Sun 23 Dec 22:22:41 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 2opl-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opl-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opl-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-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/2opl-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-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 22:22:50 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/2opl-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-4.0-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 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-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: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-4.0-parrot-hancs.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 3327 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3462 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3391 (Rfree = 0.000) for 3327 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 4.05 Search for helices and strands: 0 residues in 0 chains, 3395 seeds are put forward NCS extension: 0 residues added, 3395 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 8 peptides. Score 0.256 Round 2: 142 peptides, 26 chains. Longest chain 10 peptides. Score 0.355 Round 3: 175 peptides, 28 chains. Longest chain 11 peptides. Score 0.459 Round 4: 194 peptides, 32 chains. Longest chain 15 peptides. Score 0.465 Round 5: 186 peptides, 30 chains. Longest chain 24 peptides. Score 0.468 Taking the results from Round 5 Chains 30, Residues 156, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6511 restraints for refining 2701 atoms. 5901 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3015 (Rfree = 0.000) for 2701 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 2: After refmac, R = 0.2954 (Rfree = 0.000) for 2644 atoms. Found 12 (12 requested) and removed 29 (6 requested) atoms. Cycle 3: After refmac, R = 0.2839 (Rfree = 0.000) for 2597 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 4: After refmac, R = 0.2645 (Rfree = 0.000) for 2569 atoms. Found 8 (12 requested) and removed 10 (6 requested) atoms. Cycle 5: After refmac, R = 0.2610 (Rfree = 0.000) for 2550 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2649 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2670 seeds are put forward Round 1: 142 peptides, 30 chains. Longest chain 9 peptides. Score 0.277 Round 2: 177 peptides, 29 chains. Longest chain 12 peptides. Score 0.449 Round 3: 185 peptides, 31 chains. Longest chain 12 peptides. Score 0.447 Round 4: 187 peptides, 31 chains. Longest chain 14 peptides. Score 0.455 Round 5: 182 peptides, 30 chains. Longest chain 12 peptides. Score 0.452 Taking the results from Round 4 Chains 31, Residues 156, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5848 restraints for refining 2582 atoms. 5192 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2364 (Rfree = 0.000) for 2582 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 7: After refmac, R = 0.2488 (Rfree = 0.000) for 2547 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.2281 (Rfree = 0.000) for 2523 atoms. Found 11 (12 requested) and removed 17 (6 requested) atoms. Cycle 9: After refmac, R = 0.2227 (Rfree = 0.000) for 2503 atoms. Found 7 (11 requested) and removed 14 (5 requested) atoms. Cycle 10: After refmac, R = 0.2126 (Rfree = 0.000) for 2491 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.92 Search for helices and strands: 0 residues in 0 chains, 2598 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2614 seeds are put forward Round 1: 139 peptides, 26 chains. Longest chain 12 peptides. Score 0.341 Round 2: 177 peptides, 27 chains. Longest chain 12 peptides. Score 0.484 Round 3: 184 peptides, 28 chains. Longest chain 21 peptides. Score 0.494 Round 4: 184 peptides, 28 chains. Longest chain 14 peptides. Score 0.494 Round 5: 186 peptides, 26 chains. Longest chain 21 peptides. Score 0.534 Taking the results from Round 5 Chains 27, Residues 160, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6269 restraints for refining 2702 atoms. 5598 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2220 (Rfree = 0.000) for 2702 atoms. Found 6 (12 requested) and removed 19 (6 requested) atoms. Cycle 12: After refmac, R = 0.2300 (Rfree = 0.000) for 2663 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 13: After refmac, R = 0.1873 (Rfree = 0.000) for 2627 atoms. Found 4 (12 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.1690 (Rfree = 0.000) for 2598 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.1583 (Rfree = 0.000) for 2584 atoms. Found 0 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 4.03 Search for helices and strands: 0 residues in 0 chains, 2646 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 2677 seeds are put forward Round 1: 143 peptides, 31 chains. Longest chain 10 peptides. Score 0.262 Round 2: 161 peptides, 30 chains. Longest chain 9 peptides. Score 0.364 Round 3: 172 peptides, 31 chains. Longest chain 10 peptides. Score 0.393 Round 4: 153 peptides, 26 chains. Longest chain 11 peptides. Score 0.403 Round 5: 155 peptides, 25 chains. Longest chain 13 peptides. Score 0.430 Taking the results from Round 5 Chains 25, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6508 restraints for refining 2667 atoms. 6013 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2497 (Rfree = 0.000) for 2667 atoms. Found 12 (12 requested) and removed 30 (6 requested) atoms. Cycle 17: After refmac, R = 0.2226 (Rfree = 0.000) for 2618 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. Cycle 18: After refmac, R = 0.2353 (Rfree = 0.000) for 2598 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.2223 (Rfree = 0.000) for 2586 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.2371 (Rfree = 0.000) for 2575 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2637 seeds are put forward NCS extension: 0 residues added, 2637 seeds are put forward Round 1: 128 peptides, 29 chains. Longest chain 8 peptides. Score 0.228 Round 2: 160 peptides, 31 chains. Longest chain 9 peptides. Score 0.341 Round 3: 170 peptides, 29 chains. Longest chain 10 peptides. Score 0.421 Round 4: 157 peptides, 28 chains. Longest chain 11 peptides. Score 0.384 Round 5: 158 peptides, 26 chains. Longest chain 11 peptides. Score 0.425 Taking the results from Round 5 Chains 26, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3418 reflections ( 99.19 % complete ) and 6168 restraints for refining 2581 atoms. 