Mon 24 Dec 01:02:20 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 2op5-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-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/2op5-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-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 01:02:25 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/2op5-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-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 521 and 0 Target number of residues in the AU: 521 Target solvent content: 0.5936 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-3.2-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: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 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: 73.087 3.200 Wilson plot Bfac: 49.79 12025 reflections ( 99.86 % complete ) and 0 restraints for refining 6229 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3217 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2587 (Rfree = 0.000) for 6229 atoms. Found 29 (55 requested) and removed 97 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.95 3.15 Search for helices and strands: 0 residues in 0 chains, 6323 seeds are put forward NCS extension: 0 residues added, 6323 seeds are put forward Round 1: 367 peptides, 60 chains. Longest chain 12 peptides. Score 0.474 Round 2: 424 peptides, 56 chains. Longest chain 19 peptides. Score 0.613 Round 3: 441 peptides, 52 chains. Longest chain 19 peptides. Score 0.667 Round 4: 448 peptides, 54 chains. Longest chain 29 peptides. Score 0.664 Round 5: 457 peptides, 54 chains. Longest chain 25 peptides. Score 0.677 Taking the results from Round 5 Chains 54, Residues 403, Estimated correctness of the model 60.1 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 10983 restraints for refining 5126 atoms. 9364 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2556 (Rfree = 0.000) for 5126 atoms. Found 30 (46 requested) and removed 48 (23 requested) atoms. Cycle 2: After refmac, R = 0.2351 (Rfree = 0.000) for 5077 atoms. Found 12 (45 requested) and removed 34 (22 requested) atoms. Cycle 3: After refmac, R = 0.2284 (Rfree = 0.000) for 5041 atoms. Found 9 (45 requested) and removed 29 (22 requested) atoms. Cycle 4: After refmac, R = 0.2260 (Rfree = 0.000) for 5014 atoms. Found 9 (45 requested) and removed 24 (22 requested) atoms. Cycle 5: After refmac, R = 0.2260 (Rfree = 0.000) for 4997 atoms. Found 7 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 3.25 Search for helices and strands: 0 residues in 0 chains, 5200 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 5220 seeds are put forward Round 1: 384 peptides, 56 chains. Longest chain 19 peptides. Score 0.542 Round 2: 428 peptides, 54 chains. Longest chain 18 peptides. Score 0.634 Round 3: 456 peptides, 51 chains. Longest chain 27 peptides. Score 0.694 Round 4: 460 peptides, 52 chains. Longest chain 29 peptides. Score 0.694 Round 5: 446 peptides, 50 chains. Longest chain 21 peptides. Score 0.687 Taking the results from Round 4 Chains 52, Residues 408, Estimated correctness of the model 63.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11423 restraints for refining 5127 atoms. 9843 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2493 (Rfree = 0.000) for 5127 atoms. Found 32 (46 requested) and removed 36 (23 requested) atoms. Cycle 7: After refmac, R = 0.2307 (Rfree = 0.000) for 5113 atoms. Found 21 (45 requested) and removed 25 (22 requested) atoms. Cycle 8: After refmac, R = 0.2228 (Rfree = 0.000) for 5104 atoms. Found 6 (45 requested) and removed 23 (22 requested) atoms. Cycle 9: After refmac, R = 0.2207 (Rfree = 0.000) for 5081 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. Cycle 10: After refmac, R = 0.2197 (Rfree = 0.000) for 5065 atoms. Found 6 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.04 3.25 Search for helices and strands: 0 residues in 0 chains, 5223 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 5238 seeds are put forward Round 1: 388 peptides, 55 chains. Longest chain 18 peptides. Score 0.558 Round 2: 439 peptides, 54 chains. Longest chain 21 peptides. Score 0.651 Round 3: 429 peptides, 53 chains. Longest chain 19 peptides. Score 0.642 Round 4: 452 peptides, 54 chains. Longest chain 19 peptides. Score 0.670 Round 5: 440 peptides, 57 chains. Longest chain 27 peptides. Score 0.631 Taking the results from Round 4 Chains 54, Residues 398, Estimated correctness of the model 58.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11474 restraints for refining 5127 atoms. 