Mon 24 Dec 08:05:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vp4-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-parrot-noncs ############### 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 08:05:34 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/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-parrot-noncs/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-noncs.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-noncs.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 12520 reflections ( 99.75 % complete ) and 0 restraints for refining 7563 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3678 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3842 (Rfree = 0.000) for 7563 atoms. Found 48 (48 requested) and removed 106 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 7666 seeds are put forward NCS extension: 0 residues added, 7666 seeds are put forward Round 1: 252 peptides, 54 chains. Longest chain 11 peptides. Score 0.238 Round 2: 322 peptides, 59 chains. Longest chain 12 peptides. Score 0.325 Round 3: 361 peptides, 59 chains. Longest chain 14 peptides. Score 0.388 Round 4: 378 peptides, 64 chains. Longest chain 12 peptides. Score 0.380 Round 5: 371 peptides, 57 chains. Longest chain 16 peptides. Score 0.416 Taking the results from Round 5 Chains 57, Residues 314, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14649 restraints for refining 6160 atoms. 13390 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3511 (Rfree = 0.000) for 6160 atoms. Found 39 (39 requested) and removed 57 (19 requested) atoms. Cycle 2: After refmac, R = 0.3366 (Rfree = 0.000) for 6027 atoms. Found 39 (39 requested) and removed 45 (19 requested) atoms. Cycle 3: After refmac, R = 0.3332 (Rfree = 0.000) for 5911 atoms. Found 38 (38 requested) and removed 57 (19 requested) atoms. Cycle 4: After refmac, R = 0.3360 (Rfree = 0.000) for 5830 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. Cycle 5: After refmac, R = 0.3221 (Rfree = 0.000) for 5768 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.25 Search for helices and strands: 0 residues in 0 chains, 5983 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5999 seeds are put forward Round 1: 336 peptides, 67 chains. Longest chain 10 peptides. Score 0.290 Round 2: 404 peptides, 68 chains. Longest chain 15 peptides. Score 0.393 Round 3: 400 peptides, 62 chains. Longest chain 15 peptides. Score 0.426 Round 4: 415 peptides, 62 chains. Longest chain 17 peptides. Score 0.448 Round 5: 423 peptides, 62 chains. Longest chain 20 peptides. Score 0.460 Taking the results from Round 5 Chains 63, Residues 361, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 12922 restraints for refining 5851 atoms. 11449 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3288 (Rfree = 0.000) for 5851 atoms. Found 37 (37 requested) and removed 64 (18 requested) atoms. Cycle 7: After refmac, R = 0.3053 (Rfree = 0.000) for 5754 atoms. Found 37 (37 requested) and removed 60 (18 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2646 (Rfree = 0.000) for 5671 atoms. Found 23 (36 requested) and removed 38 (18 requested) atoms. Cycle 9: After refmac, R = 0.2843 (Rfree = 0.000) for 5624 atoms. Found 36 (36 requested) and removed 36 (18 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2873 (Rfree = 0.000) for 5582 atoms. Found 36 (36 requested) and removed 45 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 5789 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 5821 seeds are put forward Round 1: 363 peptides, 69 chains. Longest chain 15 peptides. Score 0.321 Round 2: 410 peptides, 62 chains. Longest chain 23 peptides. Score 0.441 Round 3: 428 peptides, 63 chains. Longest chain 24 peptides. Score 0.460 Round 4: 439 peptides, 62 chains. Longest chain 17 peptides. Score 0.482 Round 5: 422 peptides, 59 chains. Longest chain 22 peptides. Score 0.477 Taking the results from Round 4 Chains 62, Residues 377, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13370 restraints for refining 5957 atoms. 