null Sun 23 Dec 22:22:52 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 2afb-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2afb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2afb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.6-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/2afb-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.6-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 22:23:00 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/2afb-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.6-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 497 and 0 Target number of residues in the AU: 497 Target solvent content: 0.6332 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-3.6-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 5616 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: 97.203 3.600 Wilson plot Bfac: 68.03 8743 reflections ( 99.44 % complete ) and 0 restraints for refining 6238 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3206 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2972 (Rfree = 0.000) for 6238 atoms. Found 39 (39 requested) and removed 45 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 6358 seeds are put forward NCS extension: 0 residues added, 6358 seeds are put forward Round 1: 262 peptides, 52 chains. Longest chain 11 peptides. Score 0.306 Round 2: 340 peptides, 52 chains. Longest chain 19 peptides. Score 0.477 Round 3: 370 peptides, 49 chains. Longest chain 22 peptides. Score 0.558 Round 4: 399 peptides, 50 chains. Longest chain 25 peptides. Score 0.600 Round 5: 400 peptides, 49 chains. Longest chain 25 peptides. Score 0.609 Taking the results from Round 5 Chains 51, Residues 351, Estimated correctness of the model 18.1 % 7 chains (50 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11000 restraints for refining 5088 atoms. 9504 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2838 (Rfree = 0.000) for 5088 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. Cycle 2: After refmac, R = 0.2682 (Rfree = 0.000) for 4947 atoms. Found 28 (32 requested) and removed 27 (16 requested) atoms. Cycle 3: After refmac, R = 0.2345 (Rfree = 0.000) for 4900 atoms. Found 21 (31 requested) and removed 27 (15 requested) atoms. Cycle 4: After refmac, R = 0.2346 (Rfree = 0.000) for 4865 atoms. Found 24 (31 requested) and removed 25 (15 requested) atoms. Cycle 5: After refmac, R = 0.2262 (Rfree = 0.000) for 4843 atoms. Found 14 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 5051 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5069 seeds are put forward Round 1: 356 peptides, 58 chains. Longest chain 13 peptides. Score 0.457 Round 2: 379 peptides, 48 chains. Longest chain 26 peptides. Score 0.582 Round 3: 393 peptides, 47 chains. Longest chain 23 peptides. Score 0.612 Round 4: 393 peptides, 49 chains. Longest chain 17 peptides. Score 0.598 Round 5: 385 peptides, 48 chains. Longest chain 19 peptides. Score 0.592 Taking the results from Round 3 Chains 50, Residues 346, Estimated correctness of the model 19.3 % 6 chains (50 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 10742 restraints for refining 4944 atoms. 9271 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2347 (Rfree = 0.000) for 4944 atoms. Found 25 (31 requested) and removed 35 (15 requested) atoms. Cycle 7: After refmac, R = 0.2179 (Rfree = 0.000) for 4889 atoms. Found 19 (31 requested) and removed 24 (15 requested) atoms. Cycle 8: After refmac, R = 0.2230 (Rfree = 0.000) for 4868 atoms. Found 21 (31 requested) and removed 32 (15 requested) atoms. Cycle 9: After refmac, R = 0.2100 (Rfree = 0.000) for 4847 atoms. Found 17 (31 requested) and removed 21 (15 requested) atoms. Cycle 10: After refmac, R = 0.2088 (Rfree = 0.000) for 4826 atoms. Found 16 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 5009 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 5034 seeds are put forward Round 1: 357 peptides, 61 chains. Longest chain 15 peptides. Score 0.433 Round 2: 392 peptides, 50 chains. Longest chain 25 peptides. Score 0.588 Round 3: 389 peptides, 51 chains. Longest chain 19 peptides. Score 0.576 Round 4: 387 peptides, 47 chains. Longest chain 26 peptides. Score 0.603 Round 5: 386 peptides, 48 chains. Longest chain 23 peptides. Score 0.594 Taking the results from Round 4 Chains 49, Residues 340, Estimated correctness of the model 15.8 % 5 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11282 restraints for refining 5089 atoms. 