Mon 24 Dec 00:10:42 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 1vp4-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-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/1vp4-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-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 00:10:47 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/1vp4-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-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 695 and 0 Target number of residues in the AU: 695 Target solvent content: 0.6506 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-3.6-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6800 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 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: 142.773 3.600 Wilson plot Bfac: 78.52 Failed to save intermediate PDB 12520 reflections ( 99.75 % complete ) and 0 restraints for refining 7540 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3590 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3664 (Rfree = 0.000) for 7540 atoms. Found 48 (48 requested) and removed 78 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 7685 seeds are put forward NCS extension: 0 residues added, 7685 seeds are put forward Round 1: 299 peptides, 59 chains. Longest chain 15 peptides. Score 0.285 Round 2: 418 peptides, 66 chains. Longest chain 19 peptides. Score 0.427 Round 3: 447 peptides, 61 chains. Longest chain 22 peptides. Score 0.499 Round 4: 432 peptides, 62 chains. Longest chain 18 peptides. Score 0.472 Round 5: 448 peptides, 59 chains. Longest chain 22 peptides. Score 0.512 Taking the results from Round 5 Chains 59, Residues 389, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14049 restraints for refining 6162 atoms. 12489 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3092 (Rfree = 0.000) for 6162 atoms. Found 36 (39 requested) and removed 79 (19 requested) atoms. Cycle 2: After refmac, R = 0.2764 (Rfree = 0.000) for 5975 atoms. Found 34 (39 requested) and removed 45 (19 requested) atoms. Cycle 3: After refmac, R = 0.2821 (Rfree = 0.000) for 5893 atoms. Found 38 (38 requested) and removed 41 (19 requested) atoms. Cycle 4: After refmac, R = 0.2698 (Rfree = 0.000) for 5836 atoms. Found 30 (37 requested) and removed 35 (18 requested) atoms. Cycle 5: After refmac, R = 0.2732 (Rfree = 0.000) for 5790 atoms. Found 30 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 6065 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6080 seeds are put forward Round 1: 370 peptides, 68 chains. Longest chain 15 peptides. Score 0.340 Round 2: 431 peptides, 65 chains. Longest chain 19 peptides. Score 0.452 Round 3: 458 peptides, 68 chains. Longest chain 24 peptides. Score 0.471 Round 4: 449 peptides, 68 chains. Longest chain 15 peptides. Score 0.459 Round 5: 453 peptides, 64 chains. Longest chain 20 peptides. Score 0.489 Taking the results from Round 5 Chains 70, Residues 389, Estimated correctness of the model 0.0 % 7 chains (56 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13517 restraints for refining 6105 atoms. 11858 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2730 (Rfree = 0.000) for 6105 atoms. Found 35 (39 requested) and removed 61 (19 requested) atoms. Cycle 7: After refmac, R = 0.2539 (Rfree = 0.000) for 6010 atoms. Found 32 (39 requested) and removed 51 (19 requested) atoms. Cycle 8: After refmac, R = 0.2443 (Rfree = 0.000) for 5941 atoms. Found 18 (38 requested) and removed 43 (19 requested) atoms. Cycle 9: After refmac, R = 0.2427 (Rfree = 0.000) for 5880 atoms. Found 32 (37 requested) and removed 45 (18 requested) atoms. Cycle 10: After refmac, R = 0.2291 (Rfree = 0.000) for 5839 atoms. Found 19 (37 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 6038 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 6050 seeds are put forward Round 1: 395 peptides, 69 chains. Longest chain 15 peptides. Score 0.372 Round 2: 464 peptides, 69 chains. Longest chain 21 peptides. Score 0.473 Round 3: 456 peptides, 63 chains. Longest chain 22 peptides. Score 0.499 Round 4: 477 peptides, 70 chains. Longest chain 15 peptides. Score 0.485 Round 5: 472 peptides, 66 chains. Longest chain 18 peptides. Score 0.502 Taking the results from Round 5 Chains 66, Residues 406, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13753 restraints for refining 6164 atoms. 