Tue 25 Dec 19:27:57 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 2gvh-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-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/2gvh-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-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 ============================================================ Tue 25 Dec 19:28:07 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/2gvh-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-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 744 and 0 Target number of residues in the AU: 744 Target solvent content: 0.6651 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.85 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: 121.211 3.400 Wilson plot Bfac: 88.69 16460 reflections ( 99.72 % complete ) and 0 restraints for refining 7687 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3546 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3128 (Rfree = 0.000) for 7687 atoms. Found 47 (58 requested) and removed 178 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.05 Search for helices and strands: 0 residues in 0 chains, 7655 seeds are put forward NCS extension: 0 residues added, 7655 seeds are put forward Round 1: 396 peptides, 73 chains. Longest chain 11 peptides. Score 0.333 Round 2: 464 peptides, 67 chains. Longest chain 16 peptides. Score 0.462 Round 3: 501 peptides, 71 chains. Longest chain 17 peptides. Score 0.485 Round 4: 526 peptides, 69 chains. Longest chain 27 peptides. Score 0.526 Round 5: 495 peptides, 62 chains. Longest chain 21 peptides. Score 0.527 Taking the results from Round 5 Chains 68, Residues 433, Estimated correctness of the model 3.1 % 11 chains (84 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13557 restraints for refining 6285 atoms. 11622 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2693 (Rfree = 0.000) for 6285 atoms. Found 37 (47 requested) and removed 51 (23 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2539 (Rfree = 0.000) for 6208 atoms. Found 19 (47 requested) and removed 38 (23 requested) atoms. Cycle 3: After refmac, R = 0.2493 (Rfree = 0.000) for 6164 atoms. Found 12 (46 requested) and removed 34 (23 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2498 (Rfree = 0.000) for 6124 atoms. Found 10 (46 requested) and removed 35 (23 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2395 (Rfree = 0.000) for 6093 atoms. Found 7 (46 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.02 Search for helices and strands: 0 residues in 0 chains, 6248 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6268 seeds are put forward Round 1: 452 peptides, 68 chains. Longest chain 16 peptides. Score 0.441 Round 2: 504 peptides, 68 chains. Longest chain 24 peptides. Score 0.505 Round 3: 514 peptides, 63 chains. Longest chain 23 peptides. Score 0.543 Round 4: 509 peptides, 64 chains. Longest chain 26 peptides. Score 0.532 Round 5: 503 peptides, 60 chains. Longest chain 25 peptides. Score 0.546 Taking the results from Round 5 Chains 65, Residues 443, Estimated correctness of the model 10.1 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13874 restraints for refining 6284 atoms. 12024 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2674 (Rfree = 0.000) for 6284 atoms. Found 44 (47 requested) and removed 37 (23 requested) atoms. Cycle 7: After refmac, R = 0.2517 (Rfree = 0.000) for 6256 atoms. Found 20 (47 requested) and removed 32 (23 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2445 (Rfree = 0.000) for 6228 atoms. Found 15 (47 requested) and removed 29 (23 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2422 (Rfree = 0.000) for 6200 atoms. Found 18 (46 requested) and removed 30 (23 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2394 (Rfree = 0.000) for 6172 atoms. Found 14 (46 requested) and removed 36 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.04 Search for helices and strands: 0 residues in 0 chains, 6350 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 6364 seeds are put forward Round 1: 445 peptides, 68 chains. Longest chain 17 peptides. Score 0.431 Round 2: 477 peptides, 60 chains. Longest chain 20 peptides. Score 0.516 Round 3: 501 peptides, 65 chains. Longest chain 27 peptides. Score 0.518 Round 4: 504 peptides, 64 chains. Longest chain 25 peptides. Score 0.526 Round 5: 487 peptides, 59 chains. Longest chain 20 peptides. Score 0.533 Taking the results from Round 5 Chains 60, Residues 428, Estimated correctness of the model 5.3 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13969 restraints for refining 6283 atoms. 