Mon 24 Dec 07:52:34 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2opl-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opl-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opl-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-noncs ############### 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 07:52:38 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/noncs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-noncs/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 239 and 0 Target number of residues in the AU: 239 Target solvent content: 0.6536 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-3.8-parrot-noncs.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-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2992 target number of atoms Had to go as low as 0.75 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 3.801 Wilson plot Bfac: 79.76 3962 reflections ( 99.30 % complete ) and 0 restraints for refining 3332 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3433 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3265 (Rfree = 0.000) for 3332 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.81 Search for helices and strands: 0 residues in 0 chains, 3380 seeds are put forward NCS extension: 0 residues added, 3380 seeds are put forward Round 1: 124 peptides, 25 chains. Longest chain 8 peptides. Score 0.291 Round 2: 157 peptides, 26 chains. Longest chain 11 peptides. Score 0.420 Round 3: 178 peptides, 27 chains. Longest chain 20 peptides. Score 0.487 Round 4: 198 peptides, 30 chains. Longest chain 15 peptides. Score 0.513 Round 5: 210 peptides, 29 chains. Longest chain 20 peptides. Score 0.571 Taking the results from Round 5 Chains 30, Residues 181, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6161 restraints for refining 2703 atoms. 5417 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2488 (Rfree = 0.000) for 2703 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 2: After refmac, R = 0.2193 (Rfree = 0.000) for 2672 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 3: After refmac, R = 0.2093 (Rfree = 0.000) for 2661 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.2029 (Rfree = 0.000) for 2654 atoms. Found 0 (14 requested) and removed 14 (7 requested) atoms. Cycle 5: After refmac, R = 0.2215 (Rfree = 0.000) for 2637 atoms. Found 0 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.86 Search for helices and strands: 0 residues in 0 chains, 2727 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 2757 seeds are put forward Round 1: 185 peptides, 33 chains. Longest chain 11 peptides. Score 0.412 Round 2: 193 peptides, 27 chains. Longest chain 17 peptides. Score 0.543 Round 3: 195 peptides, 31 chains. Longest chain 15 peptides. Score 0.486 Round 4: 193 peptides, 28 chains. Longest chain 16 peptides. Score 0.527 Round 5: 201 peptides, 28 chains. Longest chain 18 peptides. Score 0.555 Taking the results from Round 5 Chains 29, Residues 173, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6215 restraints for refining 2706 atoms. 5501 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2691 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 7: After refmac, R = 0.2159 (Rfree = 0.000) for 2660 atoms. Found 9 (14 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.2091 (Rfree = 0.000) for 2635 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.1986 (Rfree = 0.000) for 2621 atoms. Found 8 (14 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.1848 (Rfree = 0.000) for 2608 atoms. Found 9 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2689 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2710 seeds are put forward Round 1: 163 peptides, 30 chains. Longest chain 11 peptides. Score 0.373 Round 2: 174 peptides, 26 chains. Longest chain 13 peptides. Score 0.489 Round 3: 183 peptides, 27 chains. Longest chain 18 peptides. Score 0.506 Round 4: 185 peptides, 25 chains. Longest chain 21 peptides. Score 0.546 Round 5: 180 peptides, 27 chains. Longest chain 24 peptides. Score 0.495 Taking the results from Round 4 Chains 25, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6460 restraints for refining 2706 atoms. 5845 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2382 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 47 (7 requested) atoms. Cycle 12: After refmac, R = 0.1967 (Rfree = 0.000) for 2658 atoms. Found 8 (14 requested) and removed 16 (7 requested) atoms. Cycle 13: After refmac, R = 0.1924 (Rfree = 0.000) for 2646 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.1748 (Rfree = 0.000) for 2634 atoms. Found 11 (14 requested) and removed 11 (7 requested) atoms. Cycle 15: After refmac, R = 0.1443 (Rfree = 0.000) for 2629 atoms. Found 0 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 2722 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2752 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 8 peptides. Score 0.275 Round 2: 188 peptides, 33 chains. Longest chain 10 peptides. Score 0.424 Round 3: 179 peptides, 28 chains. Longest chain 10 peptides. Score 0.474 Round 4: 180 peptides, 30 chains. Longest chain 11 peptides. Score 0.444 Round 5: 179 peptides, 26 chains. Longest chain 17 peptides. Score 0.508 Taking the results from Round 5 Chains 28, Residues 153, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6260 restraints for refining 2706 atoms. 5616 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2167 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 17: After refmac, R = 0.1990 (Rfree = 0.000) for 2690 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 18: After refmac, R = 0.1737 (Rfree = 0.000) for 2682 atoms. Found 6 (14 requested) and removed 14 (7 requested) atoms. Cycle 19: After refmac, R = 0.1713 (Rfree = 0.000) for 2669 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.1978 (Rfree = 0.000) for 2657 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.81 Search for helices and strands: 0 residues in 0 chains, 2753 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 2755 seeds are put forward Round 1: 128 peptides, 26 chains. Longest chain 9 peptides. Score 0.290 Round 2: 154 peptides, 24 chains. Longest chain 13 peptides. Score 0.444 Round 3: 167 peptides, 29 chains. Longest chain 11 peptides. Score 0.408 Round 4: 176 peptides, 29 chains. Longest chain 12 peptides. Score 0.445 Round 5: 182 peptides, 28 chains. Longest chain 14 peptides. Score 0.486 Taking the results from Round 5 Chains 28, Residues 154, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6276 restraints for refining 2706 atoms. 