Mon 24 Dec 00:16:04 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 1vl0-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-4.0-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/1vl0-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-4.0-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 ============================================================ Mon 24 Dec 00:16:09 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/1vl0-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-4.0-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 671 and 0 Target number of residues in the AU: 671 Target solvent content: 0.6548 Checking the provided sequence file Detected sequence length: 292 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 876 Adjusted target solvent content: 0.55 Input MTZ file: 1vl0-4.0-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: 20 Cell parameters: 106.471 130.661 151.225 90.000 90.000 90.000 Input sequence file: 1vl0-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7008 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: 29.987 4.000 Wilson plot Bfac: 81.21 9090 reflections ( 98.72 % complete ) and 0 restraints for refining 7718 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3847 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3566 (Rfree = 0.000) for 7718 atoms. Found 36 (36 requested) and removed 178 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.41 Search for helices and strands: 0 residues in 0 chains, 7622 seeds are put forward NCS extension: 0 residues added, 7622 seeds are put forward Round 1: 126 peptides, 29 chains. Longest chain 6 peptides. Score 0.194 Round 2: 202 peptides, 47 chains. Longest chain 7 peptides. Score 0.197 Round 3: 261 peptides, 59 chains. Longest chain 9 peptides. Score 0.217 Round 4: 280 peptides, 57 chains. Longest chain 13 peptides. Score 0.268 Round 5: 310 peptides, 64 chains. Longest chain 10 peptides. Score 0.269 Taking the results from Round 5 Chains 64, Residues 246, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 14989 restraints for refining 6326 atoms. 14046 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3221 (Rfree = 0.000) for 6326 atoms. Found 30 (30 requested) and removed 50 (15 requested) atoms. Cycle 2: After refmac, R = 0.3066 (Rfree = 0.000) for 6212 atoms. Found 29 (29 requested) and removed 53 (14 requested) atoms. Cycle 3: After refmac, R = 0.3005 (Rfree = 0.000) for 6131 atoms. Found 29 (29 requested) and removed 47 (14 requested) atoms. Cycle 4: After refmac, R = 0.2918 (Rfree = 0.000) for 6057 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. Cycle 5: After refmac, R = 0.2443 (Rfree = 0.000) for 6014 atoms. Found 20 (28 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.42 Search for helices and strands: 0 residues in 0 chains, 6108 seeds are put forward NCS extension: 0 residues added, 6108 seeds are put forward Round 1: 250 peptides, 56 chains. Longest chain 9 peptides. Score 0.219 Round 2: 309 peptides, 63 chains. Longest chain 10 peptides. Score 0.275 Round 3: 326 peptides, 62 chains. Longest chain 10 peptides. Score 0.312 Round 4: 331 peptides, 60 chains. Longest chain 10 peptides. Score 0.335 Round 5: 305 peptides, 54 chains. Longest chain 10 peptides. Score 0.335 Taking the results from Round 5 Chains 54, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9090 reflections ( 98.72 % complete ) and 12556 restraints for refining 5609 atoms. 11606 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2823 (Rfree = 0.000) for 5609 atoms. Found 26 (26 requested) and removed 66 (13 requested) atoms. Cycle 7: After refmac, R = 0.2760 (Rfree = 0.000) for 5500 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 8: After refmac, R = 0.2609 (Rfree = 0.000) for 5456 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. Cycle 9: After refmac, R = 0.2171 (Rfree = 0.000) for 5422 atoms. Found 13 (25 requested) and removed 21 (12 requested) atoms. Cycle 10: After refmac, R = 0.2114 (Rfree = 0.000) for 5395 atoms. Found 13 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.45 Search for helices and strands: 0 residues in 0 chains, 5506 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5518 seeds are put forward Round 1: 308 peptides, 66 chains. Longest chain 11 peptides. Score 0.250 Round 2: 355 peptides, 69 chains. Longest chain 11 peptides. Score 0.311 Round 3: 371 peptides, 66 chains. Longest chain 13 peptides. Score 0.358 Round 4: 362 peptides, 64 chains. Longest chain 12 peptides. Score 0.358 Round 5: 372 peptides, 62 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 5 Chains 63, Residues 310, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 12410 restraints for refining 5734 atoms. 