null Sun 23 Dec 22:23:10 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 1vjr-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-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/1vjr-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-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 22:23:18 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/1vjr-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-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 464 and 0 Target number of residues in the AU: 464 Target solvent content: 0.6455 Checking the provided sequence file Detected sequence length: 271 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 542 Adjusted target solvent content: 0.59 Input MTZ file: 1vjr-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: 92 Cell parameters: 93.998 93.998 160.365 90.000 90.000 90.000 Input sequence file: 1vjr-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4336 target number of atoms Had to go as low as 0.65 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: 81.094 3.600 Wilson plot Bfac: 75.06 8843 reflections ( 99.92 % complete ) and 0 restraints for refining 4812 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3529 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3547 (Rfree = 0.000) for 4812 atoms. Found 30 (30 requested) and removed 152 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.17 Search for helices and strands: 0 residues in 0 chains, 4741 seeds are put forward NCS extension: 0 residues added, 4741 seeds are put forward Round 1: 150 peptides, 22 chains. Longest chain 16 peptides. Score 0.360 Round 2: 171 peptides, 24 chains. Longest chain 19 peptides. Score 0.389 Round 3: 175 peptides, 23 chains. Longest chain 16 peptides. Score 0.410 Round 4: 192 peptides, 19 chains. Longest chain 23 peptides. Score 0.493 Round 5: 183 peptides, 17 chains. Longest chain 29 peptides. Score 0.495 Taking the results from Round 5 Chains 17, Residues 166, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8843 reflections ( 99.92 % complete ) and 7629 restraints for refining 3396 atoms. 6966 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2897 (Rfree = 0.000) for 3396 atoms. Found 21 (21 requested) and removed 70 (10 requested) atoms. Cycle 2: After refmac, R = 0.2937 (Rfree = 0.000) for 3242 atoms. Found 21 (21 requested) and removed 48 (10 requested) atoms. Cycle 3: After refmac, R = 0.2758 (Rfree = 0.000) for 3156 atoms. Found 20 (20 requested) and removed 43 (10 requested) atoms. Cycle 4: After refmac, R = 0.2653 (Rfree = 0.000) for 3102 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 5: After refmac, R = 0.2562 (Rfree = 0.000) for 3061 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.06 Search for helices and strands: 0 residues in 0 chains, 3126 seeds are put forward NCS extension: 57 residues added (4 deleted due to clashes), 3183 seeds are put forward Round 1: 192 peptides, 27 chains. Longest chain 14 peptides. Score 0.406 Round 2: 215 peptides, 23 chains. Longest chain 39 peptides. Score 0.500 Round 3: 215 peptides, 25 chains. Longest chain 21 peptides. Score 0.479 Round 4: 234 peptides, 27 chains. Longest chain 22 peptides. Score 0.500 Round 5: 228 peptides, 24 chains. Longest chain 42 peptides. Score 0.517 Taking the results from Round 5 Chains 27, Residues 204, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8843 reflections ( 99.92 % complete ) and 6233 restraints for refining 3174 atoms. 5379 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2664 (Rfree = 0.000) for 3174 atoms. Found 20 (20 requested) and removed 48 (10 requested) atoms. Cycle 7: After refmac, R = 0.2539 (Rfree = 0.000) for 3097 atoms. Found 20 (20 requested) and removed 32 (10 requested) atoms. Cycle 8: After refmac, R = 0.2466 (Rfree = 0.000) for 3069 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 9: After refmac, R = 0.2426 (Rfree = 0.000) for 3054 atoms. Found 17 (19 requested) and removed 25 (9 requested) atoms. Cycle 10: After refmac, R = 0.2403 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.07 Search for helices and strands: 0 residues in 0 chains, 3132 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3152 seeds are put forward Round 1: 201 peptides, 28 chains. Longest chain 21 peptides. Score 0.416 Round 2: 202 peptides, 24 chains. Longest chain 21 peptides. Score 0.461 Round 3: 204 peptides, 20 chains. Longest chain 40 peptides. Score 0.508 Round 4: 216 peptides, 25 chains. Longest chain 20 peptides. Score 0.482 Round 5: 206 peptides, 21 chains. Longest chain 29 peptides. Score 0.502 Taking the results from Round 3 Chains 20, Residues 184, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8843 reflections ( 99.92 % complete ) and 6154 restraints for refining 3125 atoms. 