null Sun 23 Dec 22:22:59 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 2op5-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2op5-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2op5-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-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/2op5-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-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 22:23:08 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/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-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 506 and 0 Target number of residues in the AU: 506 Target solvent content: 0.6053 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: 2op5-3.4-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: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 54.52 10070 reflections ( 99.83 % complete ) and 0 restraints for refining 6210 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3263 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2140 (Rfree = 0.000) for 6210 atoms. Found 32 (46 requested) and removed 50 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.41 Search for helices and strands: 0 residues in 0 chains, 6310 seeds are put forward NCS extension: 0 residues added, 6310 seeds are put forward Round 1: 345 peptides, 57 chains. Longest chain 16 peptides. Score 0.455 Round 2: 405 peptides, 56 chains. Longest chain 17 peptides. Score 0.580 Round 3: 433 peptides, 57 chains. Longest chain 23 peptides. Score 0.620 Round 4: 414 peptides, 53 chains. Longest chain 28 peptides. Score 0.618 Round 5: 408 peptides, 53 chains. Longest chain 18 peptides. Score 0.608 Taking the results from Round 3 Chains 57, Residues 376, Estimated correctness of the model 35.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11216 restraints for refining 5105 atoms. 9732 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2693 (Rfree = 0.000) for 5105 atoms. Found 35 (38 requested) and removed 25 (19 requested) atoms. Cycle 2: After refmac, R = 0.2576 (Rfree = 0.000) for 5081 atoms. Found 10 (38 requested) and removed 26 (19 requested) atoms. Cycle 3: After refmac, R = 0.2537 (Rfree = 0.000) for 5045 atoms. Found 10 (38 requested) and removed 20 (19 requested) atoms. Cycle 4: After refmac, R = 0.2491 (Rfree = 0.000) for 5027 atoms. Found 2 (38 requested) and removed 19 (19 requested) atoms. Cycle 5: After refmac, R = 0.2475 (Rfree = 0.000) for 5003 atoms. Found 2 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.41 Search for helices and strands: 0 residues in 0 chains, 5161 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5182 seeds are put forward Round 1: 342 peptides, 50 chains. Longest chain 22 peptides. Score 0.512 Round 2: 392 peptides, 51 chains. Longest chain 16 peptides. Score 0.596 Round 3: 403 peptides, 51 chains. Longest chain 21 peptides. Score 0.615 Round 4: 394 peptides, 52 chains. Longest chain 28 peptides. Score 0.592 Round 5: 418 peptides, 52 chains. Longest chain 21 peptides. Score 0.632 Taking the results from Round 5 Chains 52, Residues 366, Estimated correctness of the model 38.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11433 restraints for refining 5032 atoms. 10021 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2813 (Rfree = 0.000) for 5032 atoms. Found 33 (37 requested) and removed 24 (18 requested) atoms. Cycle 7: After refmac, R = 0.2704 (Rfree = 0.000) for 5036 atoms. Found 11 (38 requested) and removed 21 (19 requested) atoms. Cycle 8: After refmac, R = 0.2719 (Rfree = 0.000) for 5024 atoms. Found 5 (37 requested) and removed 18 (18 requested) atoms. Cycle 9: After refmac, R = 0.2620 (Rfree = 0.000) for 5007 atoms. Found 6 (37 requested) and removed 18 (18 requested) atoms. Cycle 10: After refmac, R = 0.2669 (Rfree = 0.000) for 4991 atoms. Found 5 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.43 Search for helices and strands: 0 residues in 0 chains, 5110 seeds are put forward NCS extension: 17 residues added (6 deleted due to clashes), 5127 seeds are put forward Round 1: 384 peptides, 58 chains. Longest chain 23 peptides. Score 0.525 Round 2: 417 peptides, 51 chains. Longest chain 26 peptides. Score 0.638 Round 3: 402 peptides, 52 chains. Longest chain 23 peptides. Score 0.606 Round 4: 415 peptides, 55 chains. Longest chain 28 peptides. Score 0.605 Round 5: 404 peptides, 46 chains. Longest chain 30 peptides. Score 0.653 Taking the results from Round 5 Chains 46, Residues 358, Estimated correctness of the model 45.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11519 restraints for refining 5049 atoms. 