11185 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2591 (Rfree = 0.000) for 5734 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 12: After refmac, R = 0.2499 (Rfree = 0.000) for 5659 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 13: After refmac, R = 0.2273 (Rfree = 0.000) for 5595 atoms. Found 19 (26 requested) and removed 29 (13 requested) atoms. Cycle 14: After refmac, R = 0.2039 (Rfree = 0.000) for 5556 atoms. Found 6 (26 requested) and removed 18 (13 requested) atoms. Cycle 15: After refmac, R = 0.2013 (Rfree = 0.000) for 5525 atoms. Found 9 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.47 Search for helices and strands: 0 residues in 0 chains, 5609 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5631 seeds are put forward Round 1: 310 peptides, 65 chains. Longest chain 9 peptides. Score 0.261 Round 2: 356 peptides, 67 chains. Longest chain 13 peptides. Score 0.327 Round 3: 357 peptides, 62 chains. Longest chain 12 peptides. Score 0.364 Round 4: 355 peptides, 58 chains. Longest chain 16 peptides. Score 0.389 Round 5: 362 peptides, 61 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 4 Chains 58, Residues 297, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 12463 restraints for refining 5717 atoms. 11333 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2396 (Rfree = 0.000) for 5717 atoms. Found 21 (27 requested) and removed 50 (13 requested) atoms. Cycle 17: After refmac, R = 0.2203 (Rfree = 0.000) for 5660 atoms. Found 14 (27 requested) and removed 30 (13 requested) atoms. Cycle 18: After refmac, R = 0.2115 (Rfree = 0.000) for 5637 atoms. Found 6 (26 requested) and removed 24 (13 requested) atoms. Cycle 19: After refmac, R = 0.2086 (Rfree = 0.000) for 5614 atoms. Found 6 (26 requested) and removed 16 (13 requested) atoms. Cycle 20: After refmac, R = 0.2069 (Rfree = 0.000) for 5603 atoms. Found 3 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.45 Search for helices and strands: 0 residues in 0 chains, 5683 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5701 seeds are put forward Round 1: 329 peptides, 65 chains. Longest chain 11 peptides. Score 0.295 Round 2: 369 peptides, 65 chains. Longest chain 14 peptides. Score 0.362 Round 3: 368 peptides, 66 chains. Longest chain 10 peptides. Score 0.353 Round 4: 390 peptides, 67 chains. Longest chain 16 peptides. Score 0.382 Round 5: 375 peptides, 67 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 4 Chains 69, Residues 323, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 13146 restraints for refining 6096 atoms. 11828 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2503 (Rfree = 0.000) for 6096 atoms. Found 28 (28 requested) and removed 55 (14 requested) atoms. Cycle 22: After refmac, R = 0.2436 (Rfree = 0.000) for 6023 atoms. Found 28 (28 requested) and removed 50 (14 requested) atoms. Cycle 23: After refmac, R = 0.2297 (Rfree = 0.000) for 5970 atoms. Found 28 (28 requested) and removed 35 (14 requested) atoms. Cycle 24: After refmac, R = 0.2437 (Rfree = 0.000) for 5937 atoms. Found 28 (28 requested) and removed 36 (14 requested) atoms. Cycle 25: After refmac, R = 0.2321 (Rfree = 0.000) for 5901 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.40 Search for helices and strands: 0 residues in 0 chains, 6017 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6033 seeds are put forward Round 1: 312 peptides, 66 chains. Longest chain 8 peptides. Score 0.258 Round 2: 335 peptides, 63 chains. Longest chain 10 peptides. Score 0.320 Round 3: 333 peptides, 59 chains. Longest chain 12 peptides. Score 0.346 Round 4: 357 peptides, 60 chains. Longest chain 13 peptides. Score 0.378 Round 5: 353 peptides, 61 chains. Longest chain 14 peptides. Score 0.364 Taking the results from Round 4 Chains 60, Residues 297, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 13631 restraints for refining 6105 atoms. 12503 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2503 (Rfree = 0.000) for 6105 atoms. Found 29 (29 requested) and removed 58 (14 requested) atoms. Cycle 27: After refmac, R = 0.2335 (Rfree = 0.000) for 6026 atoms. Found 28 (28 requested) and removed 35 (14 requested) atoms. Cycle 28: After refmac, R = 0.2311 (Rfree = 0.000) for 5979 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 29: After refmac, R = 0.2276 (Rfree = 0.000) for 5942 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 30: After refmac, R = 0.2287 (Rfree = 0.000) for 5917 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.41 Search for helices and strands: 0 residues in 0 chains, 6010 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6028 seeds are put forward Round 1: 260 peptides, 53 chains. Longest chain 15 peptides. Score 0.263 Round 2: 271 peptides, 48 chains. Longest chain 12 peptides. Score 0.322 Round 3: 291 peptides, 52 chains. Longest chain 15 peptides. Score 0.326 Round 4: 287 peptides, 54 chains. Longest chain 9 peptides. Score 0.304 Round 5: 303 peptides, 54 chains. Longest chain 11 peptides. Score 0.332 Taking the results from Round 5 Chains 54, Residues 249, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 13590 restraints for refining 6066 atoms. 