Sun 23 Dec 23:45:32 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 1vp7-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.8-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/1vp7-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.8-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 ============================================================ Sun 23 Dec 23:45:36 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/1vp7-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.8-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 509 and 0 Target number of residues in the AU: 509 Target solvent content: 0.5975 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: 1vp7-3.8-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.8-parrot-mrncs.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 3.800 Wilson plot Bfac: 51.38 7444 reflections ( 99.55 % complete ) and 0 restraints for refining 5296 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3054 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3388 (Rfree = 0.000) for 5296 atoms. Found 29 (29 requested) and removed 47 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.18 Search for helices and strands: 0 residues in 0 chains, 5395 seeds are put forward NCS extension: 0 residues added, 5395 seeds are put forward Round 1: 176 peptides, 36 chains. Longest chain 10 peptides. Score 0.264 Round 2: 227 peptides, 39 chains. Longest chain 12 peptides. Score 0.365 Round 3: 244 peptides, 35 chains. Longest chain 17 peptides. Score 0.448 Round 4: 246 peptides, 32 chains. Longest chain 22 peptides. Score 0.483 Round 5: 259 peptides, 32 chains. Longest chain 18 peptides. Score 0.511 Taking the results from Round 5 Chains 32, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 9269 restraints for refining 3930 atoms. 8393 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3056 (Rfree = 0.000) for 3930 atoms. Found 21 (21 requested) and removed 44 (10 requested) atoms. Cycle 2: After refmac, R = 0.2835 (Rfree = 0.000) for 3779 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2403 (Rfree = 0.000) for 3698 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. Cycle 4: After refmac, R = 0.2283 (Rfree = 0.000) for 3657 atoms. Found 15 (20 requested) and removed 25 (10 requested) atoms. Cycle 5: After refmac, R = 0.2525 (Rfree = 0.000) for 3630 atoms. Found 16 (20 requested) and removed 30 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 3803 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 3816 seeds are put forward Round 1: 240 peptides, 43 chains. Longest chain 12 peptides. Score 0.354 Round 2: 267 peptides, 40 chains. Longest chain 21 peptides. Score 0.450 Round 3: 256 peptides, 34 chains. Longest chain 16 peptides. Score 0.485 Round 4: 272 peptides, 38 chains. Longest chain 15 peptides. Score 0.480 Round 5: 273 peptides, 37 chains. Longest chain 15 peptides. Score 0.492 Taking the results from Round 5 Chains 38, Residues 236, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8104 restraints for refining 3680 atoms. 7151 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3096 (Rfree = 0.000) for 3680 atoms. Found 20 (20 requested) and removed 49 (10 requested) atoms. Cycle 7: After refmac, R = 0.2843 (Rfree = 0.000) for 3618 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. Cycle 8: After refmac, R = 0.2718 (Rfree = 0.000) for 3584 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 9: After refmac, R = 0.2505 (Rfree = 0.000) for 3553 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 10: After refmac, R = 0.2382 (Rfree = 0.000) for 3537 atoms. Found 16 (19 requested) and removed 31 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 3702 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3723 seeds are put forward Round 1: 240 peptides, 42 chains. Longest chain 10 peptides. Score 0.365 Round 2: 257 peptides, 37 chains. Longest chain 15 peptides. Score 0.457 Round 3: 273 peptides, 35 chains. Longest chain 18 peptides. Score 0.511 Round 4: 274 peptides, 35 chains. Longest chain 17 peptides. Score 0.514 Round 5: 286 peptides, 35 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 5 Chains 35, Residues 251, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8464 restraints for refining 3807 atoms. 