9808 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2316 (Rfree = 0.000) for 5089 atoms. Found 30 (32 requested) and removed 39 (16 requested) atoms. Cycle 12: After refmac, R = 0.2092 (Rfree = 0.000) for 5060 atoms. Found 9 (32 requested) and removed 33 (16 requested) atoms. Cycle 13: After refmac, R = 0.2116 (Rfree = 0.000) for 5020 atoms. Found 12 (32 requested) and removed 24 (16 requested) atoms. Cycle 14: After refmac, R = 0.2073 (Rfree = 0.000) for 5001 atoms. Found 15 (32 requested) and removed 23 (16 requested) atoms. Cycle 15: After refmac, R = 0.2039 (Rfree = 0.000) for 4984 atoms. Found 13 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 5195 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 5209 seeds are put forward Round 1: 339 peptides, 54 chains. Longest chain 16 peptides. Score 0.458 Round 2: 373 peptides, 49 chains. Longest chain 19 peptides. Score 0.564 Round 3: 394 peptides, 47 chains. Longest chain 32 peptides. Score 0.614 Round 4: 415 peptides, 46 chains. Longest chain 29 peptides. Score 0.653 Round 5: 420 peptides, 50 chains. Longest chain 33 peptides. Score 0.633 Taking the results from Round 4 Chains 48, Residues 369, Estimated correctness of the model 34.2 % 4 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 10948 restraints for refining 5091 atoms. 9327 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2379 (Rfree = 0.000) for 5091 atoms. Found 32 (32 requested) and removed 42 (16 requested) atoms. Cycle 17: After refmac, R = 0.2078 (Rfree = 0.000) for 5046 atoms. Found 20 (32 requested) and removed 27 (16 requested) atoms. Cycle 18: After refmac, R = 0.1998 (Rfree = 0.000) for 5026 atoms. Found 10 (32 requested) and removed 22 (16 requested) atoms. Cycle 19: After refmac, R = 0.1906 (Rfree = 0.000) for 5004 atoms. Found 8 (32 requested) and removed 29 (16 requested) atoms. Cycle 20: After refmac, R = 0.1885 (Rfree = 0.000) for 4973 atoms. Found 10 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 5152 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 5168 seeds are put forward Round 1: 330 peptides, 50 chains. Longest chain 18 peptides. Score 0.475 Round 2: 365 peptides, 54 chains. Longest chain 16 peptides. Score 0.509 Round 3: 360 peptides, 47 chains. Longest chain 19 peptides. Score 0.557 Round 4: 373 peptides, 52 chains. Longest chain 15 peptides. Score 0.540 Round 5: 369 peptides, 49 chains. Longest chain 18 peptides. Score 0.557 Taking the results from Round 5 Chains 50, Residues 320, Estimated correctness of the model 0.0 % 10 chains (66 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11269 restraints for refining 5089 atoms. 9833 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2337 (Rfree = 0.000) for 5089 atoms. Found 31 (32 requested) and removed 33 (16 requested) atoms. Cycle 22: After refmac, R = 0.2141 (Rfree = 0.000) for 5046 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 23: After refmac, R = 0.1979 (Rfree = 0.000) for 5029 atoms. Found 20 (32 requested) and removed 22 (16 requested) atoms. Cycle 24: After refmac, R = 0.1834 (Rfree = 0.000) for 5014 atoms. Found 21 (32 requested) and removed 18 (16 requested) atoms. Cycle 25: After refmac, R = 0.1889 (Rfree = 0.000) for 5007 atoms. Found 26 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 5191 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5206 seeds are put forward Round 1: 313 peptides, 59 chains. Longest chain 10 peptides. Score 0.356 Round 2: 339 peptides, 52 chains. Longest chain 17 peptides. Score 0.475 Round 3: 341 peptides, 57 chains. Longest chain 14 peptides. Score 0.435 Round 4: 367 peptides, 53 chains. Longest chain 17 peptides. Score 0.521 Round 5: 356 peptides, 50 chains. Longest chain 19 peptides. Score 0.525 Taking the results from Round 5 Chains 50, Residues 306, Estimated correctness of the model 0.0 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11488 restraints for refining 5091 atoms. 10192 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2202 (Rfree = 0.000) for 5091 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 27: After refmac, R = 0.2050 (Rfree = 0.000) for 5067 atoms. Found 16 (32 requested) and removed 17 (16 requested) atoms. Cycle 28: After refmac, R = 0.1986 (Rfree = 0.000) for 5053 atoms. Found 13 (32 requested) and removed 18 (16 requested) atoms. Cycle 29: After refmac, R = 0.2002 (Rfree = 0.000) for 5041 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 30: After refmac, R = 0.1892 (Rfree = 0.000) for 5042 atoms. Found 18 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 5234 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 5270 seeds are put forward Round 1: 291 peptides, 56 chains. Longest chain 11 peptides. Score 0.334 Round 2: 332 peptides, 52 chains. Longest chain 14 peptides. Score 0.461 Round 3: 344 peptides, 51 chains. Longest chain 16 peptides. Score 0.494 Round 4: 351 peptides, 50 chains. Longest chain 15 peptides. Score 0.516 Round 5: 356 peptides, 55 chains. Longest chain 16 peptides. Score 0.483 Taking the results from Round 4 Chains 50, Residues 301, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 11689 restraints for refining 5090 atoms. 