12244 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2427 (Rfree = 0.000) for 6283 atoms. Found 37 (47 requested) and removed 31 (23 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2280 (Rfree = 0.000) for 6255 atoms. Found 14 (47 requested) and removed 28 (23 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2231 (Rfree = 0.000) for 6221 atoms. Found 11 (47 requested) and removed 31 (23 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2239 (Rfree = 0.000) for 6193 atoms. Found 10 (46 requested) and removed 29 (23 requested) atoms. Cycle 15: After refmac, R = 0.2207 (Rfree = 0.000) for 6170 atoms. Found 11 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.05 Search for helices and strands: 0 residues in 0 chains, 6320 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6337 seeds are put forward Round 1: 459 peptides, 73 chains. Longest chain 17 peptides. Score 0.421 Round 2: 491 peptides, 64 chains. Longest chain 22 peptides. Score 0.511 Round 3: 499 peptides, 59 chains. Longest chain 35 peptides. Score 0.547 Round 4: 504 peptides, 62 chains. Longest chain 37 peptides. Score 0.537 Round 5: 510 peptides, 65 chains. Longest chain 24 peptides. Score 0.528 Taking the results from Round 3 Chains 61, Residues 440, Estimated correctness of the model 10.4 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13676 restraints for refining 6285 atoms. 11848 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2503 (Rfree = 0.000) for 6285 atoms. Found 36 (47 requested) and removed 31 (23 requested) atoms. Cycle 17: After refmac, R = 0.2398 (Rfree = 0.000) for 6265 atoms. Found 19 (47 requested) and removed 30 (23 requested) atoms. Cycle 18: After refmac, R = 0.2361 (Rfree = 0.000) for 6235 atoms. Found 11 (47 requested) and removed 27 (23 requested) atoms. Cycle 19: After refmac, R = 0.2299 (Rfree = 0.000) for 6208 atoms. Found 18 (46 requested) and removed 24 (23 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2237 (Rfree = 0.000) for 6193 atoms. Found 8 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.08 Search for helices and strands: 0 residues in 0 chains, 6351 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6370 seeds are put forward Round 1: 468 peptides, 76 chains. Longest chain 21 peptides. Score 0.415 Round 2: 498 peptides, 68 chains. Longest chain 22 peptides. Score 0.498 Round 3: 479 peptides, 60 chains. Longest chain 28 peptides. Score 0.519 Round 4: 483 peptides, 62 chains. Longest chain 26 peptides. Score 0.513 Round 5: 487 peptides, 63 chains. Longest chain 30 peptides. Score 0.512 Taking the results from Round 3 Chains 61, Residues 419, Estimated correctness of the model 0.0 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13867 restraints for refining 6285 atoms. 12154 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2483 (Rfree = 0.000) for 6285 atoms. Found 30 (47 requested) and removed 28 (23 requested) atoms. Cycle 22: After refmac, R = 0.2390 (Rfree = 0.000) for 6253 atoms. Found 22 (47 requested) and removed 28 (23 requested) atoms. Cycle 23: After refmac, R = 0.2346 (Rfree = 0.000) for 6230 atoms. Found 15 (47 requested) and removed 28 (23 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2301 (Rfree = 0.000) for 6205 atoms. Found 9 (46 requested) and removed 24 (23 requested) atoms. Cycle 25: After refmac, R = 0.2258 (Rfree = 0.000) for 6188 atoms. Found 6 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.07 Search for helices and strands: 0 residues in 0 chains, 6291 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6313 seeds are put forward Round 1: 408 peptides, 69 chains. Longest chain 14 peptides. Score 0.375 Round 2: 441 peptides, 58 chains. Longest chain 22 peptides. Score 0.484 Round 3: 461 peptides, 60 chains. Longest chain 21 peptides. Score 0.497 Round 4: 489 peptides, 57 chains. Longest chain 26 peptides. Score 0.546 Round 5: 486 peptides, 61 chains. Longest chain 26 peptides. Score 0.522 Taking the results from Round 4 Chains 63, Residues 432, Estimated correctness of the model 10.1 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13519 restraints for refining 6284 atoms. 11654 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2445 (Rfree = 0.000) for 6284 atoms. Found 30 (47 requested) and removed 40 (23 requested) atoms. Cycle 27: After refmac, R = 0.2332 (Rfree = 0.000) for 6222 atoms. Found 24 (47 requested) and removed 33 (23 requested) atoms. Cycle 28: After refmac, R = 0.2396 (Rfree = 0.000) for 6186 atoms. Found 21 (46 requested) and removed 32 (23 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2563 (Rfree = 0.000) for 6158 atoms. Found 46 (46 requested) and removed 36 (23 requested) atoms. Cycle 30: After refmac, R = 0.2575 (Rfree = 0.000) for 6147 atoms. Found 46 (46 requested) and removed 36 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.05 Search for helices and strands: 0 residues in 0 chains, 6299 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 6329 seeds are put forward Round 1: 386 peptides, 68 chains. Longest chain 14 peptides. Score 0.350 Round 2: 430 peptides, 62 chains. Longest chain 22 peptides. Score 0.447 Round 3: 441 peptides, 63 chains. Longest chain 18 peptides. Score 0.455 Round 4: 455 peptides, 66 chains. Longest chain 19 peptides. Score 0.456 Round 5: 454 peptides, 62 chains. Longest chain 19 peptides. Score 0.477 Taking the results from Round 5 Chains 68, Residues 392, Estimated correctness of the model 0.0 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13850 restraints for refining 6285 atoms. 