5353 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2558 (Rfree = 0.000) for 3125 atoms. Found 20 (20 requested) and removed 57 (10 requested) atoms. Cycle 12: After refmac, R = 0.2458 (Rfree = 0.000) for 3039 atoms. Found 19 (19 requested) and removed 40 (9 requested) atoms. Cycle 13: After refmac, R = 0.2452 (Rfree = 0.000) for 2995 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 14: After refmac, R = 0.2432 (Rfree = 0.000) for 2974 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 15: After refmac, R = 0.2330 (Rfree = 0.000) for 2960 atoms. Found 17 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.12 Search for helices and strands: 0 residues in 0 chains, 2990 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 3015 seeds are put forward Round 1: 199 peptides, 25 chains. Longest chain 20 peptides. Score 0.444 Round 2: 222 peptides, 23 chains. Longest chain 29 peptides. Score 0.514 Round 3: 214 peptides, 24 chains. Longest chain 26 peptides. Score 0.488 Round 4: 211 peptides, 22 chains. Longest chain 28 peptides. Score 0.502 Round 5: 215 peptides, 24 chains. Longest chain 20 peptides. Score 0.490 Taking the results from Round 2 Chains 23, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8843 reflections ( 99.92 % complete ) and 5911 restraints for refining 2996 atoms. 5138 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2443 (Rfree = 0.000) for 2996 atoms. Found 19 (19 requested) and removed 41 (9 requested) atoms. Cycle 17: After refmac, R = 0.2591 (Rfree = 0.000) for 2953 atoms. Found 19 (19 requested) and removed 38 (9 requested) atoms. Cycle 18: After refmac, R = 0.2321 (Rfree = 0.000) for 2906 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 19: After refmac, R = 0.2295 (Rfree = 0.000) for 2890 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 20: After refmac, R = 0.2398 (Rfree = 0.000) for 2877 atoms. Found 15 (18 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.06 Search for helices and strands: 0 residues in 0 chains, 2949 seeds are put forward NCS extension: 44 residues added (1 deleted due to clashes), 2993 seeds are put forward Round 1: 217 peptides, 24 chains. Longest chain 27 peptides. Score 0.494 Round 2: 219 peptides, 24 chains. Longest chain 35 peptides. Score 0.498 Round 3: 216 peptides, 23 chains. Longest chain 32 peptides. Score 0.502 Round 4: 226 peptides, 28 chains. Longest chain 25 peptides. Score 0.473 Round 5: 240 peptides, 25 chains. Longest chain 27 peptides. Score 0.531 Taking the results from Round 5 Chains 28, Residues 215, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8843 reflections ( 99.92 % complete ) and 5902 restraints for refining 3117 atoms. 4955 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2412 (Rfree = 0.000) for 3117 atoms. Found 20 (20 requested) and removed 42 (10 requested) atoms. Cycle 22: After refmac, R = 0.2250 (Rfree = 0.000) for 3064 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 23: After refmac, R = 0.2243 (Rfree = 0.000) for 3038 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 24: After refmac, R = 0.2202 (Rfree = 0.000) for 3016 atoms. Found 15 (19 requested) and removed 19 (9 requested) atoms. Cycle 25: After refmac, R = 0.2246 (Rfree = 0.000) for 2999 atoms. Found 17 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.09 Search for helices and strands: 0 residues in 0 chains, 3068 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3094 seeds are put forward Round 1: 205 peptides, 27 chains. Longest chain 32 peptides. Score 0.436 Round 2: 209 peptides, 26 chains. Longest chain 20 peptides. Score 0.456 Round 3: 221 peptides, 23 chains. Longest chain 21 peptides. Score 0.512 Round 4: 227 peptides, 23 chains. Longest chain 29 peptides. Score 0.525 Round 5: 218 peptides, 23 chains. Longest chain 29 peptides. Score 0.506 Taking the results from Round 4 Chains 25, Residues 204, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8843 reflections ( 99.92 % complete ) and 6408 restraints for refining 3149 atoms. 5566 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2507 (Rfree = 0.000) for 3149 atoms. Found 20 (20 requested) and removed 31 (10 requested) atoms. Cycle 27: After refmac, R = 0.2421 (Rfree = 0.000) for 3122 atoms. Found 16 (20 requested) and removed 26 (10 requested) atoms. Cycle 28: After refmac, R = 0.2439 (Rfree = 0.000) for 3094 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 29: After refmac, R = 0.2345 (Rfree = 0.000) for 3076 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 30: After refmac, R = 0.2344 (Rfree = 0.000) for 3063 atoms. Found 16 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.04 Search for helices and strands: 0 residues in 0 chains, 3146 seeds are put forward NCS extension: 43 residues added (1 deleted due to clashes), 3189 seeds are put forward Round 1: 207 peptides, 27 chains. Longest chain 20 peptides. Score 0.441 Round 2: 238 peptides, 25 chains. Longest chain 33 peptides. Score 0.527 Round 3: 230 peptides, 27 chains. Longest chain 27 peptides. Score 0.491 Round 4: 240 peptides, 22 chains. Longest chain 37 peptides. Score 0.560 Round 5: 219 peptides, 25 chains. Longest chain 21 peptides. Score 0.488 Taking the results from Round 4 Chains 23, Residues 218, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8843 reflections ( 99.92 % complete ) and 6648 restraints for refining 3282 atoms. 