null Sun 23 Dec 22:22:46 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 1vjz-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-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/1vjz-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-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 22:22:56 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/1vjz-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-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 298 and 0 Target number of residues in the AU: 298 Target solvent content: 0.6190 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.56 Input MTZ file: 1vjz-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: 96 Cell parameters: 64.677 64.677 202.367 90.000 90.000 90.000 Input sequence file: 1vjz-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 target number of atoms Had to go as low as 0.80 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 Loops will be built when appropriate and at the last cycle Resolution range: 61.607 4.000 Wilson plot Bfac: 60.56 4034 reflections ( 99.88 % complete ) and 0 restraints for refining 3012 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3556 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3411 (Rfree = 0.000) for 3012 atoms. Found 14 (14 requested) and removed 33 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.37 Search for helices and strands: 0 residues in 0 chains, 3059 seeds are put forward Round 1: 166 peptides, 29 chains. Longest chain 16 peptides. Score 0.383 Round 2: 185 peptides, 29 chains. Longest chain 13 peptides. Score 0.453 Round 3: 184 peptides, 24 chains. Longest chain 18 peptides. Score 0.526 Round 4: 176 peptides, 24 chains. Longest chain 19 peptides. Score 0.499 Round 5: 188 peptides, 24 chains. Longest chain 19 peptides. Score 0.539 Taking the results from Round 5 Chains 24, Residues 164, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4034 reflections ( 99.88 % complete ) and 5364 restraints for refining 2462 atoms. 4685 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2661 (Rfree = 0.000) for 2462 atoms. Found 8 (11 requested) and removed 16 (5 requested) atoms. Cycle 2: After refmac, R = 0.2484 (Rfree = 0.000) for 2434 atoms. Found 1 (11 requested) and removed 12 (5 requested) atoms. Cycle 3: After refmac, R = 0.2400 (Rfree = 0.000) for 2417 atoms. Found 0 (11 requested) and removed 14 (5 requested) atoms. Cycle 4: After refmac, R = 0.2384 (Rfree = 0.000) for 2398 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2344 (Rfree = 0.000) for 2389 atoms. Found 1 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.23 Search for helices and strands: 0 residues in 0 chains, 2462 seeds are put forward Round 1: 187 peptides, 31 chains. Longest chain 13 peptides. Score 0.429 Round 2: 189 peptides, 26 chains. Longest chain 16 peptides. Score 0.513 Round 3: 194 peptides, 27 chains. Longest chain 23 peptides. Score 0.514 Round 4: 183 peptides, 24 chains. Longest chain 16 peptides. Score 0.523 Round 5: 185 peptides, 29 chains. Longest chain 17 peptides. Score 0.453 Taking the results from Round 4 Chains 24, Residues 159, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4034 reflections ( 99.88 % complete ) and 5469 restraints for refining 2464 atoms. 4778 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2451 (Rfree = 0.000) for 2464 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 7: After refmac, R = 0.2301 (Rfree = 0.000) for 2436 atoms. Found 4 (11 requested) and removed 12 (5 requested) atoms. Cycle 8: After refmac, R = 0.2265 (Rfree = 0.000) for 2422 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.2256 (Rfree = 0.000) for 2418 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2234 (Rfree = 0.000) for 2412 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.26 Search for helices and strands: 0 residues in 0 chains, 2471 seeds are put forward Round 1: 155 peptides, 26 chains. Longest chain 13 peptides. Score 0.390 Round 2: 160 peptides, 22 chains. Longest chain 12 peptides. Score 0.475 Round 3: 170 peptides, 20 chains. Longest chain 18 peptides. Score 0.540 Round 4: 158 peptides, 19 chains. Longest chain 20 peptides. Score 0.516 Round 5: 163 peptides, 24 chains. Longest chain 19 peptides. Score 0.454 Taking the results from Round 3 Chains 20, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4034 reflections ( 99.88 % complete ) and 5761 restraints for refining 2463 atoms. 