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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-3.8-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 19:28:06 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-3.8-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 710 and 0 Target number of residues in the AU: 710 Target solvent content: 0.6804 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 101.15 11825 reflections ( 99.61 % complete ) and 0 restraints for refining 7609 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3623 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3302 (Rfree = 0.000) for 7609 atoms. Found 41 (41 requested) and removed 91 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.36 Search for helices and strands: 0 residues in 0 chains, 7683 seeds are put forward NCS extension: 0 residues added, 7683 seeds are put forward Round 1: 345 peptides, 63 chains. Longest chain 14 peptides. Score 0.322 Round 2: 414 peptides, 62 chains. Longest chain 29 peptides. Score 0.426 Round 3: 431 peptides, 64 chains. Longest chain 26 peptides. Score 0.436 Round 4: 431 peptides, 63 chains. Longest chain 23 peptides. Score 0.442 Round 5: 447 peptides, 65 chains. Longest chain 20 peptides. Score 0.451 Taking the results from Round 5 Chains 67, Residues 382, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11825 reflections ( 99.61 % complete ) and 14577 restraints for refining 6251 atoms. 12984 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2580 (Rfree = 0.000) for 6251 atoms. Found 14 (34 requested) and removed 57 (17 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2406 (Rfree = 0.000) for 6130 atoms. Found 15 (34 requested) and removed 58 (17 requested) atoms. Cycle 3: After refmac, R = 0.2337 (Rfree = 0.000) for 6066 atoms. Found 5 (33 requested) and removed 54 (16 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2236 (Rfree = 0.000) for 6007 atoms. Found 5 (33 requested) and removed 47 (16 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2227 (Rfree = 0.000) for 5954 atoms. Found 5 (32 requested) and removed 46 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.30 Search for helices and strands: 0 residues in 0 chains, 6081 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6105 seeds are put forward Round 1: 417 peptides, 68 chains. Longest chain 25 peptides. Score 0.394 Round 2: 472 peptides, 66 chains. Longest chain 26 peptides. Score 0.477 Round 3: 472 peptides, 65 chains. Longest chain 23 peptides. Score 0.483 Round 4: 445 peptides, 62 chains. Longest chain 22 peptides. Score 0.466 Round 5: 461 peptides, 68 chains. Longest chain 22 peptides. Score 0.452 Taking the results from Round 3 Chains 70, Residues 407, Estimated correctness of the model 0.0 % 8 chains (55 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11825 reflections ( 99.61 % complete ) and 14059 restraints for refining 6251 atoms. 12332 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2584 (Rfree = 0.000) for 6251 atoms. Found 20 (34 requested) and removed 64 (17 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2379 (Rfree = 0.000) for 6167 atoms. Found 10 (34 requested) and removed 46 (17 requested) atoms. Cycle 8: After refmac, R = 0.2242 (Rfree = 0.000) for 6111 atoms. Found 14 (33 requested) and removed 37 (16 requested) atoms. Cycle 9: After refmac, R = 0.2158 (Rfree = 0.000) for 6075 atoms. Found 10 (33 requested) and removed 31 (16 requested) atoms. Cycle 10: After refmac, R = 0.2091 (Rfree = 0.000) for 6040 atoms. Found 9 (33 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.27 Search for helices and strands: 0 residues in 0 chains, 6201 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6226 seeds are put forward Round 1: 428 peptides, 74 chains. Longest chain 13 peptides. Score 0.373 Round 2: 450 peptides, 69 chains. Longest chain 17 peptides. Score 0.432 Round 3: 450 peptides, 63 chains. Longest chain 19 peptides. Score 0.467 Round 4: 468 peptides, 69 chains. Longest chain 18 peptides. Score 0.455 Round 5: 473 peptides, 66 chains. Longest chain 19 peptides. Score 0.479 Taking the results from Round 5 Chains 69, Residues 407, Estimated correctness of the model 0.0 % 6 chains (55 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11825 reflections ( 99.61 % complete ) and 13980 restraints for refining 6252 atoms. 