null Sun 23 Dec 22:22:46 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 1vpb-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-3.4-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/1vpb-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-3.4-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 22:22:54 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/1vpb-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-3.4-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 424 and 0 Target number of residues in the AU: 424 Target solvent content: 0.6219 Checking the provided sequence file Detected sequence length: 451 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 451 Adjusted target solvent content: 0.60 Input MTZ file: 1vpb-3.4-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: 20 Cell parameters: 74.004 155.044 105.800 90.000 90.000 90.000 Input sequence file: 1vpb-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3608 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 77.522 3.400 Wilson plot Bfac: 62.04 8603 reflections ( 99.04 % complete ) and 0 restraints for refining 4026 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.2992 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3007 (Rfree = 0.000) for 4026 atoms. Found 30 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 2.88 Search for helices and strands: 0 residues in 0 chains, 4096 seeds are put forward Round 1: 246 peptides, 41 chains. Longest chain 15 peptides. Score 0.411 Round 2: 295 peptides, 41 chains. Longest chain 23 peptides. Score 0.529 Round 3: 300 peptides, 35 chains. Longest chain 21 peptides. Score 0.597 Round 4: 309 peptides, 36 chains. Longest chain 28 peptides. Score 0.606 Round 5: 321 peptides, 34 chains. Longest chain 21 peptides. Score 0.646 Taking the results from Round 5 Chains 37, Residues 287, Estimated correctness of the model 43.0 % 4 chains (52 residues) have been docked in sequence ------------------------------------------------------ 8603 reflections ( 99.04 % complete ) and 6457 restraints for refining 3281 atoms. 5146 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2826 (Rfree = 0.000) for 3281 atoms. Found 21 (24 requested) and removed 29 (12 requested) atoms. Cycle 2: After refmac, R = 0.2601 (Rfree = 0.000) for 3215 atoms. Found 5 (24 requested) and removed 21 (12 requested) atoms. Cycle 3: After refmac, R = 0.2658 (Rfree = 0.000) for 3170 atoms. Found 15 (24 requested) and removed 22 (12 requested) atoms. Cycle 4: After refmac, R = 0.2473 (Rfree = 0.000) for 3143 atoms. Found 10 (23 requested) and removed 17 (11 requested) atoms. Cycle 5: After refmac, R = 0.2389 (Rfree = 0.000) for 3124 atoms. Found 16 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 3242 seeds are put forward Round 1: 284 peptides, 39 chains. Longest chain 20 peptides. Score 0.525 Round 2: 300 peptides, 34 chains. Longest chain 25 peptides. Score 0.607 Round 3: 302 peptides, 36 chains. Longest chain 19 peptides. Score 0.592 Round 4: 325 peptides, 35 chains. Longest chain 28 peptides. Score 0.645 Round 5: 315 peptides, 36 chains. Longest chain 30 peptides. Score 0.618 Taking the results from Round 4 Chains 39, Residues 290, Estimated correctness of the model 42.7 % 5 chains (69 residues) have been docked in sequence ------------------------------------------------------ 8603 reflections ( 99.04 % complete ) and 6225 restraints for refining 3281 atoms. 4841 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2823 (Rfree = 0.000) for 3281 atoms. Found 18 (24 requested) and removed 37 (12 requested) atoms. Cycle 7: After refmac, R = 0.2594 (Rfree = 0.000) for 3228 atoms. Found 9 (24 requested) and removed 30 (12 requested) atoms. Cycle 8: After refmac, R = 0.2561 (Rfree = 0.000) for 3179 atoms. Found 9 (24 requested) and removed 24 (12 requested) atoms. Cycle 9: After refmac, R = 0.2658 (Rfree = 0.000) for 3150 atoms. Found 12 (23 requested) and removed 22 (11 requested) atoms. Cycle 10: After refmac, R = 0.2486 (Rfree = 0.000) for 3131 atoms. Found 11 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.76 Search for helices and strands: 0 residues in 0 chains, 3211 seeds are put forward Round 1: 286 peptides, 43 chains. Longest chain 23 peptides. Score 0.488 Round 2: 291 peptides, 33 chains. Longest chain 24 peptides. Score 0.598 Round 3: 298 peptides, 37 chains. Longest chain 22 peptides. Score 0.575 Round 4: 299 peptides, 31 chains. Longest chain 27 peptides. Score 0.631 Round 5: 299 peptides, 33 chains. Longest chain 20 peptides. Score 0.614 Taking the results from Round 4 Chains 31, Residues 268, Estimated correctness of the model 38.5 % 3 chains (63 residues) have been docked in sequence ------------------------------------------------------ 8603 reflections ( 99.04 % complete ) and 6249 restraints for refining 3281 atoms. 