Sun 23 Dec 23:59:16 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 2afb-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-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/2afb-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-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 ============================================================ Sun 23 Dec 23:59:21 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/2afb-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-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 506 and 0 Target number of residues in the AU: 506 Target solvent content: 0.6266 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-3.4-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.4-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: 97.203 3.400 Wilson plot Bfac: 64.64 10354 reflections ( 99.53 % complete ) and 0 restraints for refining 6220 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3093 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3100 (Rfree = 0.000) for 6220 atoms. Found 46 (46 requested) and removed 36 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 6341 seeds are put forward NCS extension: 0 residues added, 6341 seeds are put forward Round 1: 248 peptides, 50 chains. Longest chain 12 peptides. Score 0.292 Round 2: 368 peptides, 61 chains. Longest chain 19 peptides. Score 0.455 Round 3: 366 peptides, 51 chains. Longest chain 20 peptides. Score 0.535 Round 4: 395 peptides, 51 chains. Longest chain 21 peptides. Score 0.586 Round 5: 411 peptides, 53 chains. Longest chain 26 peptides. Score 0.598 Taking the results from Round 5 Chains 57, Residues 358, Estimated correctness of the model 28.0 % 6 chains (50 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11037 restraints for refining 5104 atoms. 9505 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2786 (Rfree = 0.000) for 5104 atoms. Found 38 (38 requested) and removed 50 (19 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2667 (Rfree = 0.000) for 5002 atoms. Found 30 (38 requested) and removed 29 (19 requested) atoms. Cycle 3: After refmac, R = 0.2620 (Rfree = 0.000) for 4967 atoms. Found 34 (37 requested) and removed 35 (18 requested) atoms. Cycle 4: After refmac, R = 0.2562 (Rfree = 0.000) for 4936 atoms. Found 29 (37 requested) and removed 24 (18 requested) atoms. Cycle 5: After refmac, R = 0.2491 (Rfree = 0.000) for 4909 atoms. Found 33 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 5094 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5114 seeds are put forward Round 1: 349 peptides, 54 chains. Longest chain 21 peptides. Score 0.478 Round 2: 379 peptides, 51 chains. Longest chain 25 peptides. Score 0.559 Round 3: 399 peptides, 46 chains. Longest chain 27 peptides. Score 0.629 Round 4: 398 peptides, 51 chains. Longest chain 23 peptides. Score 0.591 Round 5: 404 peptides, 51 chains. Longest chain 27 peptides. Score 0.601 Taking the results from Round 3 Chains 49, Residues 353, Estimated correctness of the model 37.9 % 9 chains (86 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 10366 restraints for refining 4985 atoms. 8724 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2572 (Rfree = 0.000) for 4985 atoms. Found 29 (37 requested) and removed 34 (18 requested) atoms. Cycle 7: After refmac, R = 0.2452 (Rfree = 0.000) for 4924 atoms. Found 32 (37 requested) and removed 28 (18 requested) atoms. Cycle 8: After refmac, R = 0.2399 (Rfree = 0.000) for 4894 atoms. Found 20 (37 requested) and removed 30 (18 requested) atoms. Cycle 9: After refmac, R = 0.2335 (Rfree = 0.000) for 4863 atoms. Found 21 (36 requested) and removed 26 (18 requested) atoms. Cycle 10: After refmac, R = 0.2073 (Rfree = 0.000) for 4841 atoms. Found 15 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 5024 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 5056 seeds are put forward Round 1: 386 peptides, 61 chains. Longest chain 16 peptides. Score 0.491 Round 2: 425 peptides, 55 chains. Longest chain 27 peptides. Score 0.606 Round 3: 434 peptides, 54 chains. Longest chain 22 peptides. Score 0.627 Round 4: 406 peptides, 50 chains. Longest chain 22 peptides. Score 0.611 Round 5: 411 peptides, 53 chains. Longest chain 20 peptides. Score 0.598 Taking the results from Round 3 Chains 57, Residues 380, Estimated correctness of the model 37.2 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 10542 restraints for refining 5023 atoms. 