12148 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2495 (Rfree = 0.000) for 6285 atoms. Found 39 (47 requested) and removed 34 (23 requested) atoms. Cycle 32: After refmac, R = 0.2756 (Rfree = 0.000) for 6263 atoms. Found 47 (47 requested) and removed 46 (23 requested) atoms. Cycle 33: After refmac, R = 0.2456 (Rfree = 0.000) for 6236 atoms. Found 14 (47 requested) and removed 28 (23 requested) atoms. Cycle 34: After refmac, R = 0.2694 (Rfree = 0.000) for 6197 atoms. Found 46 (46 requested) and removed 41 (23 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2554 (Rfree = 0.000) for 6180 atoms. Found 46 (46 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.03 Search for helices and strands: 0 residues in 0 chains, 6323 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6340 seeds are put forward Round 1: 351 peptides, 64 chains. Longest chain 17 peptides. Score 0.324 Round 2: 406 peptides, 65 chains. Longest chain 16 peptides. Score 0.397 Round 3: 429 peptides, 61 chains. Longest chain 18 peptides. Score 0.451 Round 4: 424 peptides, 59 chains. Longest chain 18 peptides. Score 0.457 Round 5: 430 peptides, 63 chains. Longest chain 18 peptides. Score 0.441 Taking the results from Round 4 Chains 60, Residues 365, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 16460 reflections ( 99.72 % complete ) and 14204 restraints for refining 6283 atoms. 12719 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2324 (Rfree = 0.000) for 6283 atoms. Found 33 (47 requested) and removed 33 (23 requested) atoms. Cycle 37: After refmac, R = 0.2168 (Rfree = 0.000) for 6267 atoms. Found 16 (47 requested) and removed 33 (23 requested) atoms. Cycle 38: After refmac, R = 0.2178 (Rfree = 0.000) for 6238 atoms. Found 17 (47 requested) and removed 35 (23 requested) atoms. Cycle 39: After refmac, R = 0.2161 (Rfree = 0.000) for 6216 atoms. Found 27 (46 requested) and removed 27 (23 requested) atoms. Cycle 40: After refmac, R = 0.2131 (Rfree = 0.000) for 6207 atoms. Found 17 (46 requested) and removed 73 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.04 Search for helices and strands: 0 residues in 0 chains, 6297 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6313 seeds are put forward Round 1: 325 peptides, 68 chains. Longest chain 11 peptides. Score 0.257 Round 2: 341 peptides, 61 chains. Longest chain 13 peptides. Score 0.329 Round 3: 360 peptides, 62 chains. Longest chain 16 peptides. Score 0.350 Round 4: 359 peptides, 57 chains. Longest chain 22 peptides. Score 0.381 Round 5: 361 peptides, 61 chains. Longest chain 14 peptides. Score 0.358 Taking the results from Round 4 Chains 59, Residues 302, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 14440 restraints for refining 6285 atoms. 13186 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2479 (Rfree = 0.000) for 6285 atoms. Found 46 (47 requested) and removed 53 (23 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2354 (Rfree = 0.000) for 6258 atoms. Found 18 (47 requested) and removed 35 (23 requested) atoms. Cycle 43: After refmac, R = 0.2315 (Rfree = 0.000) for 6220 atoms. Found 42 (47 requested) and removed 33 (23 requested) atoms. Cycle 44: After refmac, R = 0.2141 (Rfree = 0.000) for 6215 atoms. Found 11 (47 requested) and removed 24 (23 requested) atoms. Cycle 45: After refmac, R = 0.2179 (Rfree = 0.000) for 6189 atoms. Found 15 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.07 Search for helices and strands: 0 residues in 0 chains, 6327 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6345 seeds are put forward Round 1: 304 peptides, 62 chains. Longest chain 16 peptides. Score 0.264 Round 2: 355 peptides, 60 chains. Longest chain 20 peptides. Score 0.356 Round 3: 376 peptides, 62 chains. Longest chain 17 peptides. Score 0.373 Round 4: 386 peptides, 61 chains. Longest chain 21 peptides. Score 0.394 Round 5: 404 peptides, 59 chains. Longest chain 26 peptides. Score 0.431 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 345, Estimated correctness of the model 0.0 % 5 chains (47 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2gvh-3_warpNtrace.pdb as input Building loops using Loopy2018 64 chains (345 residues) following loop building 5 chains (47 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16460 reflections ( 99.72 % complete ) and 14174 restraints for refining 6283 atoms. 12713 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2389 (Rfree = 0.000) for 6283 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2311 (Rfree = 0.000) for 6232 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.2688 (Rfree = 0.000) for 6195 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2252 (Rfree = 0.000) for 6160 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Writing output files ... TimeTaking 97.67