Mon 24 Dec 01:01:42 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-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 01:01:46 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-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 231 and 0 Target number of residues in the AU: 231 Target solvent content: 0.6652 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-4.0-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-4.0-parrot-mrncs.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 4.000 Wilson plot Bfac: 88.38 3418 reflections ( 99.19 % complete ) and 0 restraints for refining 3312 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3448 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3570 (Rfree = 0.000) for 3312 atoms. Found 15 (15 requested) and removed 85 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 4.04 Search for helices and strands: 0 residues in 0 chains, 3295 seeds are put forward NCS extension: 0 residues added, 3295 seeds are put forward Round 1: 109 peptides, 20 chains. Longest chain 11 peptides. Score 0.321 Round 2: 167 peptides, 26 chains. Longest chain 13 peptides. Score 0.462 Round 3: 177 peptides, 27 chains. Longest chain 17 peptides. Score 0.484 Round 4: 199 peptides, 29 chains. Longest chain 17 peptides. Score 0.533 Round 5: 204 peptides, 29 chains. Longest chain 17 peptides. Score 0.550 Taking the results from Round 5 Chains 29, Residues 175, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5951 restraints for refining 2701 atoms. 5203 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2855 (Rfree = 0.000) for 2701 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 2: After refmac, R = 0.2779 (Rfree = 0.000) for 2636 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 3: After refmac, R = 0.2515 (Rfree = 0.000) for 2588 atoms. Found 11 (12 requested) and removed 18 (6 requested) atoms. Cycle 4: After refmac, R = 0.2456 (Rfree = 0.000) for 2559 atoms. Found 9 (12 requested) and removed 16 (6 requested) atoms. Cycle 5: After refmac, R = 0.1984 (Rfree = 0.000) for 2535 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 4.01 Search for helices and strands: 0 residues in 0 chains, 2603 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 2632 seeds are put forward Round 1: 149 peptides, 29 chains. Longest chain 10 peptides. Score 0.329 Round 2: 170 peptides, 31 chains. Longest chain 10 peptides. Score 0.385 Round 3: 180 peptides, 28 chains. Longest chain 10 peptides. Score 0.478 Round 4: 175 peptides, 26 chains. Longest chain 12 peptides. Score 0.493 Round 5: 188 peptides, 29 chains. Longest chain 12 peptides. Score 0.492 Taking the results from Round 4 Chains 26, Residues 149, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3418 reflections ( 99.19 % complete ) and 6045 restraints for refining 2617 atoms. 5434 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2397 (Rfree = 0.000) for 2617 atoms. Found 5 (12 requested) and removed 26 (6 requested) atoms. Cycle 7: After refmac, R = 0.2036 (Rfree = 0.000) for 2577 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.2028 (Rfree = 0.000) for 2555 atoms. Found 5 (12 requested) and removed 15 (6 requested) atoms. Cycle 9: After refmac, R = 0.2161 (Rfree = 0.000) for 2535 atoms. Found 9 (12 requested) and removed 18 (6 requested) atoms. Cycle 10: After refmac, R = 0.2269 (Rfree = 0.000) for 2517 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 4.04 Search for helices and strands: 0 residues in 0 chains, 2583 seeds are put forward NCS extension: 0 residues added, 2583 seeds are put forward Round 1: 141 peptides, 25 chains. Longest chain 15 peptides. Score 0.370 Round 2: 173 peptides, 28 chains. Longest chain 15 peptides. Score 0.451 Round 3: 171 peptides, 29 chains. Longest chain 12 peptides. Score 0.425 Round 4: 176 peptides, 26 chains. Longest chain 15 peptides. Score 0.497 Round 5: 194 peptides, 28 chains. Longest chain 13 peptides. Score 0.531 Taking the results from Round 5 Chains 28, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5984 restraints for refining 2639 atoms. 5348 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2495 (Rfree = 0.000) for 2639 atoms. Found 11 (12 requested) and removed 27 (6 requested) atoms. Cycle 12: After refmac, R = 0.2268 (Rfree = 0.000) for 2590 atoms. Found 10 (12 requested) and removed 19 (6 requested) atoms. Cycle 13: After refmac, R = 0.2198 (Rfree = 0.000) for 2564 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 14: After refmac, R = 0.2279 (Rfree = 0.000) for 2546 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 15: After refmac, R = 0.1999 (Rfree = 0.000) for 2523 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 4.01 Search for helices and strands: 0 residues in 0 chains, 2633 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2646 seeds are put forward Round 1: 137 peptides, 29 chains. Longest chain 7 peptides. Score 0.272 Round 2: 174 peptides, 30 chains. Longest chain 9 peptides. Score 0.419 Round 3: 184 peptides, 28 chains. Longest chain 13 peptides. Score 0.494 Round 4: 198 peptides, 27 chains. Longest chain 16 peptides. Score 0.560 Round 5: 173 peptides, 27 chains. Longest chain 11 peptides. Score 0.468 Taking the results from Round 4 Chains 27, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5982 restraints for refining 2666 atoms. 5325 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2357 (Rfree = 0.000) for 2666 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 17: After refmac, R = 0.2250 (Rfree = 0.000) for 2636 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 18: After refmac, R = 0.2323 (Rfree = 0.000) for 2618 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.2082 (Rfree = 0.000) for 2591 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 20: After refmac, R = 0.2230 (Rfree = 0.000) for 2575 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 2672 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 2701 seeds are put forward Round 1: 138 peptides, 27 chains. Longest chain 9 peptides. Score 0.317 Round 2: 163 peptides, 26 chains. Longest chain 21 peptides. Score 0.445 Round 3: 175 peptides, 27 chains. Longest chain 16 peptides. Score 0.476 Round 4: 168 peptides, 25 chains. Longest chain 11 peptides. Score 0.483 Round 5: 180 peptides, 26 chains. Longest chain 18 peptides. Score 0.512 Taking the results from Round 5 Chains 26, Residues 154, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5894 restraints for refining 2686 atoms. 