9936 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2441 (Rfree = 0.000) for 5127 atoms. Found 30 (46 requested) and removed 29 (23 requested) atoms. Cycle 12: After refmac, R = 0.2284 (Rfree = 0.000) for 5121 atoms. Found 9 (46 requested) and removed 25 (23 requested) atoms. Cycle 13: After refmac, R = 0.2277 (Rfree = 0.000) for 5097 atoms. Found 12 (45 requested) and removed 22 (22 requested) atoms. Cycle 14: After refmac, R = 0.2248 (Rfree = 0.000) for 5083 atoms. Found 7 (45 requested) and removed 22 (22 requested) atoms. Cycle 15: After refmac, R = 0.2198 (Rfree = 0.000) for 5067 atoms. Found 4 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 3.25 Search for helices and strands: 0 residues in 0 chains, 5185 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 5201 seeds are put forward Round 1: 351 peptides, 51 chains. Longest chain 24 peptides. Score 0.521 Round 2: 399 peptides, 54 chains. Longest chain 24 peptides. Score 0.585 Round 3: 398 peptides, 49 chains. Longest chain 25 peptides. Score 0.622 Round 4: 404 peptides, 53 chains. Longest chain 22 peptides. Score 0.602 Round 5: 419 peptides, 52 chains. Longest chain 26 peptides. Score 0.634 Taking the results from Round 5 Chains 53, Residues 367, Estimated correctness of the model 49.9 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11278 restraints for refining 5127 atoms. 9800 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2471 (Rfree = 0.000) for 5127 atoms. Found 26 (46 requested) and removed 33 (23 requested) atoms. Cycle 17: After refmac, R = 0.2394 (Rfree = 0.000) for 5108 atoms. Found 10 (45 requested) and removed 24 (22 requested) atoms. Cycle 18: After refmac, R = 0.2350 (Rfree = 0.000) for 5087 atoms. Found 11 (45 requested) and removed 22 (22 requested) atoms. Cycle 19: After refmac, R = 0.2282 (Rfree = 0.000) for 5070 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. Cycle 20: After refmac, R = 0.2284 (Rfree = 0.000) for 5054 atoms. Found 15 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 3.24 Search for helices and strands: 0 residues in 0 chains, 5222 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 5248 seeds are put forward Round 1: 355 peptides, 55 chains. Longest chain 19 peptides. Score 0.494 Round 2: 414 peptides, 55 chains. Longest chain 22 peptides. Score 0.604 Round 3: 413 peptides, 54 chains. Longest chain 29 peptides. Score 0.609 Round 4: 383 peptides, 52 chains. Longest chain 20 peptides. Score 0.573 Round 5: 367 peptides, 49 chains. Longest chain 27 peptides. Score 0.568 Taking the results from Round 3 Chains 54, Residues 359, Estimated correctness of the model 43.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11545 restraints for refining 5127 atoms. 10163 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2359 (Rfree = 0.000) for 5127 atoms. Found 21 (46 requested) and removed 25 (23 requested) atoms. Cycle 22: After refmac, R = 0.2271 (Rfree = 0.000) for 5114 atoms. Found 10 (45 requested) and removed 23 (22 requested) atoms. Cycle 23: After refmac, R = 0.2240 (Rfree = 0.000) for 5096 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. Cycle 24: After refmac, R = 0.2210 (Rfree = 0.000) for 5083 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. Cycle 25: After refmac, R = 0.2135 (Rfree = 0.000) for 5067 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 3.20 Search for helices and strands: 0 residues in 0 chains, 5176 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 5202 seeds are put forward Round 1: 344 peptides, 55 chains. Longest chain 14 peptides. Score 0.471 Round 2: 387 peptides, 54 chains. Longest chain 20 peptides. Score 0.564 Round 3: 396 peptides, 53 chains. Longest chain 21 peptides. Score 0.588 Round 4: 404 peptides, 53 chains. Longest chain 18 peptides. Score 0.602 Round 5: 392 peptides, 50 chains. Longest chain 20 peptides. Score 0.604 Taking the results from Round 5 Chains 50, Residues 342, Estimated correctness of the model 42.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11563 restraints for refining 5126 atoms. 10245 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2258 (Rfree = 0.000) for 5126 atoms. Found 24 (46 requested) and removed 25 (23 requested) atoms. Cycle 27: After refmac, R = 0.2164 (Rfree = 0.000) for 5122 atoms. Found 15 (45 requested) and removed 23 (22 requested) atoms. Cycle 28: After refmac, R = 0.2118 (Rfree = 0.000) for 5113 atoms. Found 11 (45 requested) and removed 24 (22 requested) atoms. Cycle 29: After refmac, R = 0.2060 (Rfree = 0.000) for 5098 atoms. Found 11 (45 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.2001 (Rfree = 0.000) for 5086 atoms. Found 12 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.98 3.19 Search for helices and strands: 0 residues in 0 chains, 5221 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5236 seeds are put forward Round 1: 345 peptides, 59 chains. Longest chain 14 peptides. Score 0.436 Round 2: 382 peptides, 51 chains. Longest chain 23 peptides. Score 0.579 Round 3: 377 peptides, 48 chains. Longest chain 21 peptides. Score 0.594 Round 4: 388 peptides, 50 chains. Longest chain 23 peptides. Score 0.597 Round 5: 370 peptides, 47 chains. Longest chain 23 peptides. Score 0.589 Taking the results from Round 4 Chains 50, Residues 338, Estimated correctness of the model 40.