5670 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2004 (Rfree = 0.000) for 2706 atoms. Found 13 (14 requested) and removed 16 (7 requested) atoms. Cycle 22: After refmac, R = 0.1847 (Rfree = 0.000) for 2677 atoms. Found 6 (14 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.1931 (Rfree = 0.000) for 2662 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. Cycle 24: After refmac, R = 0.1850 (Rfree = 0.000) for 2644 atoms. Found 8 (14 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.1764 (Rfree = 0.000) for 2634 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 2703 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2719 seeds are put forward Round 1: 133 peptides, 30 chains. Longest chain 7 peptides. Score 0.233 Round 2: 158 peptides, 29 chains. Longest chain 11 peptides. Score 0.369 Round 3: 179 peptides, 28 chains. Longest chain 14 peptides. Score 0.474 Round 4: 177 peptides, 28 chains. Longest chain 10 peptides. Score 0.467 Round 5: 171 peptides, 25 chains. Longest chain 15 peptides. Score 0.494 Taking the results from Round 5 Chains 25, Residues 146, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6155 restraints for refining 2698 atoms. 5578 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2229 (Rfree = 0.000) for 2698 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 27: After refmac, R = 0.1905 (Rfree = 0.000) for 2673 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 28: After refmac, R = 0.1896 (Rfree = 0.000) for 2663 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 29: After refmac, R = 0.1809 (Rfree = 0.000) for 2655 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.1777 (Rfree = 0.000) for 2652 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2728 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2742 seeds are put forward Round 1: 138 peptides, 29 chains. Longest chain 9 peptides. Score 0.277 Round 2: 171 peptides, 29 chains. Longest chain 14 peptides. Score 0.425 Round 3: 175 peptides, 30 chains. Longest chain 19 peptides. Score 0.424 Round 4: 172 peptides, 28 chains. Longest chain 14 peptides. Score 0.447 Round 5: 184 peptides, 30 chains. Longest chain 21 peptides. Score 0.460 Taking the results from Round 5 Chains 30, Residues 154, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6184 restraints for refining 2706 atoms. 5559 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2172 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 32: After refmac, R = 0.1953 (Rfree = 0.000) for 2675 atoms. Found 11 (14 requested) and removed 14 (7 requested) atoms. Cycle 33: After refmac, R = 0.1622 (Rfree = 0.000) for 2658 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1678 (Rfree = 0.000) for 2648 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.1838 (Rfree = 0.000) for 2631 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 2713 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 2737 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 7 peptides. Score 0.228 Round 2: 109 peptides, 19 chains. Longest chain 15 peptides. Score 0.342 Round 3: 114 peptides, 22 chains. Longest chain 10 peptides. Score 0.304 Round 4: 125 peptides, 21 chains. Longest chain 16 peptides. Score 0.376 Round 5: 109 peptides, 19 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 4 Chains 21, Residues 104, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6449 restraints for refining 2655 atoms. 6025 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2453 (Rfree = 0.000) for 2655 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. Cycle 37: After refmac, R = 0.2018 (Rfree = 0.000) for 2632 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 38: After refmac, R = 0.1992 (Rfree = 0.000) for 2624 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 39: After refmac, R = 0.2076 (Rfree = 0.000) for 2621 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.1817 (Rfree = 0.000) for 2620 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.87 Search for helices and strands: 0 residues in 0 chains, 2705 seeds are put forward NCS extension: 0 residues added, 2705 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 13 peptides. Score 0.283 Round 2: 126 peptides, 22 chains. Longest chain 13 peptides. Score 0.361 Round 3: 136 peptides, 21 chains. Longest chain 19 peptides. Score 0.424 Round 4: 125 peptides, 22 chains. Longest chain 12 peptides. Score 0.356 Round 5: 126 peptides, 19 chains. Longest chain 19 peptides. Score 0.420 Taking the results from Round 3 Chains 21, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6296 restraints for refining 2617 atoms. 5857 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2162 (Rfree = 0.000) for 2617 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 42: After refmac, R = 0.1933 (Rfree = 0.000) for 2606 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.1429 (Rfree = 0.000) for 2599 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1679 (Rfree = 0.000) for 2599 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.1820 (Rfree = 0.000) for 2602 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2672 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 2705 seeds are put forward Round 1: 96 peptides, 22 chains. Longest chain 8 peptides. Score 0.211 Round 2: 120 peptides, 25 chains. Longest chain 9 peptides. Score 0.271 Round 3: 123 peptides, 23 chains. Longest chain 10 peptides. Score 0.327 Round 4: 128 peptides, 25 chains. Longest chain 8 peptides. Score 0.310 Round 5: 119 peptides, 21 chains. Longest chain 14 peptides. Score 0.348 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 98, 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. 3962 reflections ( 99.30 % complete ) and 6403 restraints for refining 2659 atoms. 6032 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1974 (Rfree = 0.000) for 2659 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1912 (Rfree = 0.000) for 2645 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1690 (Rfree = 0.000) for 2632 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1703 (Rfree = 0.000) for 2622 atoms. TimeTaking 31.48