5229 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2247 (Rfree = 0.000) for 2686 atoms. Found 10 (12 requested) and removed 29 (6 requested) atoms. Cycle 22: After refmac, R = 0.2222 (Rfree = 0.000) for 2644 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 23: After refmac, R = 0.2167 (Rfree = 0.000) for 2624 atoms. Found 8 (12 requested) and removed 16 (6 requested) atoms. Cycle 24: After refmac, R = 0.1654 (Rfree = 0.000) for 2603 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1877 (Rfree = 0.000) for 2592 atoms. Found 5 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.86 Search for helices and strands: 0 residues in 0 chains, 2662 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2687 seeds are put forward Round 1: 115 peptides, 24 chains. Longest chain 9 peptides. Score 0.267 Round 2: 149 peptides, 26 chains. Longest chain 14 peptides. Score 0.386 Round 3: 154 peptides, 26 chains. Longest chain 14 peptides. Score 0.408 Round 4: 140 peptides, 21 chains. Longest chain 16 peptides. Score 0.441 Round 5: 130 peptides, 20 chains. Longest chain 12 peptides. Score 0.418 Taking the results from Round 4 Chains 21, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6227 restraints for refining 2670 atoms. 5772 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2444 (Rfree = 0.000) for 2670 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. Cycle 27: After refmac, R = 0.2167 (Rfree = 0.000) for 2626 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 28: After refmac, R = 0.2607 (Rfree = 0.000) for 2603 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 29: After refmac, R = 0.2146 (Rfree = 0.000) for 2598 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.2364 (Rfree = 0.000) for 2588 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 4.00 Search for helices and strands: 0 residues in 0 chains, 2671 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2688 seeds are put forward Round 1: 118 peptides, 23 chains. Longest chain 11 peptides. Score 0.303 Round 2: 135 peptides, 22 chains. Longest chain 14 peptides. Score 0.401 Round 3: 120 peptides, 21 chains. Longest chain 11 peptides. Score 0.353 Round 4: 132 peptides, 21 chains. Longest chain 19 peptides. Score 0.407 Round 5: 138 peptides, 23 chains. Longest chain 9 peptides. Score 0.395 Taking the results from Round 4 Chains 21, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5806 restraints for refining 2531 atoms. 5383 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2269 (Rfree = 0.000) for 2531 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.2350 (Rfree = 0.000) for 2519 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 33: After refmac, R = 0.2322 (Rfree = 0.000) for 2507 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 34: After refmac, R = 0.2132 (Rfree = 0.000) for 2492 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2511 (Rfree = 0.000) for 2486 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.85 4.06 Search for helices and strands: 0 residues in 0 chains, 2560 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 2590 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 8 peptides. Score 0.234 Round 2: 115 peptides, 21 chains. Longest chain 11 peptides. Score 0.329 Round 3: 112 peptides, 22 chains. Longest chain 9 peptides. Score 0.294 Round 4: 128 peptides, 25 chains. Longest chain 13 peptides. Score 0.310 Round 5: 126 peptides, 23 chains. Longest chain 13 peptides. Score 0.341 Taking the results from Round 5 Chains 23, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5685 restraints for refining 2498 atoms. 5296 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2412 (Rfree = 0.000) for 2498 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 37: After refmac, R = 0.2505 (Rfree = 0.000) for 2485 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 38: After refmac, R = 0.2392 (Rfree = 0.000) for 2468 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 39: After refmac, R = 0.2158 (Rfree = 0.000) for 2456 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 40: After refmac, R = 0.2229 (Rfree = 0.000) for 2447 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.98 Search for helices and strands: 0 residues in 0 chains, 2518 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 2528 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 6 peptides. Score 0.228 Round 2: 113 peptides, 21 chains. Longest chain 12 peptides. Score 0.320 Round 3: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.305 Round 4: 114 peptides, 23 chains. Longest chain 7 peptides. Score 0.283 Round 5: 114 peptides, 21 chains. Longest chain 8 peptides. Score 0.325 Taking the results from Round 5 Chains 21, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5622 restraints for refining 2455 atoms. 5271 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2568 (Rfree = 0.000) for 2455 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 42: After refmac, R = 0.2253 (Rfree = 0.000) for 2430 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 43: After refmac, R = 0.1981 (Rfree = 0.000) for 2412 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1918 (Rfree = 0.000) for 2406 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.2217 (Rfree = 0.000) for 2405 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.97 Search for helices and strands: 0 residues in 0 chains, 2470 seeds are put forward NCS extension: 0 residues added, 2470 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.229 Round 2: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.312 Round 3: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.312 Round 4: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.370 Round 5: 89 peptides, 15 chains. Longest chain 11 peptides. Score 0.331 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 82, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3418 reflections ( 99.19 % complete ) and 5408 restraints for refining 2363 atoms. 5095 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2474 (Rfree = 0.000) for 2363 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2306 (Rfree = 0.000) for 2342 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2354 (Rfree = 0.000) for 2332 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2283 (Rfree = 0.000) for 2323 atoms. TimeTaking 27.75