12150 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2542 (Rfree = 0.000) for 6164 atoms. Found 39 (39 requested) and removed 86 (19 requested) atoms. Cycle 12: After refmac, R = 0.2274 (Rfree = 0.000) for 6086 atoms. Found 22 (39 requested) and removed 71 (19 requested) atoms. Cycle 13: After refmac, R = 0.2186 (Rfree = 0.000) for 6026 atoms. Found 14 (38 requested) and removed 38 (19 requested) atoms. Cycle 14: After refmac, R = 0.2114 (Rfree = 0.000) for 5993 atoms. Found 3 (38 requested) and removed 35 (19 requested) atoms. Cycle 15: After refmac, R = 0.2188 (Rfree = 0.000) for 5954 atoms. Found 12 (38 requested) and removed 43 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 6160 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6181 seeds are put forward Round 1: 407 peptides, 75 chains. Longest chain 15 peptides. Score 0.351 Round 2: 444 peptides, 69 chains. Longest chain 16 peptides. Score 0.445 Round 3: 436 peptides, 64 chains. Longest chain 19 peptides. Score 0.465 Round 4: 428 peptides, 66 chains. Longest chain 14 peptides. Score 0.441 Round 5: 450 peptides, 61 chains. Longest chain 16 peptides. Score 0.503 Taking the results from Round 5 Chains 64, Residues 389, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13616 restraints for refining 6164 atoms. 12009 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2404 (Rfree = 0.000) for 6164 atoms. Found 32 (39 requested) and removed 46 (19 requested) atoms. Cycle 17: After refmac, R = 0.2246 (Rfree = 0.000) for 6105 atoms. Found 18 (39 requested) and removed 38 (19 requested) atoms. Cycle 18: After refmac, R = 0.2141 (Rfree = 0.000) for 6075 atoms. Found 12 (39 requested) and removed 26 (19 requested) atoms. Cycle 19: After refmac, R = 0.2118 (Rfree = 0.000) for 6055 atoms. Found 8 (38 requested) and removed 26 (19 requested) atoms. Cycle 20: After refmac, R = 0.2054 (Rfree = 0.000) for 6031 atoms. Found 10 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 6268 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6285 seeds are put forward Round 1: 397 peptides, 69 chains. Longest chain 11 peptides. Score 0.376 Round 2: 431 peptides, 66 chains. Longest chain 14 peptides. Score 0.446 Round 3: 424 peptides, 66 chains. Longest chain 13 peptides. Score 0.436 Round 4: 440 peptides, 65 chains. Longest chain 13 peptides. Score 0.465 Round 5: 444 peptides, 69 chains. Longest chain 18 peptides. Score 0.445 Taking the results from Round 4 Chains 65, Residues 375, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14014 restraints for refining 6164 atoms. 12560 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2336 (Rfree = 0.000) for 6164 atoms. Found 24 (39 requested) and removed 23 (19 requested) atoms. Cycle 22: After refmac, R = 0.2211 (Rfree = 0.000) for 6143 atoms. Found 10 (39 requested) and removed 29 (19 requested) atoms. Cycle 23: After refmac, R = 0.2208 (Rfree = 0.000) for 6113 atoms. Found 11 (39 requested) and removed 22 (19 requested) atoms. Cycle 24: After refmac, R = 0.2093 (Rfree = 0.000) for 6095 atoms. Found 8 (39 requested) and removed 23 (19 requested) atoms. Cycle 25: After refmac, R = 0.2049 (Rfree = 0.000) for 6064 atoms. Found 6 (39 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 6290 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6304 seeds are put forward Round 1: 376 peptides, 75 chains. Longest chain 13 peptides. Score 0.301 Round 2: 405 peptides, 70 chains. Longest chain 13 peptides. Score 0.381 Round 3: 436 peptides, 70 chains. Longest chain 15 peptides. Score 0.428 Round 4: 437 peptides, 72 chains. Longest chain 21 peptides. Score 0.416 Round 5: 433 peptides, 60 chains. Longest chain 21 peptides. Score 0.486 Taking the results from Round 5 Chains 61, Residues 373, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13943 restraints for refining 6164 atoms. 12436 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2514 (Rfree = 0.000) for 6164 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. Cycle 27: After refmac, R = 0.2411 (Rfree = 0.000) for 6124 atoms. Found 39 (39 requested) and removed 42 (19 requested) atoms. Cycle 28: After refmac, R = 0.2261 (Rfree = 0.000) for 6091 atoms. Found 28 (39 requested) and removed 33 (19 requested) atoms. Cycle 29: After refmac, R = 0.2056 (Rfree = 0.000) for 6066 atoms. Found 10 (39 requested) and removed 23 (19 requested) atoms. Cycle 30: After refmac, R = 0.2101 (Rfree = 0.000) for 6039 atoms. Found 19 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 6220 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6237 seeds are put forward Round 1: 340 peptides, 70 chains. Longest chain 9 peptides. Score 0.276 Round 2: 358 peptides, 61 chains. Longest chain 13 peptides. Score 0.369 Round 3: 383 peptides, 65 chains. Longest chain 14 peptides. Score 0.381 Round 4: 398 peptides, 68 chains. Longest chain 14 peptides. Score 0.384 Round 5: 402 peptides, 65 chains. Longest chain 12 peptides. Score 0.410 Taking the results from Round 5 Chains 65, Residues 337, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14029 restraints for refining 6163 atoms. 