7458 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2581 (Rfree = 0.000) for 3807 atoms. Found 19 (20 requested) and removed 45 (10 requested) atoms. Cycle 12: After refmac, R = 0.2378 (Rfree = 0.000) for 3749 atoms. Found 14 (20 requested) and removed 33 (10 requested) atoms. Cycle 13: After refmac, R = 0.2434 (Rfree = 0.000) for 3707 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 14: After refmac, R = 0.2290 (Rfree = 0.000) for 3682 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 15: After refmac, R = 0.2288 (Rfree = 0.000) for 3672 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.11 Search for helices and strands: 0 residues in 0 chains, 3870 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3893 seeds are put forward Round 1: 242 peptides, 43 chains. Longest chain 14 peptides. Score 0.359 Round 2: 268 peptides, 36 chains. Longest chain 13 peptides. Score 0.491 Round 3: 257 peptides, 35 chains. Longest chain 15 peptides. Score 0.477 Round 4: 271 peptides, 37 chains. Longest chain 20 peptides. Score 0.488 Round 5: 280 peptides, 38 chains. Longest chain 16 peptides. Score 0.498 Taking the results from Round 5 Chains 39, Residues 242, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8424 restraints for refining 3859 atoms. 7450 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2734 (Rfree = 0.000) for 3859 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 17: After refmac, R = 0.2616 (Rfree = 0.000) for 3789 atoms. Found 21 (21 requested) and removed 36 (10 requested) atoms. Cycle 18: After refmac, R = 0.2201 (Rfree = 0.000) for 3743 atoms. Found 17 (20 requested) and removed 23 (10 requested) atoms. Cycle 19: After refmac, R = 0.2077 (Rfree = 0.000) for 3718 atoms. Found 12 (20 requested) and removed 21 (10 requested) atoms. Cycle 20: After refmac, R = 0.2351 (Rfree = 0.000) for 3698 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 3899 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3917 seeds are put forward Round 1: 216 peptides, 39 chains. Longest chain 11 peptides. Score 0.337 Round 2: 251 peptides, 40 chains. Longest chain 15 peptides. Score 0.413 Round 3: 277 peptides, 39 chains. Longest chain 21 peptides. Score 0.482 Round 4: 272 peptides, 38 chains. Longest chain 21 peptides. Score 0.480 Round 5: 259 peptides, 37 chains. Longest chain 16 peptides. Score 0.462 Taking the results from Round 3 Chains 40, Residues 238, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8324 restraints for refining 3813 atoms. 7355 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2597 (Rfree = 0.000) for 3813 atoms. Found 20 (20 requested) and removed 35 (10 requested) atoms. Cycle 22: After refmac, R = 0.2447 (Rfree = 0.000) for 3768 atoms. Found 20 (20 requested) and removed 32 (10 requested) atoms. Cycle 23: After refmac, R = 0.2311 (Rfree = 0.000) for 3736 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 24: After refmac, R = 0.2270 (Rfree = 0.000) for 3710 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 25: After refmac, R = 0.2294 (Rfree = 0.000) for 3705 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.06 Search for helices and strands: 0 residues in 0 chains, 3931 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3951 seeds are put forward Round 1: 229 peptides, 46 chains. Longest chain 13 peptides. Score 0.293 Round 2: 262 peptides, 45 chains. Longest chain 11 peptides. Score 0.387 Round 3: 270 peptides, 47 chains. Longest chain 12 peptides. Score 0.386 Round 4: 278 peptides, 41 chains. Longest chain 15 peptides. Score 0.464 Round 5: 272 peptides, 42 chains. Longest chain 17 peptides. Score 0.441 Taking the results from Round 4 Chains 42, Residues 237, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8861 restraints for refining 3985 atoms. 7916 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2604 (Rfree = 0.000) for 3985 atoms. Found 21 (21 requested) and removed 33 (10 requested) atoms. Cycle 27: After refmac, R = 0.2305 (Rfree = 0.000) for 3930 atoms. Found 21 (21 requested) and removed 34 (10 requested) atoms. Cycle 28: After refmac, R = 0.2353 (Rfree = 0.000) for 3897 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 29: After refmac, R = 0.2253 (Rfree = 0.000) for 3871 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 30: After refmac, R = 0.2235 (Rfree = 0.000) for 3858 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 4008 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4028 seeds are put forward Round 1: 223 peptides, 47 chains. Longest chain 11 peptides. Score 0.266 Round 2: 246 peptides, 46 chains. Longest chain 10 peptides. Score 0.337 Round 3: 254 peptides, 44 chains. Longest chain 16 peptides. Score 0.378 Round 4: 263 peptides, 47 chains. Longest chain 11 peptides. Score 0.369 Round 5: 274 peptides, 47 chains. Longest chain 14 peptides. Score 0.395 Taking the results from Round 5 Chains 47, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 9357 restraints for refining 4025 atoms. 