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11552 restraints for refining 5127 atoms. 10250 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2270 (Rfree = 0.000) for 5127 atoms. Found 33 (46 requested) and removed 23 (23 requested) atoms. Cycle 32: After refmac, R = 0.2152 (Rfree = 0.000) for 5129 atoms. Found 16 (46 requested) and removed 23 (23 requested) atoms. Cycle 33: After refmac, R = 0.2079 (Rfree = 0.000) for 5121 atoms. Found 5 (45 requested) and removed 22 (22 requested) atoms. Cycle 34: After refmac, R = 0.2030 (Rfree = 0.000) for 5103 atoms. Found 12 (45 requested) and removed 22 (22 requested) atoms. Cycle 35: After refmac, R = 0.1999 (Rfree = 0.000) for 5093 atoms. Found 8 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 3.21 Search for helices and strands: 0 residues in 0 chains, 5221 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5242 seeds are put forward Round 1: 311 peptides, 47 chains. Longest chain 16 peptides. Score 0.475 Round 2: 340 peptides, 47 chains. Longest chain 19 peptides. Score 0.534 Round 3: 337 peptides, 46 chains. Longest chain 22 peptides. Score 0.537 Round 4: 355 peptides, 50 chains. Longest chain 22 peptides. Score 0.537 Round 5: 347 peptides, 46 chains. Longest chain 23 peptides. Score 0.556 Taking the results from Round 5 Chains 46, Residues 301, Estimated correctness of the model 28.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11678 restraints for refining 5126 atoms. 10520 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2159 (Rfree = 0.000) for 5126 atoms. Found 17 (46 requested) and removed 26 (23 requested) atoms. Cycle 37: After refmac, R = 0.2111 (Rfree = 0.000) for 5111 atoms. Found 8 (45 requested) and removed 22 (22 requested) atoms. Cycle 38: After refmac, R = 0.2109 (Rfree = 0.000) for 5096 atoms. Found 15 (45 requested) and removed 22 (22 requested) atoms. Cycle 39: After refmac, R = 0.2056 (Rfree = 0.000) for 5089 atoms. Found 8 (45 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.2057 (Rfree = 0.000) for 5074 atoms. Found 18 (45 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.00 3.21 Search for helices and strands: 0 residues in 0 chains, 5239 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 5264 seeds are put forward Round 1: 303 peptides, 51 chains. Longest chain 15 peptides. Score 0.420 Round 2: 351 peptides, 51 chains. Longest chain 22 peptides. Score 0.521 Round 3: 336 peptides, 51 chains. Longest chain 20 peptides. Score 0.491 Round 4: 349 peptides, 50 chains. Longest chain 21 peptides. Score 0.526 Round 5: 351 peptides, 45 chains. Longest chain 24 peptides. Score 0.572 Taking the results from Round 5 Chains 45, Residues 306, Estimated correctness of the model 33.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11665 restraints for refining 5127 atoms. 10486 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2183 (Rfree = 0.000) for 5127 atoms. Found 28 (46 requested) and removed 24 (23 requested) atoms. Cycle 42: After refmac, R = 0.2060 (Rfree = 0.000) for 5128 atoms. Found 13 (46 requested) and removed 23 (23 requested) atoms. Cycle 43: After refmac, R = 0.2054 (Rfree = 0.000) for 5117 atoms. Found 16 (45 requested) and removed 22 (22 requested) atoms. Cycle 44: After refmac, R = 0.1972 (Rfree = 0.000) for 5109 atoms. Found 11 (45 requested) and removed 22 (22 requested) atoms. Cycle 45: After refmac, R = 0.1962 (Rfree = 0.000) for 5098 atoms. Found 9 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 3.20 Search for helices and strands: 0 residues in 0 chains, 5212 seeds are put forward NCS extension: 45 residues added (0 deleted due to clashes), 5257 seeds are put forward Round 1: 277 peptides, 44 chains. Longest chain 22 peptides. Score 0.430 Round 2: 295 peptides, 43 chains. Longest chain 23 peptides. Score 0.479 Round 3: 310 peptides, 41 chains. Longest chain 23 peptides. Score 0.528 Round 4: 328 peptides, 43 chains. Longest chain 24 peptides. Score 0.545 Round 5: 304 peptides, 40 chains. Longest chain 24 peptides. Score 0.525 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 285, Estimated correctness of the model 25.4 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2op5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12025 reflections ( 99.86 % complete ) and 11643 restraints for refining 5127 atoms. 10516 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2088 (Rfree = 0.000) for 5127 atoms. Found 0 (46 requested) and removed 10 (23 requested) atoms. Cycle 47: After refmac, R = 0.2042 (Rfree = 0.000) for 5114 atoms. Found 0 (45 requested) and removed 2 (22 requested) atoms. Cycle 48: After refmac, R = 0.2091 (Rfree = 0.000) for 5110 atoms. Found 0 (45 requested) and removed 4 (22 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2022 (Rfree = 0.000) for 5102 atoms. TimeTaking 62.87