11924 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3007 (Rfree = 0.000) for 5957 atoms. Found 38 (38 requested) and removed 60 (19 requested) atoms. Cycle 12: After refmac, R = 0.2825 (Rfree = 0.000) for 5876 atoms. Found 38 (38 requested) and removed 45 (19 requested) atoms. Cycle 13: After refmac, R = 0.2791 (Rfree = 0.000) for 5807 atoms. Found 37 (37 requested) and removed 35 (18 requested) atoms. Cycle 14: After refmac, R = 0.2640 (Rfree = 0.000) for 5777 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. Cycle 15: After refmac, R = 0.2632 (Rfree = 0.000) for 5750 atoms. Found 37 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 6035 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6051 seeds are put forward Round 1: 364 peptides, 72 chains. Longest chain 14 peptides. Score 0.302 Round 2: 406 peptides, 65 chains. Longest chain 15 peptides. Score 0.416 Round 3: 419 peptides, 67 chains. Longest chain 20 peptides. Score 0.422 Round 4: 431 peptides, 64 chains. Longest chain 20 peptides. Score 0.458 Round 5: 418 peptides, 58 chains. Longest chain 25 peptides. Score 0.478 Taking the results from Round 5 Chains 58, Residues 360, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14396 restraints for refining 6165 atoms. 13014 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2872 (Rfree = 0.000) for 6165 atoms. Found 39 (39 requested) and removed 83 (19 requested) atoms. Cycle 17: After refmac, R = 0.2824 (Rfree = 0.000) for 6063 atoms. Found 39 (39 requested) and removed 42 (19 requested) atoms. Cycle 18: After refmac, R = 0.2582 (Rfree = 0.000) for 6015 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. Cycle 19: After refmac, R = 0.2741 (Rfree = 0.000) for 5987 atoms. Found 38 (38 requested) and removed 35 (19 requested) atoms. Cycle 20: After refmac, R = 0.2582 (Rfree = 0.000) for 5967 atoms. Found 38 (38 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.17 Search for helices and strands: 0 residues in 0 chains, 6229 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6253 seeds are put forward Round 1: 348 peptides, 73 chains. Longest chain 8 peptides. Score 0.268 Round 2: 377 peptides, 65 chains. Longest chain 16 peptides. Score 0.371 Round 3: 419 peptides, 69 chains. Longest chain 19 peptides. Score 0.409 Round 4: 427 peptides, 67 chains. Longest chain 14 peptides. Score 0.434 Round 5: 417 peptides, 69 chains. Longest chain 14 peptides. Score 0.406 Taking the results from Round 4 Chains 67, Residues 360, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13812 restraints for refining 6164 atoms. 12425 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2894 (Rfree = 0.000) for 6164 atoms. Found 39 (39 requested) and removed 55 (19 requested) atoms. Cycle 22: After refmac, R = 0.2695 (Rfree = 0.000) for 6078 atoms. Found 39 (39 requested) and removed 40 (19 requested) atoms. Cycle 23: After refmac, R = 0.2515 (Rfree = 0.000) for 6038 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 24: After refmac, R = 0.2491 (Rfree = 0.000) for 6014 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 25: After refmac, R = 0.2312 (Rfree = 0.000) for 6000 atoms. Found 37 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 6246 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6259 seeds are put forward Round 1: 300 peptides, 61 chains. Longest chain 9 peptides. Score 0.272 Round 2: 337 peptides, 58 chains. Longest chain 11 peptides. Score 0.356 Round 3: 377 peptides, 63 chains. Longest chain 15 peptides. Score 0.385 Round 4: 369 peptides, 58 chains. Longest chain 16 peptides. Score 0.407 Round 5: 355 peptides, 56 chains. Longest chain 19 peptides. Score 0.399 Taking the results from Round 4 Chains 58, Residues 311, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14413 restraints for refining 6165 atoms. 13227 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2467 (Rfree = 0.000) for 6165 atoms. Found 39 (39 requested) and removed 36 (19 requested) atoms. Cycle 27: After refmac, R = 0.2258 (Rfree = 0.000) for 6139 atoms. Found 36 (39 requested) and removed 25 (19 requested) atoms. Cycle 28: After refmac, R = 0.2113 (Rfree = 0.000) for 6122 atoms. Found 30 (39 requested) and removed 31 (19 requested) atoms. Cycle 29: After refmac, R = 0.2075 (Rfree = 0.000) for 6108 atoms. Found 26 (39 requested) and removed 26 (19 requested) atoms. Cycle 30: After refmac, R = 0.2025 (Rfree = 0.000) for 6096 atoms. Found 29 (39 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 6304 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6326 seeds are put forward Round 1: 322 peptides, 68 chains. Longest chain 10 peptides. Score 0.259 Round 2: 369 peptides, 64 chains. Longest chain 12 peptides. Score 0.366 Round 3: 363 peptides, 63 chains. Longest chain 12 peptides. Score 0.363 Round 4: 366 peptides, 62 chains. Longest chain 15 peptides. Score 0.375 Round 5: 355 peptides, 58 chains. Longest chain 18 peptides. Score 0.385 Taking the results from Round 5 Chains 58, Residues 297, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14286 restraints for refining 6165 atoms. 