5703 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2576 (Rfree = 0.000) for 3282 atoms. Found 21 (21 requested) and removed 57 (10 requested) atoms. Cycle 32: After refmac, R = 0.2593 (Rfree = 0.000) for 3226 atoms. Found 20 (20 requested) and removed 40 (10 requested) atoms. Cycle 33: After refmac, R = 0.2458 (Rfree = 0.000) for 3190 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 34: After refmac, R = 0.2358 (Rfree = 0.000) for 3174 atoms. Found 14 (20 requested) and removed 27 (10 requested) atoms. Cycle 35: After refmac, R = 0.2401 (Rfree = 0.000) for 3146 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.08 Search for helices and strands: 0 residues in 0 chains, 3242 seeds are put forward NCS extension: 43 residues added (2 deleted due to clashes), 3285 seeds are put forward Round 1: 206 peptides, 29 chains. Longest chain 24 peptides. Score 0.417 Round 2: 209 peptides, 28 chains. Longest chain 24 peptides. Score 0.435 Round 3: 228 peptides, 24 chains. Longest chain 32 peptides. Score 0.517 Round 4: 230 peptides, 18 chains. Longest chain 40 peptides. Score 0.578 Round 5: 213 peptides, 22 chains. Longest chain 23 peptides. Score 0.506 Taking the results from Round 4 Chains 19, Residues 212, Estimated correctness of the model 5.9 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 8843 reflections ( 99.92 % complete ) and 6476 restraints for refining 3312 atoms. 5471 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2546 (Rfree = 0.000) for 3312 atoms. Found 21 (21 requested) and removed 56 (10 requested) atoms. Cycle 37: After refmac, R = 0.2362 (Rfree = 0.000) for 3256 atoms. Found 16 (21 requested) and removed 29 (10 requested) atoms. Cycle 38: After refmac, R = 0.2395 (Rfree = 0.000) for 3232 atoms. Found 7 (20 requested) and removed 36 (10 requested) atoms. Cycle 39: After refmac, R = 0.2257 (Rfree = 0.000) for 3188 atoms. Found 12 (20 requested) and removed 17 (10 requested) atoms. Cycle 40: After refmac, R = 0.2220 (Rfree = 0.000) for 3177 atoms. Found 9 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.08 Search for helices and strands: 0 residues in 0 chains, 3256 seeds are put forward NCS extension: 38 residues added (4 deleted due to clashes), 3294 seeds are put forward Round 1: 204 peptides, 30 chains. Longest chain 15 peptides. Score 0.402 Round 2: 217 peptides, 25 chains. Longest chain 19 peptides. Score 0.484 Round 3: 214 peptides, 26 chains. Longest chain 17 peptides. Score 0.467 Round 4: 213 peptides, 24 chains. Longest chain 27 peptides. Score 0.485 Round 5: 206 peptides, 23 chains. Longest chain 19 peptides. Score 0.481 Taking the results from Round 4 Chains 24, Residues 189, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8843 reflections ( 99.92 % complete ) and 7051 restraints for refining 3340 atoms. 6251 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2614 (Rfree = 0.000) for 3340 atoms. Found 21 (21 requested) and removed 59 (10 requested) atoms. Cycle 42: After refmac, R = 0.2818 (Rfree = 0.000) for 3279 atoms. Found 21 (21 requested) and removed 40 (10 requested) atoms. Cycle 43: After refmac, R = 0.2423 (Rfree = 0.000) for 3242 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 44: After refmac, R = 0.2537 (Rfree = 0.000) for 3230 atoms. Found 20 (20 requested) and removed 43 (10 requested) atoms. Cycle 45: After refmac, R = 0.2382 (Rfree = 0.000) for 3194 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.08 Search for helices and strands: 0 residues in 0 chains, 3301 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3328 seeds are put forward Round 1: 185 peptides, 28 chains. Longest chain 13 peptides. Score 0.378 Round 2: 206 peptides, 27 chains. Longest chain 16 peptides. Score 0.439 Round 3: 203 peptides, 20 chains. Longest chain 29 peptides. Score 0.506 Round 4: 202 peptides, 24 chains. Longest chain 24 peptides. Score 0.461 Round 5: 218 peptides, 22 chains. Longest chain 24 peptides. Score 0.516 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 196, 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 1vjr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8843 reflections ( 99.92 % complete ) and 6853 restraints for refining 3233 atoms. 6091 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2591 (Rfree = 0.000) for 3233 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2409 (Rfree = 0.000) for 3202 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2320 (Rfree = 0.000) for 3183 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2259 (Rfree = 0.000) for 3166 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:22:58 GMT 2018 Job finished. TimeTaking 59.8 Used memory is bytes: 21755208