12232 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2502 (Rfree = 0.000) for 6252 atoms. Found 21 (34 requested) and removed 35 (17 requested) atoms. Cycle 12: After refmac, R = 0.2246 (Rfree = 0.000) for 6191 atoms. Found 5 (34 requested) and removed 33 (17 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2152 (Rfree = 0.000) for 6150 atoms. Found 10 (33 requested) and removed 31 (16 requested) atoms. Cycle 14: After refmac, R = 0.2110 (Rfree = 0.000) for 6123 atoms. Found 6 (33 requested) and removed 26 (16 requested) atoms. Cycle 15: After refmac, R = 0.2073 (Rfree = 0.000) for 6093 atoms. Found 9 (33 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.28 Search for helices and strands: 0 residues in 0 chains, 6226 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6247 seeds are put forward Round 1: 388 peptides, 73 chains. Longest chain 15 peptides. Score 0.321 Round 2: 418 peptides, 68 chains. Longest chain 12 peptides. Score 0.395 Round 3: 445 peptides, 64 chains. Longest chain 17 peptides. Score 0.455 Round 4: 441 peptides, 62 chains. Longest chain 14 peptides. Score 0.461 Round 5: 438 peptides, 66 chains. Longest chain 14 peptides. Score 0.434 Taking the results from Round 4 Chains 63, Residues 379, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14409 restraints for refining 6252 atoms. 12867 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2485 (Rfree = 0.000) for 6252 atoms. Found 25 (34 requested) and removed 32 (17 requested) atoms. Cycle 17: After refmac, R = 0.2303 (Rfree = 0.000) for 6223 atoms. Found 17 (34 requested) and removed 40 (17 requested) atoms. Cycle 18: After refmac, R = 0.2238 (Rfree = 0.000) for 6185 atoms. Found 16 (34 requested) and removed 31 (17 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2250 (Rfree = 0.000) for 6156 atoms. Found 16 (33 requested) and removed 27 (16 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2081 (Rfree = 0.000) for 6133 atoms. Found 13 (33 requested) and removed 30 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.32 Search for helices and strands: 0 residues in 0 chains, 6264 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6278 seeds are put forward Round 1: 383 peptides, 71 chains. Longest chain 10 peptides. Score 0.327 Round 2: 428 peptides, 67 chains. Longest chain 19 peptides. Score 0.415 Round 3: 420 peptides, 63 chains. Longest chain 13 peptides. Score 0.428 Round 4: 433 peptides, 62 chains. Longest chain 14 peptides. Score 0.451 Round 5: 436 peptides, 62 chains. Longest chain 18 peptides. Score 0.455 Taking the results from Round 5 Chains 62, Residues 374, Estimated correctness of the model 0.0 % 6 chains (41 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14141 restraints for refining 6250 atoms. 12580 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2447 (Rfree = 0.000) for 6250 atoms. Found 20 (34 requested) and removed 50 (17 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2247 (Rfree = 0.000) for 6184 atoms. Found 10 (34 requested) and removed 36 (17 requested) atoms. Cycle 23: After refmac, R = 0.2195 (Rfree = 0.000) for 6143 atoms. Found 9 (33 requested) and removed 36 (16 requested) atoms. Cycle 24: After refmac, R = 0.2077 (Rfree = 0.000) for 6100 atoms. Found 9 (33 requested) and removed 31 (16 requested) atoms. Cycle 25: After refmac, R = 0.2024 (Rfree = 0.000) for 6065 atoms. Found 6 (33 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 3.32 Search for helices and strands: 0 residues in 0 chains, 6201 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6216 seeds are put forward Round 1: 375 peptides, 71 chains. Longest chain 10 peptides. Score 0.315 Round 2: 420 peptides, 75 chains. Longest chain 14 peptides. Score 0.355 Round 3: 426 peptides, 68 chains. Longest chain 15 peptides. Score 0.406 Round 4: 433 peptides, 64 chains. Longest chain 27 peptides. Score 0.439 Round 5: 438 peptides, 67 chains. Longest chain 20 peptides. Score 0.428 Taking the results from Round 4 Chains 65, Residues 369, Estimated correctness of the model 0.0 % 13 chains (83 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11825 reflections ( 99.61 % complete ) and 13818 restraints for refining 6252 atoms. 12138 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2387 (Rfree = 0.000) for 6252 atoms. Found 19 (34 requested) and removed 40 (17 requested) atoms. Cycle 27: After refmac, R = 0.2320 (Rfree = 0.000) for 6210 atoms. Found 23 (34 requested) and removed 38 (17 requested) atoms. Cycle 28: After refmac, R = 0.2163 (Rfree = 0.000) for 6186 atoms. Found 11 (34 requested) and removed 30 (17 requested) atoms. Cycle 29: After refmac, R = 0.2102 (Rfree = 0.000) for 6157 atoms. Found 13 (33 requested) and removed 27 (16 requested) atoms. Cycle 30: After refmac, R = 0.2043 (Rfree = 0.000) for 6133 atoms. Found 8 (33 requested) and removed 30 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.30 Search for helices and strands: 0 residues in 0 chains, 6272 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 6302 seeds are put forward Round 1: 358 peptides, 70 chains. Longest chain 11 peptides. Score 0.295 Round 2: 363 peptides, 61 chains. Longest chain 15 peptides. Score 0.361 Round 3: 381 peptides, 65 chains. Longest chain 22 peptides. Score 0.362 Round 4: 379 peptides, 62 chains. Longest chain 18 peptides. Score 0.378 Round 5: 393 peptides, 58 chains. Longest chain 25 peptides. Score 0.422 Taking the results from Round 5 Chains 58, Residues 335, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11825 reflections ( 99.61 % complete ) and 14768 restraints for refining 6250 atoms. 