12627 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2344 (Rfree = 0.000) for 6066 atoms. Found 28 (28 requested) and removed 52 (14 requested) atoms. Cycle 32: After refmac, R = 0.2394 (Rfree = 0.000) for 6000 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 33: After refmac, R = 0.2232 (Rfree = 0.000) for 5959 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 34: After refmac, R = 0.2394 (Rfree = 0.000) for 5932 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. Cycle 35: After refmac, R = 0.2320 (Rfree = 0.000) for 5904 atoms. Found 28 (28 requested) and removed 30 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.44 Search for helices and strands: 0 residues in 0 chains, 5985 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6001 seeds are put forward Round 1: 244 peptides, 56 chains. Longest chain 7 peptides. Score 0.208 Round 2: 290 peptides, 58 chains. Longest chain 10 peptides. Score 0.279 Round 3: 295 peptides, 55 chains. Longest chain 12 peptides. Score 0.310 Round 4: 294 peptides, 54 chains. Longest chain 12 peptides. Score 0.316 Round 5: 288 peptides, 52 chains. Longest chain 10 peptides. Score 0.321 Taking the results from Round 5 Chains 52, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 13389 restraints for refining 5929 atoms. 12497 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2365 (Rfree = 0.000) for 5929 atoms. Found 28 (28 requested) and removed 61 (14 requested) atoms. Cycle 37: After refmac, R = 0.2274 (Rfree = 0.000) for 5862 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. Cycle 38: After refmac, R = 0.2389 (Rfree = 0.000) for 5828 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 39: After refmac, R = 0.1734 (Rfree = 0.000) for 5808 atoms. Found 17 (27 requested) and removed 15 (13 requested) atoms. Cycle 40: After refmac, R = 0.1648 (Rfree = 0.000) for 5799 atoms. Found 10 (27 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.45 Search for helices and strands: 0 residues in 0 chains, 5856 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5868 seeds are put forward Round 1: 247 peptides, 56 chains. Longest chain 7 peptides. Score 0.214 Round 2: 268 peptides, 56 chains. Longest chain 8 peptides. Score 0.254 Round 3: 275 peptides, 52 chains. Longest chain 12 peptides. Score 0.298 Round 4: 273 peptides, 53 chains. Longest chain 9 peptides. Score 0.287 Round 5: 292 peptides, 57 chains. Longest chain 12 peptides. Score 0.290 Taking the results from Round 3 Chains 52, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 13090 restraints for refining 5829 atoms. 12250 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2246 (Rfree = 0.000) for 5829 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 42: After refmac, R = 0.2238 (Rfree = 0.000) for 5771 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 43: After refmac, R = 0.2278 (Rfree = 0.000) for 5737 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 44: After refmac, R = 0.2204 (Rfree = 0.000) for 5711 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 45: After refmac, R = 0.1726 (Rfree = 0.000) for 5700 atoms. Found 17 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.44 Search for helices and strands: 0 residues in 0 chains, 5776 seeds are put forward NCS extension: 0 residues added, 5776 seeds are put forward Round 1: 232 peptides, 51 chains. Longest chain 10 peptides. Score 0.225 Round 2: 278 peptides, 55 chains. Longest chain 10 peptides. Score 0.280 Round 3: 250 peptides, 49 chains. Longest chain 10 peptides. Score 0.276 Round 4: 263 peptides, 50 chains. Longest chain 11 peptides. Score 0.292 Round 5: 262 peptides, 52 chains. Longest chain 8 peptides. Score 0.274 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 213, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vl0-4_warpNtrace.pdb as input Building loops using Loopy2018 50 chains (213 residues) following loop building 3 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9090 reflections ( 98.72 % complete ) and 12961 restraints for refining 5798 atoms. 12115 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2159 (Rfree = 0.000) for 5798 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2132 (Rfree = 0.000) for 5753 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1727 (Rfree = 0.000) for 5718 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1611 (Rfree = 0.000) for 5694 atoms. TimeTaking 67.73