Score 0.650 Round 4: 234 peptides, 27 chains. Longest chain 22 peptides. Score 0.670 Round 5: 225 peptides, 28 chains. Longest chain 26 peptides. Score 0.632 Taking the results from Round 4 Chains 27, Residues 207, Estimated correctness of the model 49.8 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 5887 restraints for refining 2719 atoms. 4987 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2259 (Rfree = 0.000) for 2719 atoms. Found 14 (16 requested) and removed 22 (10 requested) atoms. Cycle 27: After refmac, R = 0.2017 (Rfree = 0.000) for 2707 atoms. Found 10 (16 requested) and removed 14 (10 requested) atoms. Cycle 28: After refmac, R = 0.2035 (Rfree = 0.000) for 2700 atoms. Found 11 (16 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.1978 (Rfree = 0.000) for 2697 atoms. Found 8 (16 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1905 (Rfree = 0.000) for 2690 atoms. Found 5 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.48 Search for helices and strands: 0 residues in 0 chains, 2754 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 2769 seeds are put forward Round 1: 195 peptides, 29 chains. Longest chain 22 peptides. Score 0.518 Round 2: 219 peptides, 28 chains. Longest chain 21 peptides. Score 0.614 Round 3: 217 peptides, 26 chains. Longest chain 22 peptides. Score 0.635 Round 4: 210 peptides, 28 chains. Longest chain 21 peptides. Score 0.586 Round 5: 211 peptides, 29 chains. Longest chain 26 peptides. Score 0.574 Taking the results from Round 3 Chains 26, Residues 191, Estimated correctness of the model 39.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6269 restraints for refining 2720 atoms. 5531 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2144 (Rfree = 0.000) for 2720 atoms. Found 11 (16 requested) and removed 10 (10 requested) atoms. Cycle 32: After refmac, R = 0.2049 (Rfree = 0.000) for 2716 atoms. Found 15 (16 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.2019 (Rfree = 0.000) for 2719 atoms. Found 9 (16 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.1907 (Rfree = 0.000) for 2716 atoms. Found 8 (16 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1897 (Rfree = 0.000) for 2712 atoms. Found 5 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.50 Search for helices and strands: 0 residues in 0 chains, 2813 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2830 seeds are put forward Round 1: 171 peptides, 31 chains. Longest chain 10 peptides. Score 0.389 Round 2: 187 peptides, 24 chains. Longest chain 23 peptides. Score 0.569 Round 3: 208 peptides, 29 chains. Longest chain 14 peptides. Score 0.564 Round 4: 210 peptides, 30 chains. Longest chain 12 peptides. Score 0.556 Round 5: 219 peptides, 31 chains. Longest chain 18 peptides. Score 0.571 Taking the results from Round 5 Chains 31, Residues 188, Estimated correctness of the model 18.9 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6142 restraints for refining 2720 atoms. 5376 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2309 (Rfree = 0.000) for 2720 atoms. Found 9 (16 requested) and removed 11 (10 requested) atoms. Cycle 37: After refmac, R = 0.2220 (Rfree = 0.000) for 2705 atoms. Found 16 (16 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.2033 (Rfree = 0.000) for 2697 atoms. Found 10 (16 requested) and removed 12 (10 requested) atoms. Cycle 39: After refmac, R = 0.1955 (Rfree = 0.000) for 2693 atoms. Found 9 (16 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.1935 (Rfree = 0.000) for 2686 atoms. Found 11 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2770 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 2801 seeds are put forward Round 1: 158 peptides, 30 chains. Longest chain 12 peptides. Score 0.350 Round 2: 165 peptides, 26 chains. Longest chain 11 peptides. Score 0.453 Round 3: 179 peptides, 26 chains. Longest chain 20 peptides. Score 0.508 Round 4: 162 peptides, 22 chains. Longest chain 25 peptides. Score 0.511 Round 5: 161 peptides, 21 chains. Longest chain 16 peptides. Score 0.524 Taking the results from Round 5 Chains 21, Residues 140, Estimated correctness of the model 1.9 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5475 reflections ( 99.44 % complete ) and 6510 restraints for refining 2720 atoms. 5953 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2183 (Rfree = 0.000) for 2720 atoms. Found 16 (16 requested) and removed 11 (10 requested) atoms. Cycle 42: After refmac, R = 0.1948 (Rfree = 0.000) for 2718 atoms. Found 12 (16 requested) and removed 13 (10 requested) atoms. Cycle 43: After refmac, R = 0.1854 (Rfree = 0.000) for 2714 atoms. Found 13 (16 requested) and removed 12 (10 requested) atoms. Cycle 44: After refmac, R = 0.1864 (Rfree = 0.000) for 2715 atoms. Found 16 (16 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1806 (Rfree = 0.000) for 2717 atoms. Found 15 (16 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.47 Search for helices and strands: 0 residues in 0 chains, 2821 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2837 seeds are put forward Round 1: 156 peptides, 28 chains. Longest chain 11 peptides. Score 0.379 Round 2: 171 peptides, 24 chains. Longest chain 16 peptides. Score 0.511 Round 3: 175 peptides, 26 chains. Longest chain 18 peptides. Score 0.493 Round 4: 185 peptides, 28 chains. Longest chain 16 peptides. Score 0.498 Round 5: 169 peptides, 24 chains. Longest chain 18 peptides. Score 0.504 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 147, 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 2opl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5475 reflections ( 99.44 % complete ) and 6466 restraints for refining 2718 atoms. 5902 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1942 (Rfree = 0.000) for 2718 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1967 (Rfree = 0.000) for 2704 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1948 (Rfree = 0.000) for 2692 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2002 (Rfree = 0.000) for 2675 atoms. Found 0 (16 requested) and removed 10 (10 requested) atoms. Writing output files ... TimeTaking 39.47