10479 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2299 (Rfree = 0.000) for 5090 atoms. Found 32 (32 requested) and removed 17 (16 requested) atoms. Cycle 32: After refmac, R = 0.2182 (Rfree = 0.000) for 5085 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 33: After refmac, R = 0.1987 (Rfree = 0.000) for 5073 atoms. Found 29 (32 requested) and removed 18 (16 requested) atoms. Cycle 34: After refmac, R = 0.1956 (Rfree = 0.000) for 5072 atoms. Found 27 (32 requested) and removed 19 (16 requested) atoms. Cycle 35: After refmac, R = 0.1908 (Rfree = 0.000) for 5064 atoms. Found 31 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 5296 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5312 seeds are put forward Round 1: 288 peptides, 55 chains. Longest chain 13 peptides. Score 0.337 Round 2: 305 peptides, 50 chains. Longest chain 17 peptides. Score 0.423 Round 3: 312 peptides, 49 chains. Longest chain 19 peptides. Score 0.447 Round 4: 318 peptides, 47 chains. Longest chain 17 peptides. Score 0.477 Round 5: 317 peptides, 49 chains. Longest chain 14 peptides. Score 0.457 Taking the results from Round 4 Chains 47, Residues 271, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 12105 restraints for refining 5091 atoms. 11038 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2237 (Rfree = 0.000) for 5091 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 37: After refmac, R = 0.2107 (Rfree = 0.000) for 5079 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. Cycle 38: After refmac, R = 0.1944 (Rfree = 0.000) for 5077 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 39: After refmac, R = 0.1981 (Rfree = 0.000) for 5069 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 40: After refmac, R = 0.1777 (Rfree = 0.000) for 5073 atoms. Found 24 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 5273 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5289 seeds are put forward Round 1: 225 peptides, 44 chains. Longest chain 12 peptides. Score 0.298 Round 2: 252 peptides, 43 chains. Longest chain 13 peptides. Score 0.373 Round 3: 262 peptides, 41 chains. Longest chain 16 peptides. Score 0.415 Round 4: 283 peptides, 42 chains. Longest chain 20 peptides. Score 0.451 Round 5: 262 peptides, 40 chains. Longest chain 28 peptides. Score 0.425 Taking the results from Round 4 Chains 42, Residues 241, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8743 reflections ( 99.44 % complete ) and 12169 restraints for refining 5090 atoms. 11247 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2099 (Rfree = 0.000) for 5090 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 42: After refmac, R = 0.1894 (Rfree = 0.000) for 5072 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 43: After refmac, R = 0.1956 (Rfree = 0.000) for 5074 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. Cycle 44: After refmac, R = 0.1759 (Rfree = 0.000) for 5073 atoms. Found 26 (32 requested) and removed 19 (16 requested) atoms. Cycle 45: After refmac, R = 0.1810 (Rfree = 0.000) for 5073 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 5244 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 5258 seeds are put forward Round 1: 269 peptides, 56 chains. Longest chain 9 peptides. Score 0.282 Round 2: 280 peptides, 49 chains. Longest chain 16 peptides. Score 0.378 Round 3: 281 peptides, 44 chains. Longest chain 22 peptides. Score 0.428 Round 4: 292 peptides, 49 chains. Longest chain 22 peptides. Score 0.404 Round 5: 301 peptides, 48 chains. Longest chain 26 peptides. Score 0.433 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 253, Estimated correctness of the model 0.0 % 7 chains (56 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (253 residues) following loop building 7 chains (56 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8743 reflections ( 99.44 % complete ) and 11421 restraints for refining 5090 atoms. 10255 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2067 (Rfree = 0.000) for 5090 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1947 (Rfree = 0.000) for 5042 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1908 (Rfree = 0.000) for 4998 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1860 (Rfree = 0.000) for 4970 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:44:17 GMT 2018 Job finished. TimeTaking 81.41 Used memory is bytes: 3235216