Mon 24 Dec 00:34:04 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-3.2-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-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-3.2-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 00:34:08 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-3.2-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 266 and 0 Target number of residues in the AU: 266 Target solvent content: 0.6145 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 58.42 6543 reflections ( 99.53 % complete ) and 0 restraints for refining 3340 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3131 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2876 (Rfree = 0.000) for 3340 atoms. Found 29 (29 requested) and removed 37 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.28 Search for helices and strands: 0 residues in 0 chains, 3406 seeds are put forward NCS extension: 0 residues added, 3406 seeds are put forward Round 1: 191 peptides, 37 chains. Longest chain 9 peptides. Score 0.366 Round 2: 220 peptides, 29 chains. Longest chain 18 peptides. Score 0.603 Round 3: 258 peptides, 34 chains. Longest chain 21 peptides. Score 0.650 Round 4: 259 peptides, 30 chains. Longest chain 29 peptides. Score 0.699 Round 5: 274 peptides, 29 chains. Longest chain 29 peptides. Score 0.744 Taking the results from Round 5 Chains 30, Residues 245, Estimated correctness of the model 74.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5591 restraints for refining 2730 atoms. 4569 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2371 (Rfree = 0.000) for 2730 atoms. Found 19 (24 requested) and removed 20 (12 requested) atoms. Cycle 2: After refmac, R = 0.2170 (Rfree = 0.000) for 2691 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. Cycle 3: After refmac, R = 0.2087 (Rfree = 0.000) for 2678 atoms. Found 5 (23 requested) and removed 12 (12 requested) atoms. Cycle 4: After refmac, R = 0.2090 (Rfree = 0.000) for 2666 atoms. Found 4 (22 requested) and removed 12 (11 requested) atoms. Cycle 5: After refmac, R = 0.2023 (Rfree = 0.000) for 2657 atoms. Found 3 (21 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.09 3.26 Search for helices and strands: 0 residues in 0 chains, 2737 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 2753 seeds are put forward Round 1: 239 peptides, 31 chains. Longest chain 24 peptides. Score 0.634 Round 2: 240 peptides, 28 chains. Longest chain 18 peptides. Score 0.674 Round 3: 255 peptides, 29 chains. Longest chain 24 peptides. Score 0.701 Round 4: 267 peptides, 27 chains. Longest chain 30 peptides. Score 0.749 Round 5: 257 peptides, 30 chains. Longest chain 18 peptides. Score 0.694 Taking the results from Round 4 Chains 29, Residues 240, Estimated correctness of the model 74.9 % 5 chains (77 residues) have been docked in sequence Building loops using Loopy2018 29 chains (240 residues) following loop building 5 chains (77 residues) in sequence following loop building ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5204 restraints for refining 2731 atoms. 3991 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2484 (Rfree = 0.000) for 2731 atoms. Found 22 (22 requested) and removed 24 (12 requested) atoms. Cycle 7: After refmac, R = 0.2401 (Rfree = 0.000) for 2718 atoms. Found 13 (21 requested) and removed 15 (12 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2292 (Rfree = 0.000) for 2706 atoms. Found 13 (21 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.2215 (Rfree = 0.000) for 2705 atoms. Found 4 (20 requested) and removed 13 (12 requested) atoms. Cycle 10: After refmac, R = 0.2048 (Rfree = 0.000) for 2695 atoms. Found 6 (20 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.29 Search for helices and strands: 0 residues in 0 chains, 2778 seeds are put forward NCS extension: 20 residues added (10 deleted due to clashes), 2798 seeds are put forward Round 1: 238 peptides, 32 chains. Longest chain 23 peptides. Score 0.618 Round 2: 249 peptides, 28 chains. Longest chain 31 peptides. Score 0.697 Round 3: 259 peptides, 27 chains. Longest chain 31 peptides. Score 0.732 Round 4: 260 peptides, 30 chains. Longest chain 35 peptides. Score 0.702 Round 5: 260 peptides, 27 chains. Longest chain 25 peptides. Score 0.734 Taking the results from Round 5 Chains 27, Residues 233, Estimated correctness of the model 72.1 % 3 chains (45 residues) have been docked in sequence Building loops using Loopy2018 27 chains (233 residues) following loop building 3 chains (45 residues) in sequence following loop building ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5551 restraints for refining 2732 atoms. 