Sun 23 Dec 22:22:52 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 1vp4-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-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/1vp4-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-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 ============================================================ Sun 23 Dec 22:23:02 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/1vp4-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.6-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 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-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.6-parrot-hancs.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 7516 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3585 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3772 (Rfree = 0.000) for 7516 atoms. Found 48 (48 requested) and removed 126 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.28 Search for helices and strands: 0 residues in 0 chains, 7618 seeds are put forward NCS extension: 0 residues added, 7618 seeds are put forward Round 1: 278 peptides, 58 chains. Longest chain 10 peptides. Score 0.255 Round 2: 361 peptides, 63 chains. Longest chain 15 peptides. Score 0.360 Round 3: 412 peptides, 67 chains. Longest chain 17 peptides. Score 0.412 Round 4: 419 peptides, 63 chains. Longest chain 14 peptides. Score 0.448 Round 5: 425 peptides, 61 chains. Longest chain 15 peptides. Score 0.469 Taking the results from Round 5 Chains 61, Residues 364, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13999 restraints for refining 6161 atoms. 12569 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3325 (Rfree = 0.000) for 6161 atoms. Found 39 (39 requested) and removed 81 (19 requested) atoms. Cycle 2: After refmac, R = 0.3090 (Rfree = 0.000) for 6003 atoms. Found 39 (39 requested) and removed 54 (19 requested) atoms. Cycle 3: After refmac, R = 0.3048 (Rfree = 0.000) for 5922 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 4: After refmac, R = 0.2983 (Rfree = 0.000) for 5839 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. Cycle 5: After refmac, R = 0.3058 (Rfree = 0.000) for 5818 atoms. Found 37 (37 requested) and removed 35 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.26 Search for helices and strands: 0 residues in 0 chains, 6075 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6092 seeds are put forward Round 1: 362 peptides, 67 chains. Longest chain 11 peptides. Score 0.334 Round 2: 411 peptides, 60 chains. Longest chain 22 peptides. Score 0.455 Round 3: 423 peptides, 63 chains. Longest chain 15 peptides. Score 0.453 Round 4: 442 peptides, 64 chains. Longest chain 16 peptides. Score 0.474 Round 5: 440 peptides, 62 chains. Longest chain 16 peptides. Score 0.483 Taking the results from Round 5 Chains 63, Residues 378, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14069 restraints for refining 6138 atoms. 12558 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3242 (Rfree = 0.000) for 6138 atoms. Found 39 (39 requested) and removed 89 (19 requested) atoms. Cycle 7: After refmac, R = 0.2893 (Rfree = 0.000) for 6011 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. Cycle 8: After refmac, R = 0.2760 (Rfree = 0.000) for 5955 atoms. Found 38 (38 requested) and removed 42 (19 requested) atoms. Cycle 9: After refmac, R = 0.2696 (Rfree = 0.000) for 5910 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. Cycle 10: After refmac, R = 0.2600 (Rfree = 0.000) for 5889 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 6087 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 6097 seeds are put forward Round 1: 367 peptides, 64 chains. Longest chain 26 peptides. Score 0.363 Round 2: 446 peptides, 71 chains. Longest chain 15 peptides. Score 0.436 Round 3: 453 peptides, 66 chains. Longest chain 20 peptides. Score 0.477 Round 4: 432 peptides, 64 chains. Longest chain 33 peptides. Score 0.460 Round 5: 420 peptides, 64 chains. Longest chain 16 peptides. Score 0.443 Taking the results from Round 3 Chains 67, Residues 387, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13681 restraints for refining 6140 atoms. 