8879 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2524 (Rfree = 0.000) for 5023 atoms. Found 31 (37 requested) and removed 41 (18 requested) atoms. Cycle 12: After refmac, R = 0.2488 (Rfree = 0.000) for 4977 atoms. Found 37 (37 requested) and removed 26 (18 requested) atoms. Cycle 13: After refmac, R = 0.2449 (Rfree = 0.000) for 4966 atoms. Found 23 (37 requested) and removed 26 (18 requested) atoms. Cycle 14: After refmac, R = 0.2140 (Rfree = 0.000) for 4945 atoms. Found 17 (37 requested) and removed 20 (18 requested) atoms. Cycle 15: After refmac, R = 0.2091 (Rfree = 0.000) for 4931 atoms. Found 8 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 5088 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 5101 seeds are put forward Round 1: 350 peptides, 57 chains. Longest chain 20 peptides. Score 0.454 Round 2: 404 peptides, 54 chains. Longest chain 22 peptides. Score 0.579 Round 3: 402 peptides, 51 chains. Longest chain 22 peptides. Score 0.598 Round 4: 402 peptides, 53 chains. Longest chain 22 peptides. Score 0.583 Round 5: 400 peptides, 52 chains. Longest chain 22 peptides. Score 0.587 Taking the results from Round 3 Chains 51, Residues 351, Estimated correctness of the model 28.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11391 restraints for refining 5086 atoms. 9948 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2633 (Rfree = 0.000) for 5086 atoms. Found 37 (38 requested) and removed 47 (19 requested) atoms. Cycle 17: After refmac, R = 0.2541 (Rfree = 0.000) for 5056 atoms. Found 38 (38 requested) and removed 29 (19 requested) atoms. Cycle 18: After refmac, R = 0.2431 (Rfree = 0.000) for 5041 atoms. Found 24 (38 requested) and removed 26 (19 requested) atoms. Cycle 19: After refmac, R = 0.2088 (Rfree = 0.000) for 5020 atoms. Found 12 (38 requested) and removed 23 (19 requested) atoms. Cycle 20: After refmac, R = 0.2048 (Rfree = 0.000) for 5003 atoms. Found 6 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 5178 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 5211 seeds are put forward Round 1: 368 peptides, 61 chains. Longest chain 16 peptides. Score 0.455 Round 2: 431 peptides, 56 chains. Longest chain 22 peptides. Score 0.608 Round 3: 429 peptides, 50 chains. Longest chain 31 peptides. Score 0.646 Round 4: 427 peptides, 54 chains. Longest chain 24 peptides. Score 0.616 Round 5: 435 peptides, 56 chains. Longest chain 23 peptides. Score 0.614 Taking the results from Round 3 Chains 53, Residues 379, Estimated correctness of the model 43.0 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 10889 restraints for refining 5103 atoms. 9244 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2445 (Rfree = 0.000) for 5103 atoms. Found 27 (38 requested) and removed 27 (19 requested) atoms. Cycle 22: After refmac, R = 0.2420 (Rfree = 0.000) for 5074 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. Cycle 23: After refmac, R = 0.2293 (Rfree = 0.000) for 5073 atoms. Found 32 (38 requested) and removed 25 (19 requested) atoms. Cycle 24: After refmac, R = 0.2244 (Rfree = 0.000) for 5063 atoms. Found 31 (38 requested) and removed 23 (19 requested) atoms. Cycle 25: After refmac, R = 0.2154 (Rfree = 0.000) for 5058 atoms. Found 29 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 5238 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5254 seeds are put forward Round 1: 334 peptides, 56 chains. Longest chain 13 peptides. Score 0.429 Round 2: 401 peptides, 61 chains. Longest chain 19 peptides. Score 0.519 Round 3: 392 peptides, 55 chains. Longest chain 22 peptides. Score 0.550 Round 4: 422 peptides, 57 chains. Longest chain 20 peptides. Score 0.586 Round 5: 411 peptides, 56 chains. Longest chain 17 peptides. Score 0.575 Taking the results from Round 4 Chains 59, Residues 365, Estimated correctness of the model 24.0 % 9 chains (55 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 10980 restraints for refining 5106 atoms. 9390 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2349 (Rfree = 0.000) for 5106 atoms. Found 29 (38 requested) and removed 26 (19 requested) atoms. Cycle 27: After refmac, R = 0.2136 (Rfree = 0.000) for 5091 atoms. Found 11 (38 requested) and removed 21 (19 requested) atoms. Cycle 28: After refmac, R = 0.2053 (Rfree = 0.000) for 5071 atoms. Found 13 (38 requested) and removed 21 (19 requested) atoms. Cycle 29: After refmac, R = 0.2026 (Rfree = 0.000) for 5060 atoms. Found 11 (38 requested) and removed 21 (19 requested) atoms. Cycle 30: After refmac, R = 0.2013 (Rfree = 0.000) for 5049 atoms. Found 13 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 5218 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5230 seeds are put forward Round 1: 372 peptides, 58 chains. Longest chain 20 peptides. Score 0.489 Round 2: 405 peptides, 52 chains. Longest chain 22 peptides. Score 0.595 Round 3: 404 peptides, 51 chains. Longest chain 22 peptides. Score 0.601 Round 4: 423 peptides, 52 chains. Longest chain 21 peptides. Score 0.624 Round 5: 427 peptides, 58 chains. Longest chain 19 peptides. Score 0.587 Taking the results from Round 4 Chains 57, Residues 371, Estimated correctness of the model 36.3 % 9 chains (77 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 10834 restraints for refining 5106 atoms. 