10133 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2784 (Rfree = 0.000) for 5049 atoms. Found 19 (38 requested) and removed 26 (19 requested) atoms. Cycle 12: After refmac, R = 0.2663 (Rfree = 0.000) for 5036 atoms. Found 8 (38 requested) and removed 22 (19 requested) atoms. Cycle 13: After refmac, R = 0.2606 (Rfree = 0.000) for 5017 atoms. Found 7 (37 requested) and removed 19 (18 requested) atoms. Cycle 14: After refmac, R = 0.2586 (Rfree = 0.000) for 5003 atoms. Found 5 (37 requested) and removed 18 (18 requested) atoms. Cycle 15: After refmac, R = 0.2542 (Rfree = 0.000) for 4989 atoms. Found 2 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.38 Search for helices and strands: 0 residues in 0 chains, 5112 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 5129 seeds are put forward Round 1: 366 peptides, 51 chains. Longest chain 22 peptides. Score 0.550 Round 2: 390 peptides, 48 chains. Longest chain 22 peptides. Score 0.616 Round 3: 413 peptides, 48 chains. Longest chain 33 peptides. Score 0.652 Round 4: 397 peptides, 50 chains. Longest chain 23 peptides. Score 0.612 Round 5: 414 peptides, 47 chains. Longest chain 25 peptides. Score 0.661 Taking the results from Round 5 Chains 48, Residues 367, Estimated correctness of the model 47.3 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11480 restraints for refining 5059 atoms. 10015 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2839 (Rfree = 0.000) for 5059 atoms. Found 22 (38 requested) and removed 29 (19 requested) atoms. Cycle 17: After refmac, R = 0.2705 (Rfree = 0.000) for 5045 atoms. Found 8 (38 requested) and removed 21 (19 requested) atoms. Cycle 18: After refmac, R = 0.2644 (Rfree = 0.000) for 5031 atoms. Found 4 (37 requested) and removed 19 (18 requested) atoms. Cycle 19: After refmac, R = 0.2586 (Rfree = 0.000) for 5016 atoms. Found 3 (37 requested) and removed 18 (18 requested) atoms. Cycle 20: After refmac, R = 0.2562 (Rfree = 0.000) for 4998 atoms. Found 4 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 5123 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 5145 seeds are put forward Round 1: 333 peptides, 55 chains. Longest chain 13 peptides. Score 0.448 Round 2: 362 peptides, 49 chains. Longest chain 22 peptides. Score 0.559 Round 3: 380 peptides, 52 chains. Longest chain 18 peptides. Score 0.567 Round 4: 390 peptides, 56 chains. Longest chain 22 peptides. Score 0.553 Round 5: 371 peptides, 50 chains. Longest chain 23 peptides. Score 0.567 Taking the results from Round 5 Chains 50, Residues 321, Estimated correctness of the model 17.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 12050 restraints for refining 5105 atoms. 10816 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2661 (Rfree = 0.000) for 5105 atoms. Found 17 (38 requested) and removed 25 (19 requested) atoms. Cycle 22: After refmac, R = 0.2592 (Rfree = 0.000) for 5090 atoms. Found 14 (38 requested) and removed 19 (19 requested) atoms. Cycle 23: After refmac, R = 0.2528 (Rfree = 0.000) for 5083 atoms. Found 1 (38 requested) and removed 20 (19 requested) atoms. Cycle 24: After refmac, R = 0.2506 (Rfree = 0.000) for 5063 atoms. Found 1 (38 requested) and removed 19 (19 requested) atoms. Cycle 25: After refmac, R = 0.2464 (Rfree = 0.000) for 5042 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.38 Search for helices and strands: 0 residues in 0 chains, 5175 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 5202 seeds are put forward Round 1: 342 peptides, 54 chains. Longest chain 14 peptides. Score 0.476 Round 2: 360 peptides, 47 chains. Longest chain 28 peptides. Score 0.572 Round 3: 372 peptides, 52 chains. Longest chain 15 peptides. Score 0.553 Round 4: 374 peptides, 53 chains. Longest chain 28 peptides. Score 0.548 Round 5: 375 peptides, 51 chains. Longest chain 28 peptides. Score 0.566 Taking the results from Round 2 Chains 47, Residues 313, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11883 restraints for refining 5095 atoms. 10678 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2607 (Rfree = 0.000) for 5095 atoms. Found 17 (38 requested) and removed 20 (19 requested) atoms. Cycle 27: After refmac, R = 0.2504 (Rfree = 0.000) for 5088 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. Cycle 28: After refmac, R = 0.2461 (Rfree = 0.000) for 5071 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. Cycle 29: After refmac, R = 0.2421 (Rfree = 0.000) for 5057 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. Cycle 30: After refmac, R = 0.2399 (Rfree = 0.000) for 5044 atoms. Found 3 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.40 Search for helices and strands: 0 residues in 0 chains, 5200 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 5228 seeds are put forward Round 1: 335 peptides, 55 chains. Longest chain 14 peptides. Score 0.452 Round 2: 360 peptides, 51 chains. Longest chain 17 peptides. Score 0.538 Round 3: 356 peptides, 45 chains. Longest chain 17 peptides. Score 0.581 Round 4: 363 peptides, 50 chains. Longest chain 18 peptides. Score 0.552 Round 5: 357 peptides, 42 chains. Longest chain 20 peptides. Score 0.606 Taking the results from Round 5 Chains 42, Residues 315, Estimated correctness of the model 30.