12120 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2711 (Rfree = 0.000) for 6140 atoms. Found 39 (39 requested) and removed 71 (19 requested) atoms. Cycle 12: After refmac, R = 0.2660 (Rfree = 0.000) for 6037 atoms. Found 39 (39 requested) and removed 46 (19 requested) atoms. Cycle 13: After refmac, R = 0.2573 (Rfree = 0.000) for 5980 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 14: After refmac, R = 0.2754 (Rfree = 0.000) for 5939 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 15: After refmac, R = 0.2615 (Rfree = 0.000) for 5899 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.25 Search for helices and strands: 0 residues in 0 chains, 6169 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 6197 seeds are put forward Round 1: 417 peptides, 85 chains. Longest chain 10 peptides. Score 0.299 Round 2: 437 peptides, 73 chains. Longest chain 15 peptides. Score 0.410 Round 3: 447 peptides, 75 chains. Longest chain 12 peptides. Score 0.412 Round 4: 456 peptides, 72 chains. Longest chain 15 peptides. Score 0.444 Round 5: 466 peptides, 67 chains. Longest chain 22 peptides. Score 0.488 Taking the results from Round 5 Chains 67, Residues 399, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13814 restraints for refining 6165 atoms. 12252 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3011 (Rfree = 0.000) for 6165 atoms. Found 39 (39 requested) and removed 61 (19 requested) atoms. Cycle 17: After refmac, R = 0.2807 (Rfree = 0.000) for 6060 atoms. Found 39 (39 requested) and removed 76 (19 requested) atoms. Cycle 18: After refmac, R = 0.2665 (Rfree = 0.000) for 5957 atoms. Found 38 (38 requested) and removed 38 (19 requested) atoms. Cycle 19: After refmac, R = 0.2599 (Rfree = 0.000) for 5906 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 20: After refmac, R = 0.2567 (Rfree = 0.000) for 5881 atoms. Found 37 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.24 Search for helices and strands: 0 residues in 0 chains, 6127 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6146 seeds are put forward Round 1: 376 peptides, 74 chains. Longest chain 10 peptides. Score 0.308 Round 2: 404 peptides, 65 chains. Longest chain 14 peptides. Score 0.413 Round 3: 446 peptides, 70 chains. Longest chain 16 peptides. Score 0.442 Round 4: 430 peptides, 64 chains. Longest chain 16 peptides. Score 0.457 Round 5: 441 peptides, 65 chains. Longest chain 19 peptides. Score 0.466 Taking the results from Round 5 Chains 68, Residues 376, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13815 restraints for refining 6163 atoms. 12322 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2884 (Rfree = 0.000) for 6163 atoms. Found 39 (39 requested) and removed 82 (19 requested) atoms. Cycle 22: After refmac, R = 0.2724 (Rfree = 0.000) for 6057 atoms. Found 39 (39 requested) and removed 74 (19 requested) atoms. Cycle 23: After refmac, R = 0.2622 (Rfree = 0.000) for 5973 atoms. Found 38 (38 requested) and removed 41 (19 requested) atoms. Cycle 24: After refmac, R = 0.2535 (Rfree = 0.000) for 5930 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. Cycle 25: After refmac, R = 0.2405 (Rfree = 0.000) for 5922 atoms. Found 38 (38 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 6164 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6177 seeds are put forward Round 1: 371 peptides, 74 chains. Longest chain 11 peptides. Score 0.299 Round 2: 426 peptides, 75 chains. Longest chain 13 peptides. Score 0.380 Round 3: 414 peptides, 67 chains. Longest chain 13 peptides. Score 0.415 Round 4: 438 peptides, 68 chains. Longest chain 16 peptides. Score 0.443 Round 5: 414 peptides, 62 chains. Longest chain 18 peptides. Score 0.447 Taking the results from Round 5 Chains 62, Residues 352, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14069 restraints for refining 6165 atoms. 12709 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2422 (Rfree = 0.000) for 6165 atoms. Found 38 (39 requested) and removed 54 (19 requested) atoms. Cycle 27: After refmac, R = 0.2251 (Rfree = 0.000) for 6108 atoms. Found 33 (39 requested) and removed 53 (19 requested) atoms. Cycle 28: After refmac, R = 0.2186 (Rfree = 0.000) for 6071 atoms. Found 34 (39 requested) and removed 39 (19 requested) atoms. Cycle 29: After refmac, R = 0.2115 (Rfree = 0.000) for 6053 atoms. Found 26 (38 requested) and removed 25 (19 requested) atoms. Cycle 30: After refmac, R = 0.2079 (Rfree = 0.000) for 6043 atoms. Found 25 (38 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 6312 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 6340 seeds are put forward Round 1: 347 peptides, 64 chains. Longest chain 13 peptides. Score 0.330 Round 2: 396 peptides, 63 chains. Longest chain 15 peptides. Score 0.414 Round 3: 404 peptides, 62 chains. Longest chain 19 peptides. Score 0.432 Round 4: 415 peptides, 62 chains. Longest chain 16 peptides. Score 0.448 Round 5: 389 peptides, 56 chains. Longest chain 19 peptides. Score 0.450 Taking the results from Round 5 Chains 56, Residues 333, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13898 restraints for refining 6165 atoms. 