5181 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2469 (Rfree = 0.000) for 2463 atoms. Found 7 (11 requested) and removed 18 (5 requested) atoms. Cycle 12: After refmac, R = 0.2239 (Rfree = 0.000) for 2441 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 13: After refmac, R = 0.2226 (Rfree = 0.000) for 2429 atoms. Found 1 (11 requested) and removed 10 (5 requested) atoms. Cycle 14: After refmac, R = 0.2148 (Rfree = 0.000) for 2409 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 15: After refmac, R = 0.2141 (Rfree = 0.000) for 2400 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 2473 seeds are put forward Round 1: 158 peptides, 26 chains. Longest chain 11 peptides. Score 0.402 Round 2: 152 peptides, 22 chains. Longest chain 13 peptides. Score 0.446 Round 3: 168 peptides, 24 chains. Longest chain 18 peptides. Score 0.471 Round 4: 171 peptides, 23 chains. Longest chain 14 peptides. Score 0.498 Round 5: 176 peptides, 25 chains. Longest chain 12 peptides. Score 0.484 Taking the results from Round 4 Chains 23, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4034 reflections ( 99.88 % complete ) and 5732 restraints for refining 2464 atoms. 5163 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2485 (Rfree = 0.000) for 2464 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.2305 (Rfree = 0.000) for 2449 atoms. Found 3 (11 requested) and removed 12 (5 requested) atoms. Cycle 18: After refmac, R = 0.2222 (Rfree = 0.000) for 2437 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2207 (Rfree = 0.000) for 2432 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2152 (Rfree = 0.000) for 2425 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.24 Search for helices and strands: 0 residues in 0 chains, 2481 seeds are put forward Round 1: 165 peptides, 29 chains. Longest chain 11 peptides. Score 0.379 Round 2: 180 peptides, 25 chains. Longest chain 15 peptides. Score 0.497 Round 3: 164 peptides, 24 chains. Longest chain 14 peptides. Score 0.457 Round 4: 175 peptides, 24 chains. Longest chain 16 peptides. Score 0.496 Round 5: 177 peptides, 24 chains. Longest chain 12 peptides. Score 0.503 Taking the results from Round 5 Chains 24, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4034 reflections ( 99.88 % complete ) and 5586 restraints for refining 2464 atoms. 4998 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2464 (Rfree = 0.000) for 2464 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 22: After refmac, R = 0.2206 (Rfree = 0.000) for 2458 atoms. Found 5 (11 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.2204 (Rfree = 0.000) for 2446 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.2113 (Rfree = 0.000) for 2436 atoms. Found 1 (11 requested) and removed 11 (5 requested) atoms. Cycle 25: After refmac, R = 0.2130 (Rfree = 0.000) for 2423 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.24 Search for helices and strands: 0 residues in 0 chains, 2498 seeds are put forward Round 1: 150 peptides, 27 chains. Longest chain 10 peptides. Score 0.353 Round 2: 182 peptides, 29 chains. Longest chain 12 peptides. Score 0.442 Round 3: 167 peptides, 23 chains. Longest chain 17 peptides. Score 0.484 Round 4: 176 peptides, 25 chains. Longest chain 16 peptides. Score 0.484 Round 5: 190 peptides, 24 chains. Longest chain 17 peptides. Score 0.545 Taking the results from Round 5 Chains 24, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4034 reflections ( 99.88 % complete ) and 5471 restraints for refining 2464 atoms. 4831 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2397 (Rfree = 0.000) for 2464 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 27: After refmac, R = 0.2256 (Rfree = 0.000) for 2452 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.2185 (Rfree = 0.000) for 2443 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.2191 (Rfree = 0.000) for 2435 atoms. Found 1 (11 requested) and removed 14 (5 requested) atoms. Cycle 30: After refmac, R = 0.2176 (Rfree = 0.000) for 2421 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 2494 seeds are put forward Round 1: 154 peptides, 27 chains. Longest chain 12 peptides. Score 0.369 Round 2: 165 peptides, 26 chains. Longest chain 16 peptides. Score 0.428 Round 3: 168 peptides, 23 chains. Longest chain 13 peptides. Score 0.487 Round 4: 180 peptides, 25 chains. Longest chain 15 peptides. Score 0.497 Round 5: 165 peptides, 24 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 4 Chains 25, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4034 reflections ( 99.88 % complete ) and 5744 restraints for refining 2464 atoms. 