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11915 restraints for refining 5106 atoms. 10697 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2496 (Rfree = 0.000) for 5106 atoms. Found 23 (38 requested) and removed 22 (19 requested) atoms. Cycle 32: After refmac, R = 0.2350 (Rfree = 0.000) for 5099 atoms. Found 10 (38 requested) and removed 20 (19 requested) atoms. Cycle 33: After refmac, R = 0.2313 (Rfree = 0.000) for 5086 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. Cycle 34: After refmac, R = 0.2263 (Rfree = 0.000) for 5076 atoms. Found 2 (38 requested) and removed 19 (19 requested) atoms. Cycle 35: After refmac, R = 0.2231 (Rfree = 0.000) for 5058 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.38 Search for helices and strands: 0 residues in 0 chains, 5185 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 5196 seeds are put forward Round 1: 277 peptides, 51 chains. Longest chain 10 peptides. Score 0.359 Round 2: 342 peptides, 50 chains. Longest chain 19 peptides. Score 0.512 Round 3: 355 peptides, 52 chains. Longest chain 19 peptides. Score 0.520 Round 4: 339 peptides, 49 chains. Longest chain 13 peptides. Score 0.515 Round 5: 347 peptides, 48 chains. Longest chain 17 peptides. Score 0.539 Taking the results from Round 5 Chains 48, Residues 299, Estimated correctness of the model 7.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11896 restraints for refining 5106 atoms. 10748 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2444 (Rfree = 0.000) for 5106 atoms. Found 22 (38 requested) and removed 19 (19 requested) atoms. Cycle 37: After refmac, R = 0.2281 (Rfree = 0.000) for 5108 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. Cycle 38: After refmac, R = 0.2231 (Rfree = 0.000) for 5091 atoms. Found 12 (38 requested) and removed 19 (19 requested) atoms. Cycle 39: After refmac, R = 0.2200 (Rfree = 0.000) for 5082 atoms. Found 2 (38 requested) and removed 19 (19 requested) atoms. Cycle 40: After refmac, R = 0.2179 (Rfree = 0.000) for 5064 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 5206 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5221 seeds are put forward Round 1: 311 peptides, 57 chains. Longest chain 16 peptides. Score 0.379 Round 2: 334 peptides, 50 chains. Longest chain 14 peptides. Score 0.496 Round 3: 324 peptides, 51 chains. Longest chain 13 peptides. Score 0.466 Round 4: 332 peptides, 46 chains. Longest chain 17 peptides. Score 0.527 Round 5: 320 peptides, 49 chains. Longest chain 12 peptides. Score 0.476 Taking the results from Round 4 Chains 46, Residues 286, Estimated correctness of the model 3.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 12062 restraints for refining 5106 atoms. 10964 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2441 (Rfree = 0.000) for 5106 atoms. Found 23 (38 requested) and removed 19 (19 requested) atoms. Cycle 42: After refmac, R = 0.2285 (Rfree = 0.000) for 5108 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. Cycle 43: After refmac, R = 0.2255 (Rfree = 0.000) for 5094 atoms. Found 11 (38 requested) and removed 19 (19 requested) atoms. Cycle 44: After refmac, R = 0.2150 (Rfree = 0.000) for 5084 atoms. Found 3 (38 requested) and removed 19 (19 requested) atoms. Cycle 45: After refmac, R = 0.2184 (Rfree = 0.000) for 5066 atoms. Found 5 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 5194 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 5212 seeds are put forward Round 1: 278 peptides, 50 chains. Longest chain 16 peptides. Score 0.372 Round 2: 306 peptides, 49 chains. Longest chain 14 peptides. Score 0.446 Round 3: 328 peptides, 47 chains. Longest chain 23 peptides. Score 0.510 Round 4: 290 peptides, 44 chains. Longest chain 16 peptides. Score 0.459 Round 5: 297 peptides, 42 chains. Longest chain 23 peptides. Score 0.492 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 47, Residues 281, 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 2op5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10070 reflections ( 99.83 % complete ) and 12002 restraints for refining 5106 atoms. 10925 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2273 (Rfree = 0.000) for 5106 atoms. Found 0 (38 requested) and removed 8 (19 requested) atoms. Cycle 47: After refmac, R = 0.2178 (Rfree = 0.000) for 5097 atoms. Found 0 (38 requested) and removed 8 (19 requested) atoms. Cycle 48: After refmac, R = 0.2155 (Rfree = 0.000) for 5087 atoms. Found 0 (38 requested) and removed 2 (19 requested) atoms. Cycle 49: After refmac, R = 0.2220 (Rfree = 0.000) for 5085 atoms. Found 0 (38 requested) and removed 4 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:32:27 GMT 2018 Job finished. TimeTaking 69.48 Used memory is bytes: 6010784