4925 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2827 (Rfree = 0.000) for 3281 atoms. Found 15 (24 requested) and removed 32 (12 requested) atoms. Cycle 12: After refmac, R = 0.2594 (Rfree = 0.000) for 3243 atoms. Found 8 (24 requested) and removed 19 (12 requested) atoms. Cycle 13: After refmac, R = 0.2567 (Rfree = 0.000) for 3224 atoms. Found 9 (24 requested) and removed 20 (12 requested) atoms. Cycle 14: After refmac, R = 0.2535 (Rfree = 0.000) for 3204 atoms. Found 11 (24 requested) and removed 21 (12 requested) atoms. Cycle 15: After refmac, R = 0.2546 (Rfree = 0.000) for 3189 atoms. Found 8 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.73 Search for helices and strands: 0 residues in 0 chains, 3285 seeds are put forward Round 1: 274 peptides, 40 chains. Longest chain 17 peptides. Score 0.491 Round 2: 311 peptides, 40 chains. Longest chain 20 peptides. Score 0.573 Round 3: 298 peptides, 39 chains. Longest chain 19 peptides. Score 0.556 Round 4: 305 peptides, 39 chains. Longest chain 19 peptides. Score 0.570 Round 5: 303 peptides, 36 chains. Longest chain 19 peptides. Score 0.594 Taking the results from Round 5 Chains 37, Residues 267, Estimated correctness of the model 26.7 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8603 reflections ( 99.04 % complete ) and 6938 restraints for refining 3281 atoms. 5874 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2462 (Rfree = 0.000) for 3281 atoms. Found 14 (24 requested) and removed 15 (12 requested) atoms. Cycle 17: After refmac, R = 0.2349 (Rfree = 0.000) for 3268 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.2287 (Rfree = 0.000) for 3254 atoms. Found 5 (24 requested) and removed 17 (12 requested) atoms. Cycle 19: After refmac, R = 0.2293 (Rfree = 0.000) for 3240 atoms. Found 10 (24 requested) and removed 20 (12 requested) atoms. Cycle 20: After refmac, R = 0.2270 (Rfree = 0.000) for 3227 atoms. Found 8 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 2.79 Search for helices and strands: 0 residues in 0 chains, 3328 seeds are put forward Round 1: 280 peptides, 44 chains. Longest chain 20 peptides. Score 0.463 Round 2: 299 peptides, 33 chains. Longest chain 37 peptides. Score 0.614 Round 3: 291 peptides, 35 chains. Longest chain 20 peptides. Score 0.579 Round 4: 284 peptides, 33 chains. Longest chain 27 peptides. Score 0.584 Round 5: 312 peptides, 34 chains. Longest chain 19 peptides. Score 0.630 Taking the results from Round 5 Chains 36, Residues 278, Estimated correctness of the model 38.2 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 8603 reflections ( 99.04 % complete ) and 6429 restraints for refining 3281 atoms. 5168 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2494 (Rfree = 0.000) for 3281 atoms. Found 17 (24 requested) and removed 25 (12 requested) atoms. Cycle 22: After refmac, R = 0.2311 (Rfree = 0.000) for 3251 atoms. Found 9 (24 requested) and removed 16 (12 requested) atoms. Cycle 23: After refmac, R = 0.2267 (Rfree = 0.000) for 3236 atoms. Found 6 (24 requested) and removed 17 (12 requested) atoms. Cycle 24: After refmac, R = 0.2108 (Rfree = 0.000) for 3222 atoms. Found 6 (24 requested) and removed 15 (12 requested) atoms. Cycle 25: After refmac, R = 0.2122 (Rfree = 0.000) for 3205 atoms. Found 13 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 2.81 Search for helices and strands: 0 residues in 0 chains, 3291 seeds are put forward Round 1: 295 peptides, 42 chains. Longest chain 22 peptides. Score 0.519 Round 2: 306 peptides, 37 chains. Longest chain 21 peptides. Score 0.591 Round 3: 307 peptides, 35 chains. Longest chain 24 peptides. Score 0.611 Round 4: 306 peptides, 36 chains. Longest chain 27 peptides. Score 0.600 Round 5: 295 peptides, 35 chains. Longest chain 18 peptides. Score 0.587 Taking the results from Round 3 Chains 38, Residues 272, Estimated correctness of the model 32.2 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 8603 reflections ( 99.04 % complete ) and 6520 restraints for refining 3281 atoms. 5314 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2338 (Rfree = 0.000) for 3281 atoms. Found 12 (24 requested) and removed 16 (12 requested) atoms. Cycle 27: After refmac, R = 0.2147 (Rfree = 0.000) for 3261 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2093 (Rfree = 0.000) for 3248 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 29: After refmac, R = 0.2040 (Rfree = 0.000) for 3235 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.2025 (Rfree = 0.000) for 3227 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 2.80 Search for helices and strands: 0 residues in 0 chains, 3318 seeds are put forward Round 1: 274 peptides, 40 chains. Longest chain 23 peptides. Score 0.491 Round 2: 288 peptides, 35 chains. Longest chain 22 peptides. Score 0.573 Round 3: 294 peptides, 36 chains. Longest chain 20 peptides. Score 0.576 Round 4: 310 peptides, 33 chains. Longest chain 31 peptides. Score 0.634 Round 5: 308 peptides, 34 chains. Longest chain 20 peptides. Score 0.622 Taking the results from Round 4 Chains 35, Residues 277, Estimated correctness of the model 39.4 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8603 reflections ( 99.04 % complete ) and 6440 restraints for refining 3281 atoms. 