13111 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2374 (Rfree = 0.000) for 6165 atoms. Found 39 (39 requested) and removed 24 (19 requested) atoms. Cycle 32: After refmac, R = 0.2268 (Rfree = 0.000) for 6145 atoms. Found 39 (39 requested) and removed 25 (19 requested) atoms. Cycle 33: After refmac, R = 0.2360 (Rfree = 0.000) for 6134 atoms. Found 39 (39 requested) and removed 24 (19 requested) atoms. Cycle 34: After refmac, R = 0.2116 (Rfree = 0.000) for 6131 atoms. Found 33 (39 requested) and removed 22 (19 requested) atoms. Cycle 35: After refmac, R = 0.2248 (Rfree = 0.000) for 6132 atoms. Found 39 (39 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 6348 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6364 seeds are put forward Round 1: 305 peptides, 67 chains. Longest chain 8 peptides. Score 0.236 Round 2: 351 peptides, 61 chains. Longest chain 13 peptides. Score 0.358 Round 3: 339 peptides, 59 chains. Longest chain 13 peptides. Score 0.353 Round 4: 350 peptides, 62 chains. Longest chain 17 peptides. Score 0.349 Round 5: 359 peptides, 62 chains. Longest chain 18 peptides. Score 0.364 Taking the results from Round 5 Chains 63, Residues 297, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14316 restraints for refining 6165 atoms. 13127 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2375 (Rfree = 0.000) for 6165 atoms. Found 37 (39 requested) and removed 31 (19 requested) atoms. Cycle 37: After refmac, R = 0.2215 (Rfree = 0.000) for 6138 atoms. Found 36 (39 requested) and removed 22 (19 requested) atoms. Cycle 38: After refmac, R = 0.2171 (Rfree = 0.000) for 6136 atoms. Found 27 (39 requested) and removed 23 (19 requested) atoms. Cycle 39: After refmac, R = 0.1941 (Rfree = 0.000) for 6124 atoms. Found 6 (39 requested) and removed 21 (19 requested) atoms. Cycle 40: After refmac, R = 0.2041 (Rfree = 0.000) for 6104 atoms. Found 22 (39 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.13 Search for helices and strands: 0 residues in 0 chains, 6318 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 6333 seeds are put forward Round 1: 310 peptides, 68 chains. Longest chain 9 peptides. Score 0.238 Round 2: 331 peptides, 61 chains. Longest chain 13 peptides. Score 0.325 Round 3: 332 peptides, 60 chains. Longest chain 14 peptides. Score 0.334 Round 4: 341 peptides, 57 chains. Longest chain 13 peptides. Score 0.370 Round 5: 353 peptides, 56 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 5 Chains 56, Residues 297, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12520 reflections ( 99.75 % complete ) and 14466 restraints for refining 6165 atoms. 13334 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2339 (Rfree = 0.000) for 6165 atoms. Found 39 (39 requested) and removed 24 (19 requested) atoms. Cycle 42: After refmac, R = 0.2492 (Rfree = 0.000) for 6148 atoms. Found 39 (39 requested) and removed 38 (19 requested) atoms. Cycle 43: After refmac, R = 0.2401 (Rfree = 0.000) for 6133 atoms. Found 39 (39 requested) and removed 25 (19 requested) atoms. Cycle 44: After refmac, R = 0.2283 (Rfree = 0.000) for 6119 atoms. Found 39 (39 requested) and removed 23 (19 requested) atoms. Cycle 45: After refmac, R = 0.2264 (Rfree = 0.000) for 6122 atoms. Found 39 (39 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 6375 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6391 seeds are put forward Round 1: 267 peptides, 60 chains. Longest chain 8 peptides. Score 0.219 Round 2: 312 peptides, 64 chains. Longest chain 9 peptides. Score 0.271 Round 3: 319 peptides, 61 chains. Longest chain 9 peptides. Score 0.305 Round 4: 305 peptides, 56 chains. Longest chain 9 peptides. Score 0.318 Round 5: 320 peptides, 57 chains. Longest chain 10 peptides. Score 0.336 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 263, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (263 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12520 reflections ( 99.75 % complete ) and 14673 restraints for refining 6165 atoms. 13667 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2226 (Rfree = 0.000) for 6165 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2283 (Rfree = 0.000) for 6129 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2290 (Rfree = 0.000) for 6099 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2339 (Rfree = 0.000) for 6066 atoms. TimeTaking 72.15