8496 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2680 (Rfree = 0.000) for 4025 atoms. Found 22 (22 requested) and removed 68 (11 requested) atoms. Cycle 32: After refmac, R = 0.2557 (Rfree = 0.000) for 3951 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 33: After refmac, R = 0.2477 (Rfree = 0.000) for 3916 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 34: After refmac, R = 0.2323 (Rfree = 0.000) for 3901 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Cycle 35: After refmac, R = 0.2256 (Rfree = 0.000) for 3890 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 4088 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4104 seeds are put forward Round 1: 194 peptides, 42 chains. Longest chain 9 peptides. Score 0.243 Round 2: 238 peptides, 44 chains. Longest chain 9 peptides. Score 0.338 Round 3: 239 peptides, 43 chains. Longest chain 11 peptides. Score 0.352 Round 4: 238 peptides, 40 chains. Longest chain 14 peptides. Score 0.382 Round 5: 245 peptides, 41 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 5 Chains 41, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 9445 restraints for refining 4083 atoms. 8670 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2674 (Rfree = 0.000) for 4083 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 37: After refmac, R = 0.2711 (Rfree = 0.000) for 4038 atoms. Found 22 (22 requested) and removed 39 (11 requested) atoms. Cycle 38: After refmac, R = 0.2460 (Rfree = 0.000) for 3994 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 39: After refmac, R = 0.2485 (Rfree = 0.000) for 3977 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 40: After refmac, R = 0.2362 (Rfree = 0.000) for 3956 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 4090 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4105 seeds are put forward Round 1: 195 peptides, 41 chains. Longest chain 8 peptides. Score 0.258 Round 2: 240 peptides, 45 chains. Longest chain 10 peptides. Score 0.333 Round 3: 225 peptides, 41 chains. Longest chain 11 peptides. Score 0.338 Round 4: 220 peptides, 39 chains. Longest chain 11 peptides. Score 0.348 Round 5: 221 peptides, 39 chains. Longest chain 9 peptides. Score 0.350 Taking the results from Round 5 Chains 39, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 9445 restraints for refining 3999 atoms. 8756 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2741 (Rfree = 0.000) for 3999 atoms. Found 21 (21 requested) and removed 36 (10 requested) atoms. Cycle 42: After refmac, R = 0.2785 (Rfree = 0.000) for 3949 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 43: After refmac, R = 0.2562 (Rfree = 0.000) for 3920 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 44: After refmac, R = 0.2520 (Rfree = 0.000) for 3896 atoms. Found 21 (21 requested) and removed 31 (10 requested) atoms. Cycle 45: After refmac, R = 0.2068 (Rfree = 0.000) for 3873 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 4048 seeds are put forward NCS extension: 0 residues added, 4048 seeds are put forward Round 1: 162 peptides, 34 chains. Longest chain 9 peptides. Score 0.248 Round 2: 208 peptides, 37 chains. Longest chain 10 peptides. Score 0.339 Round 3: 217 peptides, 38 chains. Longest chain 11 peptides. Score 0.351 Round 4: 227 peptides, 39 chains. Longest chain 11 peptides. Score 0.365 Round 5: 221 peptides, 37 chains. Longest chain 11 peptides. Score 0.372 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 184, 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. 7444 reflections ( 99.55 % complete ) and 9040 restraints for refining 3879 atoms. 8341 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3091 (Rfree = 0.000) for 3879 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2960 (Rfree = 0.000) for 3844 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2934 (Rfree = 0.000) for 3799 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2800 (Rfree = 0.000) for 3776 atoms. TimeTaking 61.13