5666 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2512 (Rfree = 0.000) for 2581 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 22: After refmac, R = 0.2212 (Rfree = 0.000) for 2560 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.1686 (Rfree = 0.000) for 2546 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.1546 (Rfree = 0.000) for 2529 atoms. Found 2 (12 requested) and removed 14 (6 requested) atoms. Cycle 25: After refmac, R = 0.1744 (Rfree = 0.000) for 2512 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.99 Search for helices and strands: 0 residues in 0 chains, 2590 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2603 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 7 peptides. Score 0.243 Round 2: 143 peptides, 29 chains. Longest chain 8 peptides. Score 0.301 Round 3: 158 peptides, 26 chains. Longest chain 13 peptides. Score 0.425 Round 4: 153 peptides, 24 chains. Longest chain 11 peptides. Score 0.440 Round 5: 145 peptides, 24 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 4 Chains 24, Residues 129, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6216 restraints for refining 2677 atoms. 5684 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2306 (Rfree = 0.000) for 2677 atoms. Found 11 (12 requested) and removed 24 (6 requested) atoms. Cycle 27: After refmac, R = 0.2297 (Rfree = 0.000) for 2651 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 28: After refmac, R = 0.2462 (Rfree = 0.000) for 2629 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.2046 (Rfree = 0.000) for 2610 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 30: After refmac, R = 0.2162 (Rfree = 0.000) for 2597 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.97 Search for helices and strands: 0 residues in 0 chains, 2676 seeds are put forward NCS extension: 0 residues added, 2676 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 9 peptides. Score 0.259 Round 2: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.337 Round 3: 137 peptides, 23 chains. Longest chain 11 peptides. Score 0.391 Round 4: 135 peptides, 22 chains. Longest chain 14 peptides. Score 0.401 Round 5: 136 peptides, 24 chains. Longest chain 11 peptides. Score 0.367 Taking the results from Round 4 Chains 22, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 6278 restraints for refining 2620 atoms. 5848 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2262 (Rfree = 0.000) for 2620 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 32: After refmac, R = 0.2284 (Rfree = 0.000) for 2591 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 33: After refmac, R = 0.2057 (Rfree = 0.000) for 2574 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 34: After refmac, R = 0.2327 (Rfree = 0.000) for 2564 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 35: After refmac, R = 0.2089 (Rfree = 0.000) for 2555 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2623 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2639 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 9 peptides. Score 0.268 Round 2: 124 peptides, 25 chains. Longest chain 11 peptides. Score 0.291 Round 3: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.315 Round 4: 113 peptides, 21 chains. Longest chain 11 peptides. Score 0.320 Round 5: 106 peptides, 20 chains. Longest chain 11 peptides. Score 0.307 Taking the results from Round 4 Chains 21, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5930 restraints for refining 2490 atoms. 5583 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2651 (Rfree = 0.000) for 2490 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 37: After refmac, R = 0.2214 (Rfree = 0.000) for 2470 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 38: After refmac, R = 0.2317 (Rfree = 0.000) for 2459 atoms. Found 9 (11 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2220 (Rfree = 0.000) for 2452 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.1845 (Rfree = 0.000) for 2443 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 4.01 Search for helices and strands: 0 residues in 0 chains, 2509 seeds are put forward NCS extension: 0 residues added, 2509 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 8 peptides. Score 0.212 Round 2: 74 peptides, 16 chains. Longest chain 8 peptides. Score 0.228 Round 3: 84 peptides, 17 chains. Longest chain 9 peptides. Score 0.260 Round 4: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.274 Round 5: 85 peptides, 17 chains. Longest chain 10 peptides. Score 0.265 Taking the results from Round 4 Chains 18, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3418 reflections ( 99.19 % complete ) and 5557 restraints for refining 2353 atoms. 5283 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2336 (Rfree = 0.000) for 2353 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.2379 (Rfree = 0.000) for 2345 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2290 (Rfree = 0.000) for 2337 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2263 (Rfree = 0.000) for 2333 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 45: After refmac, R = 0.2121 (Rfree = 0.000) for 2327 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 2383 seeds are put forward NCS extension: 0 residues added, 2383 seeds are put forward Round 1: 68 peptides, 16 chains. Longest chain 6 peptides. Score 0.192 Round 2: 80 peptides, 16 chains. Longest chain 7 peptides. Score 0.261 Round 3: 87 peptides, 17 chains. Longest chain 7 peptides. Score 0.276 Round 4: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.285 Round 5: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.285 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 65, 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 5264 restraints for refining 2254 atoms. 5019 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2275 (Rfree = 0.000) for 2254 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2080 (Rfree = 0.000) for 2229 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2378 (Rfree = 0.000) for 2219 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2244 (Rfree = 0.000) for 2207 atoms. TimeTaking 46.98