13398 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2285 (Rfree = 0.000) for 6250 atoms. Found 24 (34 requested) and removed 32 (17 requested) atoms. Cycle 32: After refmac, R = 0.2199 (Rfree = 0.000) for 6203 atoms. Found 15 (34 requested) and removed 27 (17 requested) atoms. Cycle 33: After refmac, R = 0.2098 (Rfree = 0.000) for 6181 atoms. Found 9 (34 requested) and removed 30 (17 requested) atoms. Cycle 34: After refmac, R = 0.2144 (Rfree = 0.000) for 6155 atoms. Found 19 (33 requested) and removed 35 (16 requested) atoms. Cycle 35: After refmac, R = 0.2106 (Rfree = 0.000) for 6133 atoms. Found 13 (33 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.27 Search for helices and strands: 0 residues in 0 chains, 6267 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 6291 seeds are put forward Round 1: 348 peptides, 67 chains. Longest chain 14 peptides. Score 0.300 Round 2: 380 peptides, 64 chains. Longest chain 12 peptides. Score 0.367 Round 3: 385 peptides, 62 chains. Longest chain 16 peptides. Score 0.386 Round 4: 404 peptides, 65 chains. Longest chain 17 peptides. Score 0.394 Round 5: 390 peptides, 61 chains. Longest chain 18 peptides. Score 0.399 Taking the results from Round 5 Chains 61, Residues 329, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14770 restraints for refining 6251 atoms. 13445 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2276 (Rfree = 0.000) for 6251 atoms. Found 25 (34 requested) and removed 38 (17 requested) atoms. Cycle 37: After refmac, R = 0.2182 (Rfree = 0.000) for 6230 atoms. Found 22 (34 requested) and removed 39 (17 requested) atoms. Cycle 38: After refmac, R = 0.2208 (Rfree = 0.000) for 6204 atoms. Found 19 (34 requested) and removed 41 (17 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2152 (Rfree = 0.000) for 6177 atoms. Found 12 (33 requested) and removed 31 (16 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2147 (Rfree = 0.000) for 6152 atoms. Found 16 (33 requested) and removed 39 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.28 Search for helices and strands: 0 residues in 0 chains, 6311 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6332 seeds are put forward Round 1: 330 peptides, 68 chains. Longest chain 13 peptides. Score 0.265 Round 2: 366 peptides, 61 chains. Longest chain 29 peptides. Score 0.365 Round 3: 390 peptides, 63 chains. Longest chain 20 peptides. Score 0.387 Round 4: 364 peptides, 56 chains. Longest chain 20 peptides. Score 0.394 Round 5: 371 peptides, 57 chains. Longest chain 24 peptides. Score 0.398 Taking the results from Round 5 Chains 61, Residues 314, Estimated correctness of the model 0.0 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14355 restraints for refining 6251 atoms. 13005 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2187 (Rfree = 0.000) for 6251 atoms. Found 25 (34 requested) and removed 36 (17 requested) atoms. Cycle 42: After refmac, R = 0.2103 (Rfree = 0.000) for 6214 atoms. Found 27 (34 requested) and removed 28 (17 requested) atoms. Cycle 43: After refmac, R = 0.2066 (Rfree = 0.000) for 6204 atoms. Found 17 (34 requested) and removed 30 (17 requested) atoms. Cycle 44: After refmac, R = 0.1964 (Rfree = 0.000) for 6186 atoms. Found 18 (34 requested) and removed 31 (17 requested) atoms. Cycle 45: After refmac, R = 0.1986 (Rfree = 0.000) for 6166 atoms. Found 15 (33 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.24 Search for helices and strands: 0 residues in 0 chains, 6320 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6333 seeds are put forward Round 1: 308 peptides, 63 chains. Longest chain 12 peptides. Score 0.264 Round 2: 333 peptides, 57 chains. Longest chain 20 peptides. Score 0.343 Round 3: 328 peptides, 54 chains. Longest chain 20 peptides. Score 0.355 Round 4: 339 peptides, 51 chains. Longest chain 17 peptides. Score 0.391 Round 5: 348 peptides, 53 chains. Longest chain 19 peptides. Score 0.391 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 295, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2gvh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11825 reflections ( 99.61 % complete ) and 15038 restraints for refining 6251 atoms. 13876 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2170 (Rfree = 0.000) for 6251 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2143 (Rfree = 0.000) for 6208 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2127 (Rfree = 0.000) for 6183 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2045 (Rfree = 0.000) for 6161 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 94.22