12667 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2471 (Rfree = 0.000) for 6163 atoms. Found 39 (39 requested) and removed 41 (19 requested) atoms. Cycle 32: After refmac, R = 0.2375 (Rfree = 0.000) for 6126 atoms. Found 33 (39 requested) and removed 29 (19 requested) atoms. Cycle 33: After refmac, R = 0.2260 (Rfree = 0.000) for 6103 atoms. Found 24 (39 requested) and removed 28 (19 requested) atoms. Cycle 34: After refmac, R = 0.2315 (Rfree = 0.000) for 6086 atoms. Found 39 (39 requested) and removed 28 (19 requested) atoms. Cycle 35: After refmac, R = 0.2176 (Rfree = 0.000) for 6078 atoms. Found 28 (39 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.17 Search for helices and strands: 0 residues in 0 chains, 6283 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6296 seeds are put forward Round 1: 340 peptides, 74 chains. Longest chain 7 peptides. Score 0.247 Round 2: 376 peptides, 69 chains. Longest chain 13 peptides. Score 0.342 Round 3: 365 peptides, 67 chains. Longest chain 12 peptides. Score 0.339 Round 4: 368 peptides, 63 chains. Longest chain 11 peptides. Score 0.371 Round 5: 399 peptides, 69 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 5 Chains 70, Residues 330, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12520 reflections ( 99.75 % complete ) and 14067 restraints for refining 6165 atoms. 12758 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2424 (Rfree = 0.000) for 6165 atoms. Found 39 (39 requested) and removed 55 (19 requested) atoms. Cycle 37: After refmac, R = 0.2181 (Rfree = 0.000) for 6103 atoms. Found 24 (39 requested) and removed 21 (19 requested) atoms. Cycle 38: After refmac, R = 0.2074 (Rfree = 0.000) for 6080 atoms. Found 8 (39 requested) and removed 20 (19 requested) atoms. Cycle 39: After refmac, R = 0.2086 (Rfree = 0.000) for 6056 atoms. Found 9 (38 requested) and removed 20 (19 requested) atoms. Cycle 40: After refmac, R = 0.2062 (Rfree = 0.000) for 6038 atoms. Found 13 (38 requested) and removed 39 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 6216 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6229 seeds are put forward Round 1: 330 peptides, 66 chains. Longest chain 12 peptides. Score 0.287 Round 2: 354 peptides, 60 chains. Longest chain 14 peptides. Score 0.370 Round 3: 375 peptides, 62 chains. Longest chain 15 peptides. Score 0.389 Round 4: 379 peptides, 66 chains. Longest chain 13 peptides. Score 0.368 Round 5: 380 peptides, 70 chains. Longest chain 13 peptides. Score 0.342 Taking the results from Round 3 Chains 62, Residues 313, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13860 restraints for refining 6105 atoms. 12656 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2194 (Rfree = 0.000) for 6105 atoms. Found 25 (39 requested) and removed 29 (19 requested) atoms. Cycle 42: After refmac, R = 0.2114 (Rfree = 0.000) for 6087 atoms. Found 20 (39 requested) and removed 25 (19 requested) atoms. Cycle 43: After refmac, R = 0.2108 (Rfree = 0.000) for 6077 atoms. Found 19 (39 requested) and removed 24 (19 requested) atoms. Cycle 44: After refmac, R = 0.2156 (Rfree = 0.000) for 6065 atoms. Found 23 (38 requested) and removed 23 (19 requested) atoms. Cycle 45: After refmac, R = 0.1954 (Rfree = 0.000) for 6057 atoms. Found 0 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 6262 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6281 seeds are put forward Round 1: 308 peptides, 64 chains. Longest chain 11 peptides. Score 0.264 Round 2: 350 peptides, 63 chains. Longest chain 11 peptides. Score 0.342 Round 3: 358 peptides, 64 chains. Longest chain 13 peptides. Score 0.348 Round 4: 365 peptides, 61 chains. Longest chain 16 peptides. Score 0.380 Round 5: 363 peptides, 63 chains. Longest chain 18 peptides. Score 0.363 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 304, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (304 residues) following loop building 3 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12520 reflections ( 99.75 % complete ) and 14074 restraints for refining 6165 atoms. 12896 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2371 (Rfree = 0.000) for 6165 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2307 (Rfree = 0.000) for 6110 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2273 (Rfree = 0.000) for 6063 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2099 (Rfree = 0.000) for 6029 atoms. TimeTaking 60.35