Mon 24 Dec 07:29:54 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 1vp7-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vp7-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vp7-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.6-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/1vp7-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.6-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 07:29:59 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/1vp7-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.6-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 544 and 0 Target number of residues in the AU: 544 Target solvent content: 0.5698 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 600 Adjusted target solvent content: 0.53 Input MTZ file: 1vp7-3.6-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.60 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: 207.138 3.600 Wilson plot Bfac: 41.56 8705 reflections ( 99.61 % complete ) and 0 restraints for refining 5290 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3171 (Rfree = 0.000) for 5290 atoms. Found 33 (33 requested) and removed 38 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 2.97 Search for helices and strands: 0 residues in 0 chains, 5383 seeds are put forward NCS extension: 0 residues added, 5383 seeds are put forward Round 1: 188 peptides, 41 chains. Longest chain 7 peptides. Score 0.238 Round 2: 233 peptides, 39 chains. Longest chain 12 peptides. Score 0.380 Round 3: 255 peptides, 38 chains. Longest chain 13 peptides. Score 0.443 Round 4: 250 peptides, 36 chains. Longest chain 13 peptides. Score 0.452 Round 5: 256 peptides, 38 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 4 Chains 36, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 9487 restraints for refining 3995 atoms. 8667 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2845 (Rfree = 0.000) for 3995 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 2: After refmac, R = 0.2771 (Rfree = 0.000) for 3880 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 3: After refmac, R = 0.2714 (Rfree = 0.000) for 3838 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Cycle 4: After refmac, R = 0.2722 (Rfree = 0.000) for 3822 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 5: After refmac, R = 0.2599 (Rfree = 0.000) for 3817 atoms. Found 18 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 2.93 Search for helices and strands: 0 residues in 0 chains, 3971 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3983 seeds are put forward Round 1: 240 peptides, 41 chains. Longest chain 13 peptides. Score 0.376 Round 2: 269 peptides, 39 chains. Longest chain 17 peptides. Score 0.464 Round 3: 279 peptides, 38 chains. Longest chain 15 peptides. Score 0.495 Round 4: 278 peptides, 34 chains. Longest chain 16 peptides. Score 0.531 Round 5: 277 peptides, 38 chains. Longest chain 17 peptides. Score 0.491 Taking the results from Round 4 Chains 34, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8068 restraints for refining 3660 atoms. 7126 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2793 (Rfree = 0.000) for 3660 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 7: After refmac, R = 0.2604 (Rfree = 0.000) for 3625 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 8: After refmac, R = 0.2468 (Rfree = 0.000) for 3612 atoms. Found 19 (23 requested) and removed 16 (11 requested) atoms. Cycle 9: After refmac, R = 0.2426 (Rfree = 0.000) for 3604 atoms. Found 15 (23 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.2365 (Rfree = 0.000) for 3596 atoms. Found 11 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.93 Search for helices and strands: 0 residues in 0 chains, 3787 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3810 seeds are put forward Round 1: 254 peptides, 45 chains. Longest chain 12 peptides. Score 0.368 Round 2: 277 peptides, 41 chains. Longest chain 14 peptides. Score 0.462 Round 3: 267 peptides, 38 chains. Longest chain 19 peptides. Score 0.470 Round 4: 284 peptides, 42 chains. Longest chain 23 peptides. Score 0.468 Round 5: 289 peptides, 40 chains. Longest chain 20 peptides. Score 0.498 Taking the results from Round 5 Chains 40, Residues 249, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8108 restraints for refining 3701 atoms. 