9167 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2584 (Rfree = 0.000) for 5106 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 32: After refmac, R = 0.2622 (Rfree = 0.000) for 5085 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 33: After refmac, R = 0.2408 (Rfree = 0.000) for 5066 atoms. Found 30 (38 requested) and removed 24 (19 requested) atoms. Cycle 34: After refmac, R = 0.2457 (Rfree = 0.000) for 5056 atoms. Found 27 (38 requested) and removed 26 (19 requested) atoms. Cycle 35: After refmac, R = 0.2354 (Rfree = 0.000) for 5039 atoms. Found 38 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 5215 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 5246 seeds are put forward Round 1: 322 peptides, 56 chains. Longest chain 14 peptides. Score 0.404 Round 2: 370 peptides, 54 chains. Longest chain 18 peptides. Score 0.518 Round 3: 396 peptides, 54 chains. Longest chain 26 peptides. Score 0.565 Round 4: 402 peptides, 58 chains. Longest chain 19 peptides. Score 0.544 Round 5: 392 peptides, 51 chains. Longest chain 22 peptides. Score 0.581 Taking the results from Round 5 Chains 51, Residues 341, Estimated correctness of the model 22.4 % 5 chains (30 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11395 restraints for refining 5106 atoms. 10000 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2354 (Rfree = 0.000) for 5106 atoms. Found 31 (38 requested) and removed 21 (19 requested) atoms. Cycle 37: After refmac, R = 0.2401 (Rfree = 0.000) for 5096 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. Cycle 38: After refmac, R = 0.2267 (Rfree = 0.000) for 5093 atoms. Found 38 (38 requested) and removed 22 (19 requested) atoms. Cycle 39: After refmac, R = 0.2319 (Rfree = 0.000) for 5103 atoms. Found 38 (38 requested) and removed 24 (19 requested) atoms. Cycle 40: After refmac, R = 0.2144 (Rfree = 0.000) for 5105 atoms. Found 35 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 5303 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 5332 seeds are put forward Round 1: 274 peptides, 48 chains. Longest chain 12 peptides. Score 0.374 Round 2: 342 peptides, 53 chains. Longest chain 18 peptides. Score 0.473 Round 3: 331 peptides, 54 chains. Longest chain 11 peptides. Score 0.441 Round 4: 340 peptides, 49 chains. Longest chain 21 peptides. Score 0.503 Round 5: 319 peptides, 51 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 4 Chains 51, Residues 291, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11657 restraints for refining 5106 atoms. 10451 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2340 (Rfree = 0.000) for 5106 atoms. Found 31 (38 requested) and removed 26 (19 requested) atoms. Cycle 42: After refmac, R = 0.2204 (Rfree = 0.000) for 5095 atoms. Found 30 (38 requested) and removed 26 (19 requested) atoms. Cycle 43: After refmac, R = 0.2097 (Rfree = 0.000) for 5088 atoms. Found 21 (38 requested) and removed 21 (19 requested) atoms. Cycle 44: After refmac, R = 0.1879 (Rfree = 0.000) for 5082 atoms. Found 8 (38 requested) and removed 19 (19 requested) atoms. Cycle 45: After refmac, R = 0.1856 (Rfree = 0.000) for 5068 atoms. Found 5 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 5158 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5178 seeds are put forward Round 1: 271 peptides, 51 chains. Longest chain 11 peptides. Score 0.337 Round 2: 316 peptides, 47 chains. Longest chain 15 peptides. Score 0.473 Round 3: 324 peptides, 53 chains. Longest chain 17 peptides. Score 0.436 Round 4: 307 peptides, 44 chains. Longest chain 20 peptides. Score 0.482 Round 5: 305 peptides, 49 chains. Longest chain 16 peptides. Score 0.432 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 263, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10354 reflections ( 99.53 % complete ) and 11939 restraints for refining 5105 atoms. 10856 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2117 (Rfree = 0.000) for 5105 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2080 (Rfree = 0.000) for 5069 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2148 (Rfree = 0.000) for 5046 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2101 (Rfree = 0.000) for 5025 atoms. TimeTaking 68.93