4446 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2586 (Rfree = 0.000) for 2732 atoms. Found 14 (19 requested) and removed 14 (12 requested) atoms. Cycle 12: After refmac, R = 0.2178 (Rfree = 0.000) for 2720 atoms. Found 6 (19 requested) and removed 13 (12 requested) atoms. Cycle 13: After refmac, R = 0.2118 (Rfree = 0.000) for 2708 atoms. Found 8 (18 requested) and removed 13 (12 requested) atoms. Cycle 14: After refmac, R = 0.1997 (Rfree = 0.000) for 2700 atoms. Found 6 (18 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.1982 (Rfree = 0.000) for 2694 atoms. Found 3 (17 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.11 3.28 Search for helices and strands: 0 residues in 0 chains, 2773 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 2788 seeds are put forward Round 1: 225 peptides, 31 chains. Longest chain 16 peptides. Score 0.591 Round 2: 254 peptides, 31 chains. Longest chain 18 peptides. Score 0.675 Round 3: 250 peptides, 28 chains. Longest chain 22 peptides. Score 0.700 Round 4: 255 peptides, 27 chains. Longest chain 18 peptides. Score 0.722 Round 5: 252 peptides, 28 chains. Longest chain 26 peptides. Score 0.705 Taking the results from Round 4 Chains 29, Residues 228, Estimated correctness of the model 69.7 % 2 chains (27 residues) have been docked in sequence Building loops using Loopy2018 29 chains (228 residues) following loop building 2 chains (27 residues) in sequence following loop building ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5810 restraints for refining 2732 atoms. 4824 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2404 (Rfree = 0.000) for 2732 atoms. Found 14 (17 requested) and removed 15 (12 requested) atoms. Cycle 17: After refmac, R = 0.2239 (Rfree = 0.000) for 2720 atoms. Found 8 (16 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.2252 (Rfree = 0.000) for 2707 atoms. Found 12 (16 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.2143 (Rfree = 0.000) for 2706 atoms. Found 9 (15 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2294 (Rfree = 0.000) for 2696 atoms. Found 15 (15 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.25 Search for helices and strands: 0 residues in 0 chains, 2784 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2810 seeds are put forward Round 1: 224 peptides, 33 chains. Longest chain 16 peptides. Score 0.559 Round 2: 244 peptides, 29 chains. Longest chain 22 peptides. Score 0.673 Round 3: 245 peptides, 30 chains. Longest chain 21 peptides. Score 0.663 Round 4: 245 peptides, 27 chains. Longest chain 24 peptides. Score 0.699 Round 5: 231 peptides, 26 chains. Longest chain 20 peptides. Score 0.674 Taking the results from Round 4 Chains 31, Residues 218, Estimated correctness of the model 65.0 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5708 restraints for refining 2732 atoms. 4717 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2362 (Rfree = 0.000) for 2732 atoms. Found 14 (14 requested) and removed 16 (12 requested) atoms. Cycle 22: After refmac, R = 0.2175 (Rfree = 0.000) for 2726 atoms. Found 8 (14 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.2078 (Rfree = 0.000) for 2719 atoms. Found 6 (14 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.1966 (Rfree = 0.000) for 2712 atoms. Found 6 (14 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.1955 (Rfree = 0.000) for 2704 atoms. Found 8 (14 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 3.30 Search for helices and strands: 0 residues in 0 chains, 2772 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 2787 seeds are put forward Round 1: 191 peptides, 27 chains. Longest chain 15 peptides. Score 0.536 Round 2: 224 peptides, 28 chains. Longest chain 20 peptides. Score 0.629 Round 3: 226 peptides, 26 chains. Longest chain 25 peptides. Score 0.661 Round 4: 222 peptides, 25 chains. Longest chain 26 peptides. Score 0.663 Round 5: 233 peptides, 27 chains. Longest chain 24 peptides. Score 0.668 Taking the results from Round 5 Chains 28, Residues 206, Estimated correctness of the model 58.1 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5895 restraints for refining 2732 atoms. 5019 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2226 (Rfree = 0.000) for 2732 atoms. Found 14 (14 requested) and removed 14 (12 requested) atoms. Cycle 27: After refmac, R = 0.2068 (Rfree = 0.000) for 2726 atoms. Found 11 (14 requested) and removed 15 (12 requested) atoms. Cycle 28: After refmac, R = 0.1942 (Rfree = 0.000) for 2717 atoms. Found 8 (14 requested) and removed 13 (12 requested) atoms. Cycle 29: After refmac, R = 0.1887 (Rfree = 0.000) for 2706 atoms. Found 8 (14 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.1918 (Rfree = 0.000) for 2700 atoms. Found 9 (14 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.27 Search for helices and strands: 0 residues in 0 chains, 2762 seeds are put forward NCS extension: 27 residues added (10 deleted due to clashes), 2789 seeds are put forward Round 1: 205 peptides, 31 chains. Longest chain 16 peptides. Score 0.523 Round 2: 223 peptides, 27 chains. Longest chain 17 peptides. Score 0.639 Round 3: 227 peptides, 29 chains. Longest chain 20 peptides. Score 0.625 Round 4: 220 peptides, 27 chains. Longest chain 18 peptides. Score 0.631 Round 5: 226 peptides, 27 chains. Longest chain 18 peptides. Score 0.648 Taking the results from Round 5 Chains 27, Residues 199, Estimated correctness of the model 53.4 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5776 restraints for refining 2732 atoms. 