5202 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2382 (Rfree = 0.000) for 3281 atoms. Found 14 (24 requested) and removed 17 (12 requested) atoms. Cycle 32: After refmac, R = 0.2232 (Rfree = 0.000) for 3258 atoms. Found 5 (24 requested) and removed 14 (12 requested) atoms. Cycle 33: After refmac, R = 0.2163 (Rfree = 0.000) for 3244 atoms. Found 4 (24 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.2137 (Rfree = 0.000) for 3227 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2072 (Rfree = 0.000) for 3221 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 2.79 Search for helices and strands: 0 residues in 0 chains, 3304 seeds are put forward Round 1: 283 peptides, 41 chains. Longest chain 21 peptides. Score 0.502 Round 2: 314 peptides, 36 chains. Longest chain 30 peptides. Score 0.616 Round 3: 302 peptides, 37 chains. Longest chain 22 peptides. Score 0.583 Round 4: 313 peptides, 36 chains. Longest chain 20 peptides. Score 0.614 Round 5: 300 peptides, 33 chains. Longest chain 23 peptides. Score 0.616 Taking the results from Round 5 Chains 33, Residues 267, Estimated correctness of the model 33.8 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 8603 reflections ( 99.04 % complete ) and 6630 restraints for refining 3280 atoms. 5461 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2470 (Rfree = 0.000) for 3280 atoms. Found 16 (24 requested) and removed 18 (12 requested) atoms. Cycle 37: After refmac, R = 0.2477 (Rfree = 0.000) for 3266 atoms. Found 13 (24 requested) and removed 16 (12 requested) atoms. Cycle 38: After refmac, R = 0.2466 (Rfree = 0.000) for 3255 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.2310 (Rfree = 0.000) for 3246 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2305 (Rfree = 0.000) for 3234 atoms. Found 3 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 2.80 Search for helices and strands: 0 residues in 0 chains, 3310 seeds are put forward Round 1: 251 peptides, 40 chains. Longest chain 13 peptides. Score 0.435 Round 2: 297 peptides, 36 chains. Longest chain 21 peptides. Score 0.582 Round 3: 291 peptides, 38 chains. Longest chain 20 peptides. Score 0.550 Round 4: 291 peptides, 35 chains. Longest chain 18 peptides. Score 0.579 Round 5: 288 peptides, 32 chains. Longest chain 21 peptides. Score 0.601 Taking the results from Round 5 Chains 34, Residues 256, Estimated correctness of the model 29.0 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8603 reflections ( 99.04 % complete ) and 6607 restraints for refining 3281 atoms. 5435 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2537 (Rfree = 0.000) for 3281 atoms. Found 11 (24 requested) and removed 21 (12 requested) atoms. Cycle 42: After refmac, R = 0.2440 (Rfree = 0.000) for 3255 atoms. Found 11 (24 requested) and removed 22 (12 requested) atoms. Cycle 43: After refmac, R = 0.2374 (Rfree = 0.000) for 3240 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. Cycle 44: After refmac, R = 0.2339 (Rfree = 0.000) for 3223 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. Cycle 45: After refmac, R = 0.2230 (Rfree = 0.000) for 3209 atoms. Found 7 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 2.80 Search for helices and strands: 0 residues in 0 chains, 3270 seeds are put forward Round 1: 228 peptides, 38 chains. Longest chain 18 peptides. Score 0.397 Round 2: 265 peptides, 40 chains. Longest chain 15 peptides. Score 0.470 Round 3: 259 peptides, 36 chains. Longest chain 20 peptides. Score 0.498 Round 4: 264 peptides, 33 chains. Longest chain 16 peptides. Score 0.541 Round 5: 270 peptides, 36 chains. Longest chain 18 peptides. Score 0.523 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 231, Estimated correctness of the model 8.3 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vpb-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (231 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8603 reflections ( 99.04 % complete ) and 6950 restraints for refining 3281 atoms. 5962 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2479 (Rfree = 0.000) for 3281 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2323 (Rfree = 0.000) for 3259 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2305 (Rfree = 0.000) for 3244 atoms. Found 0 (24 requested) and removed 6 (12 requested) atoms. Cycle 49: After refmac, R = 0.2312 (Rfree = 0.000) for 3237 atoms. Found 0 (24 requested) and removed 3 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:22:24 GMT 2018 Job finished. TimeTaking 59.64 Used memory is bytes: 20574048