7152 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2755 (Rfree = 0.000) for 3701 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 12: After refmac, R = 0.2605 (Rfree = 0.000) for 3673 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 13: After refmac, R = 0.2561 (Rfree = 0.000) for 3659 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 14: After refmac, R = 0.2337 (Rfree = 0.000) for 3641 atoms. Found 12 (23 requested) and removed 19 (11 requested) atoms. Cycle 15: After refmac, R = 0.2376 (Rfree = 0.000) for 3621 atoms. Found 12 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 3816 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 3840 seeds are put forward Round 1: 256 peptides, 47 chains. Longest chain 12 peptides. Score 0.351 Round 2: 273 peptides, 43 chains. Longest chain 12 peptides. Score 0.433 Round 3: 270 peptides, 39 chains. Longest chain 19 peptides. Score 0.466 Round 4: 262 peptides, 38 chains. Longest chain 18 peptides. Score 0.458 Round 5: 271 peptides, 38 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 5 Chains 38, Residues 233, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8478 restraints for refining 3828 atoms. 7514 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2766 (Rfree = 0.000) for 3828 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 17: After refmac, R = 0.2594 (Rfree = 0.000) for 3780 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 18: After refmac, R = 0.2580 (Rfree = 0.000) for 3755 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 19: After refmac, R = 0.2425 (Rfree = 0.000) for 3735 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 20: After refmac, R = 0.2354 (Rfree = 0.000) for 3721 atoms. Found 23 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.00 2.88 Search for helices and strands: 0 residues in 0 chains, 3913 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3933 seeds are put forward Round 1: 207 peptides, 39 chains. Longest chain 14 peptides. Score 0.314 Round 2: 255 peptides, 43 chains. Longest chain 12 peptides. Score 0.391 Round 3: 257 peptides, 41 chains. Longest chain 19 peptides. Score 0.417 Round 4: 265 peptides, 42 chains. Longest chain 14 peptides. Score 0.425 Round 5: 268 peptides, 42 chains. Longest chain 17 peptides. Score 0.432 Taking the results from Round 5 Chains 42, Residues 226, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8785 restraints for refining 3833 atoms. 7893 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2870 (Rfree = 0.000) for 3833 atoms. Found 24 (24 requested) and removed 38 (12 requested) atoms. Cycle 22: After refmac, R = 0.2579 (Rfree = 0.000) for 3787 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 23: After refmac, R = 0.2494 (Rfree = 0.000) for 3760 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 24: After refmac, R = 0.2454 (Rfree = 0.000) for 3745 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 25: After refmac, R = 0.2490 (Rfree = 0.000) for 3740 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 2.96 Search for helices and strands: 0 residues in 0 chains, 3953 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3976 seeds are put forward Round 1: 222 peptides, 44 chains. Longest chain 11 peptides. Score 0.297 Round 2: 244 peptides, 44 chains. Longest chain 11 peptides. Score 0.353 Round 3: 247 peptides, 40 chains. Longest chain 12 peptides. Score 0.403 Round 4: 254 peptides, 39 chains. Longest chain 16 peptides. Score 0.430 Round 5: 250 peptides, 37 chains. Longest chain 17 peptides. Score 0.441 Taking the results from Round 5 Chains 37, Residues 213, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8887 restraints for refining 3962 atoms. 8007 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2743 (Rfree = 0.000) for 3962 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 27: After refmac, R = 0.2696 (Rfree = 0.000) for 3924 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 28: After refmac, R = 0.2329 (Rfree = 0.000) for 3909 atoms. Found 18 (25 requested) and removed 22 (12 requested) atoms. Cycle 29: After refmac, R = 0.2346 (Rfree = 0.000) for 3895 atoms. Found 9 (25 requested) and removed 16 (12 requested) atoms. Cycle 30: After refmac, R = 0.2318 (Rfree = 0.000) for 3881 atoms. Found 10 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.04 2.92 Search for helices and strands: 0 residues in 0 chains, 4012 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4035 seeds are put forward Round 1: 201 peptides, 39 chains. Longest chain 10 peptides. Score 0.298 Round 2: 225 peptides, 41 chains. Longest chain 9 peptides. Score 0.338 Round 3: 238 peptides, 39 chains. Longest chain 17 peptides. Score 0.392 Round 4: 245 peptides, 38 chains. Longest chain 13 peptides. Score 0.420 Round 5: 249 peptides, 37 chains. Longest chain 15 peptides. Score 0.439 Taking the results from Round 5 Chains 37, Residues 212, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 9030 restraints for refining 3944 atoms. 