12578 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2594 (Rfree = 0.000) for 6165 atoms. Found 39 (39 requested) and removed 43 (19 requested) atoms. Cycle 32: After refmac, R = 0.2394 (Rfree = 0.000) for 6099 atoms. Found 39 (39 requested) and removed 30 (19 requested) atoms. Cycle 33: After refmac, R = 0.2092 (Rfree = 0.000) for 6088 atoms. Found 22 (39 requested) and removed 23 (19 requested) atoms. Cycle 34: After refmac, R = 0.1975 (Rfree = 0.000) for 6065 atoms. Found 11 (39 requested) and removed 21 (19 requested) atoms. Cycle 35: After refmac, R = 0.1928 (Rfree = 0.000) for 6046 atoms. Found 7 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 6255 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 6273 seeds are put forward Round 1: 326 peptides, 64 chains. Longest chain 13 peptides. Score 0.295 Round 2: 360 peptides, 62 chains. Longest chain 13 peptides. Score 0.365 Round 3: 367 peptides, 59 chains. Longest chain 14 peptides. Score 0.397 Round 4: 382 peptides, 57 chains. Longest chain 21 peptides. Score 0.433 Round 5: 375 peptides, 57 chains. Longest chain 14 peptides. Score 0.422 Taking the results from Round 4 Chains 57, Residues 325, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 13956 restraints for refining 6164 atoms. 12660 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2386 (Rfree = 0.000) for 6164 atoms. Found 39 (39 requested) and removed 23 (19 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2383 (Rfree = 0.000) for 6147 atoms. Found 39 (39 requested) and removed 28 (19 requested) atoms. Cycle 38: After refmac, R = 0.2288 (Rfree = 0.000) for 6142 atoms. Found 36 (39 requested) and removed 26 (19 requested) atoms. Cycle 39: After refmac, R = 0.1902 (Rfree = 0.000) for 6129 atoms. Found 14 (39 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.1849 (Rfree = 0.000) for 6104 atoms. Found 13 (39 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 6325 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 6341 seeds are put forward Round 1: 325 peptides, 66 chains. Longest chain 11 peptides. Score 0.279 Round 2: 358 peptides, 62 chains. Longest chain 13 peptides. Score 0.362 Round 3: 372 peptides, 61 chains. Longest chain 12 peptides. Score 0.391 Round 4: 364 peptides, 60 chains. Longest chain 15 peptides. Score 0.385 Round 5: 388 peptides, 63 chains. Longest chain 14 peptides. Score 0.402 Taking the results from Round 5 Chains 63, Residues 325, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12520 reflections ( 99.75 % complete ) and 14083 restraints for refining 6164 atoms. 12832 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2479 (Rfree = 0.000) for 6164 atoms. Found 39 (39 requested) and removed 24 (19 requested) atoms. Cycle 42: After refmac, R = 0.2413 (Rfree = 0.000) for 6144 atoms. Found 39 (39 requested) and removed 32 (19 requested) atoms. Cycle 43: After refmac, R = 0.2502 (Rfree = 0.000) for 6118 atoms. Found 39 (39 requested) and removed 34 (19 requested) atoms. Cycle 44: After refmac, R = 0.2294 (Rfree = 0.000) for 6108 atoms. Found 39 (39 requested) and removed 28 (19 requested) atoms. Cycle 45: After refmac, R = 0.2303 (Rfree = 0.000) for 6090 atoms. Found 39 (39 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 6330 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6342 seeds are put forward Round 1: 264 peptides, 56 chains. Longest chain 10 peptides. Score 0.245 Round 2: 314 peptides, 60 chains. Longest chain 9 peptides. Score 0.304 Round 3: 327 peptides, 57 chains. Longest chain 13 peptides. Score 0.347 Round 4: 338 peptides, 55 chains. Longest chain 12 peptides. Score 0.379 Round 5: 331 peptides, 55 chains. Longest chain 13 peptides. Score 0.368 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 283, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12520 reflections ( 99.75 % complete ) and 13995 restraints for refining 6135 atoms. 12887 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2366 (Rfree = 0.000) for 6135 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2310 (Rfree = 0.000) for 6073 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2439 (Rfree = 0.000) for 6024 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2219 (Rfree = 0.000) for 5977 atoms. TimeTaking 84.62