5149 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2502 (Rfree = 0.000) for 2464 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 32: After refmac, R = 0.2312 (Rfree = 0.000) for 2457 atoms. Found 1 (11 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.2281 (Rfree = 0.000) for 2442 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2234 (Rfree = 0.000) for 2433 atoms. Found 0 (11 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2212 (Rfree = 0.000) for 2423 atoms. Found 0 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.26 Search for helices and strands: 0 residues in 0 chains, 2483 seeds are put forward Round 1: 144 peptides, 27 chains. Longest chain 9 peptides. Score 0.329 Round 2: 170 peptides, 25 chains. Longest chain 16 peptides. Score 0.463 Round 3: 173 peptides, 26 chains. Longest chain 14 peptides. Score 0.458 Round 4: 181 peptides, 27 chains. Longest chain 20 peptides. Score 0.470 Round 5: 174 peptides, 23 chains. Longest chain 18 peptides. Score 0.508 Taking the results from Round 5 Chains 23, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4034 reflections ( 99.88 % complete ) and 5734 restraints for refining 2464 atoms. 5153 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2645 (Rfree = 0.000) for 2464 atoms. Found 2 (11 requested) and removed 16 (5 requested) atoms. Cycle 37: After refmac, R = 0.2488 (Rfree = 0.000) for 2440 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.2307 (Rfree = 0.000) for 2433 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2206 (Rfree = 0.000) for 2424 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.2183 (Rfree = 0.000) for 2416 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 2466 seeds are put forward Round 1: 160 peptides, 28 chains. Longest chain 16 peptides. Score 0.376 Round 2: 181 peptides, 28 chains. Longest chain 16 peptides. Score 0.455 Round 3: 168 peptides, 24 chains. Longest chain 15 peptides. Score 0.471 Round 4: 173 peptides, 27 chains. Longest chain 13 peptides. Score 0.442 Round 5: 175 peptides, 24 chains. Longest chain 14 peptides. Score 0.496 Taking the results from Round 5 Chains 24, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4034 reflections ( 99.88 % complete ) and 5596 restraints for refining 2464 atoms. 5016 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2539 (Rfree = 0.000) for 2464 atoms. Found 5 (11 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.2403 (Rfree = 0.000) for 2448 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. Cycle 43: After refmac, R = 0.2398 (Rfree = 0.000) for 2435 atoms. Found 4 (11 requested) and removed 19 (5 requested) atoms. Cycle 44: After refmac, R = 0.2191 (Rfree = 0.000) for 2417 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. Cycle 45: After refmac, R = 0.2180 (Rfree = 0.000) for 2406 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.54 Search for helices and strands: 0 residues in 0 chains, 2476 seeds are put forward Round 1: 140 peptides, 28 chains. Longest chain 10 peptides. Score 0.294 Round 2: 160 peptides, 26 chains. Longest chain 17 peptides. Score 0.410 Round 3: 153 peptides, 26 chains. Longest chain 19 peptides. Score 0.383 Round 4: 146 peptides, 24 chains. Longest chain 13 peptides. Score 0.389 Round 5: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 134, 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 1vjz-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4034 reflections ( 99.88 % complete ) and 5603 restraints for refining 2464 atoms. 5093 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2368 (Rfree = 0.000) for 2464 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2351 (Rfree = 0.000) for 2455 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2447 (Rfree = 0.000) for 2447 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2123 (Rfree = 0.000) for 2436 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:09:53 GMT 2018 Job finished. TimeTaking 47.11 Used memory is bytes: 4218728