8201 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2684 (Rfree = 0.000) for 3944 atoms. Found 25 (25 requested) and removed 42 (12 requested) atoms. Cycle 32: After refmac, R = 0.2557 (Rfree = 0.000) for 3888 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2318 (Rfree = 0.000) for 3862 atoms. Found 16 (24 requested) and removed 17 (12 requested) atoms. Cycle 34: After refmac, R = 0.2238 (Rfree = 0.000) for 3854 atoms. Found 12 (24 requested) and removed 19 (12 requested) atoms. Cycle 35: After refmac, R = 0.2261 (Rfree = 0.000) for 3844 atoms. Found 9 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 2.90 Search for helices and strands: 0 residues in 0 chains, 3996 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 4017 seeds are put forward Round 1: 189 peptides, 38 chains. Longest chain 8 peptides. Score 0.277 Round 2: 237 peptides, 39 chains. Longest chain 16 peptides. Score 0.390 Round 3: 256 peptides, 41 chains. Longest chain 14 peptides. Score 0.414 Round 4: 250 peptides, 42 chains. Longest chain 13 peptides. Score 0.390 Round 5: 254 peptides, 43 chains. Longest chain 17 peptides. Score 0.389 Taking the results from Round 3 Chains 41, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8742 restraints for refining 3856 atoms. 7923 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2544 (Rfree = 0.000) for 3856 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 37: After refmac, R = 0.2380 (Rfree = 0.000) for 3836 atoms. Found 20 (24 requested) and removed 24 (12 requested) atoms. Cycle 38: After refmac, R = 0.2355 (Rfree = 0.000) for 3816 atoms. Found 18 (24 requested) and removed 18 (12 requested) atoms. Cycle 39: After refmac, R = 0.2418 (Rfree = 0.000) for 3807 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 40: After refmac, R = 0.2388 (Rfree = 0.000) for 3803 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.01 2.89 Search for helices and strands: 0 residues in 0 chains, 3970 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 3992 seeds are put forward Round 1: 226 peptides, 45 chains. Longest chain 14 peptides. Score 0.296 Round 2: 247 peptides, 43 chains. Longest chain 17 peptides. Score 0.372 Round 3: 260 peptides, 42 chains. Longest chain 19 peptides. Score 0.413 Round 4: 255 peptides, 37 chains. Longest chain 19 peptides. Score 0.453 Round 5: 256 peptides, 37 chains. Longest chain 20 peptides. Score 0.455 Taking the results from Round 5 Chains 37, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8731 restraints for refining 3915 atoms. 7892 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2842 (Rfree = 0.000) for 3915 atoms. Found 25 (25 requested) and removed 41 (12 requested) atoms. Cycle 42: After refmac, R = 0.2656 (Rfree = 0.000) for 3880 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 43: After refmac, R = 0.2612 (Rfree = 0.000) for 3877 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 44: After refmac, R = 0.2434 (Rfree = 0.000) for 3872 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.2400 (Rfree = 0.000) for 3878 atoms. Found 17 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 2.96 Search for helices and strands: 0 residues in 0 chains, 4057 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 4093 seeds are put forward Round 1: 182 peptides, 37 chains. Longest chain 10 peptides. Score 0.269 Round 2: 230 peptides, 41 chains. Longest chain 17 peptides. Score 0.351 Round 3: 227 peptides, 34 chains. Longest chain 19 peptides. Score 0.419 Round 4: 231 peptides, 38 chains. Longest chain 19 peptides. Score 0.386 Round 5: 242 peptides, 38 chains. Longest chain 15 peptides. Score 0.412 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vp7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8705 reflections ( 99.61 % complete ) and 9082 restraints for refining 3911 atoms. 8344 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2725 (Rfree = 0.000) for 3911 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2636 (Rfree = 0.000) for 3881 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2533 (Rfree = 0.000) for 3862 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2476 (Rfree = 0.000) for 3848 atoms. TimeTaking 62.3