4845 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2334 (Rfree = 0.000) for 2732 atoms. Found 14 (14 requested) and removed 13 (12 requested) atoms. Cycle 32: After refmac, R = 0.2280 (Rfree = 0.000) for 2726 atoms. Found 11 (14 requested) and removed 12 (12 requested) atoms. Cycle 33: After refmac, R = 0.2072 (Rfree = 0.000) for 2719 atoms. Found 7 (14 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.2220 (Rfree = 0.000) for 2704 atoms. Found 14 (14 requested) and removed 14 (12 requested) atoms. Cycle 35: After refmac, R = 0.1899 (Rfree = 0.000) for 2699 atoms. Found 3 (14 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 3.27 Search for helices and strands: 0 residues in 0 chains, 2750 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2764 seeds are put forward Round 1: 175 peptides, 28 chains. Longest chain 16 peptides. Score 0.459 Round 2: 205 peptides, 26 chains. Longest chain 20 peptides. Score 0.598 Round 3: 220 peptides, 30 chains. Longest chain 18 peptides. Score 0.589 Round 4: 213 peptides, 25 chains. Longest chain 24 peptides. Score 0.637 Round 5: 210 peptides, 24 chains. Longest chain 24 peptides. Score 0.641 Taking the results from Round 5 Chains 25, Residues 186, Estimated correctness of the model 51.6 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5721 restraints for refining 2732 atoms. 4828 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2216 (Rfree = 0.000) for 2732 atoms. Found 14 (14 requested) and removed 21 (12 requested) atoms. Cycle 37: After refmac, R = 0.2090 (Rfree = 0.000) for 2720 atoms. Found 11 (14 requested) and removed 16 (12 requested) atoms. Cycle 38: After refmac, R = 0.2024 (Rfree = 0.000) for 2714 atoms. Found 9 (14 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.1987 (Rfree = 0.000) for 2709 atoms. Found 6 (14 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.1942 (Rfree = 0.000) for 2703 atoms. Found 5 (14 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 3.30 Search for helices and strands: 0 residues in 0 chains, 2769 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 2798 seeds are put forward Round 1: 186 peptides, 28 chains. Longest chain 18 peptides. Score 0.501 Round 2: 202 peptides, 26 chains. Longest chain 18 peptides. Score 0.589 Round 3: 204 peptides, 28 chains. Longest chain 20 peptides. Score 0.566 Round 4: 222 peptides, 28 chains. Longest chain 17 peptides. Score 0.623 Round 5: 216 peptides, 29 chains. Longest chain 18 peptides. Score 0.591 Taking the results from Round 4 Chains 29, Residues 194, Estimated correctness of the model 47.1 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 6159 restraints for refining 2732 atoms. 5361 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2115 (Rfree = 0.000) for 2732 atoms. Found 14 (14 requested) and removed 13 (12 requested) atoms. Cycle 42: After refmac, R = 0.1974 (Rfree = 0.000) for 2723 atoms. Found 4 (14 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.2187 (Rfree = 0.000) for 2712 atoms. Found 14 (14 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.1897 (Rfree = 0.000) for 2712 atoms. Found 10 (14 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.2318 (Rfree = 0.000) for 2708 atoms. Found 14 (14 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.04 3.21 Search for helices and strands: 0 residues in 0 chains, 2790 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2806 seeds are put forward Round 1: 168 peptides, 28 chains. Longest chain 13 peptides. Score 0.430 Round 2: 210 peptides, 28 chains. Longest chain 15 peptides. Score 0.586 Round 3: 200 peptides, 26 chains. Longest chain 15 peptides. Score 0.582 Round 4: 209 peptides, 26 chains. Longest chain 30 peptides. Score 0.611 Round 5: 218 peptides, 24 chains. Longest chain 28 peptides. Score 0.664 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 194, Estimated correctness of the model 57.2 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2opl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6543 reflections ( 99.53 % complete ) and 5976 restraints for refining 2732 atoms. 5178 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2118 (Rfree = 0.000) for 2732 atoms. Found 0 (14 requested) and removed 10 (12 requested) atoms. Cycle 47: After refmac, R = 0.2101 (Rfree = 0.000) for 2719 atoms. Found 0 (14 requested) and removed 5 (12 requested) atoms. Cycle 48: After refmac, R = 0.2096 (Rfree = 0.000) for 2711 atoms. Found 0 (14 requested) and removed 9 (12 requested) atoms. Cycle 49: After refmac, R = 0.2357 (Rfree = 0.000) for 2700 atoms. Found 0 (14 requested) and removed 12 (12 requested) atoms. Writing output files ... TimeTaking 35.73