Sun 23 Dec 22:22:44 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-3.2-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 22:22:52 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-3.2-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 439 and 0 Target number of residues in the AU: 439 Target solvent content: 0.6086 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-3.2-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-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3608 target number of atoms Had to go as low as 0.70 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 3.200 Wilson plot Bfac: 55.94 10285 reflections ( 99.08 % complete ) and 0 restraints for refining 3981 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.2986 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2494 (Rfree = 0.000) for 3981 atoms. Found 31 (35 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.98 2.60 Search for helices and strands: 0 residues in 0 chains, 4035 seeds are put forward Round 1: 266 peptides, 43 chains. Longest chain 16 peptides. Score 0.440 Round 2: 323 peptides, 40 chains. Longest chain 22 peptides. Score 0.598 Round 3: 335 peptides, 34 chains. Longest chain 36 peptides. Score 0.670 Round 4: 351 peptides, 27 chains. Longest chain 49 peptides. Score 0.746 Round 5: 358 peptides, 27 chains. Longest chain 43 peptides. Score 0.756 Taking the results from Round 5 Chains 28, Residues 331, Estimated correctness of the model 76.1 % 6 chains (159 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 A and 146 A 27 chains (333 residues) following loop building 5 chains (161 residues) in sequence following loop building ------------------------------------------------------ 10285 reflections ( 99.08 % complete ) and 5123 restraints for refining 3293 atoms. 3179 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2881 (Rfree = 0.000) for 3293 atoms. Found 29 (29 requested) and removed 46 (14 requested) atoms. Cycle 2: After refmac, R = 0.2674 (Rfree = 0.000) for 3226 atoms. Found 25 (28 requested) and removed 18 (14 requested) atoms. Cycle 3: After refmac, R = 0.2450 (Rfree = 0.000) for 3208 atoms. Found 17 (28 requested) and removed 19 (14 requested) atoms. Cycle 4: After refmac, R = 0.2320 (Rfree = 0.000) for 3188 atoms. Found 11 (26 requested) and removed 17 (14 requested) atoms. Cycle 5: After refmac, R = 0.2282 (Rfree = 0.000) for 3172 atoms. Found 9 (26 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 2.67 Search for helices and strands: 0 residues in 0 chains, 3241 seeds are put forward Round 1: 353 peptides, 30 chains. Longest chain 43 peptides. Score 0.728 Round 2: 373 peptides, 26 chains. Longest chain 51 peptides. Score 0.781 Round 3: 364 peptides, 25 chains. Longest chain 42 peptides. Score 0.776 Round 4: 360 peptides, 28 chains. Longest chain 39 peptides. Score 0.752 Round 5: 347 peptides, 26 chains. Longest chain 40 peptides. Score 0.748 Taking the results from Round 2 Chains 31, Residues 347, Estimated correctness of the model 80.4 % 10 chains (211 residues) have been docked in sequence Building loops using Loopy2018 31 chains (347 residues) following loop building 10 chains (211 residues) in sequence following loop building ------------------------------------------------------ 10285 reflections ( 99.08 % complete ) and 4729 restraints for refining 3294 atoms. 2562 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2622 (Rfree = 0.000) for 3294 atoms. Found 17 (26 requested) and removed 36 (14 requested) atoms. Cycle 7: After refmac, R = 0.2386 (Rfree = 0.000) for 3249 atoms. Found 10 (26 requested) and removed 18 (14 requested) atoms. Cycle 8: After refmac, R = 0.2404 (Rfree = 0.000) for 3217 atoms. Found 17 (25 requested) and removed 18 (14 requested) atoms. Cycle 9: After refmac, R = 0.2200 (Rfree = 0.000) for 3206 atoms. Found 7 (24 requested) and removed 20 (14 requested) atoms. Cycle 10: After refmac, R = 0.2155 (Rfree = 0.000) for 3186 atoms. Found 8 (23 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.66 Search for helices and strands: 0 residues in 0 chains, 3251 seeds are put forward Round 1: 350 peptides, 30 chains. Longest chain 33 peptides. Score 0.724 Round 2: 366 peptides, 28 chains. Longest chain 34 peptides. Score 0.760 Round 3: 369 peptides, 23 chains. Longest chain 73 peptides. Score 0.794 Round 4: 365 peptides, 24 chains. Longest chain 44 peptides. Score 0.783 Round 5: 368 peptides, 28 chains. Longest chain 51 peptides. Score 0.762 Taking the results from Round 3 Chains 28, Residues 346, Estimated correctness of the model 82.5 % 8 chains (166 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 A and 89 A Built loop between residues 178 A and 181 A Built loop between residues 304 A and 310 A Built loop between residues 323 A and 326 A 23 chains (356 residues) following loop building 4 chains (179 residues) in sequence following loop building ------------------------------------------------------ 10285 reflections ( 99.08 % complete ) and 5003 restraints for refining 3294 atoms. 2991 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2765 (Rfree = 0.000) for 3294 atoms. Found 23 (23 requested) and removed 34 (14 requested) atoms. Cycle 12: After refmac, R = 0.2447 (Rfree = 0.000) for 3268 atoms. Found 15 (23 requested) and removed 22 (14 requested) atoms. Cycle 13: After refmac, R = 0.2465 (Rfree = 0.000) for 3246 atoms. Found 22 (22 requested) and removed 23 (14 requested) atoms. Cycle 14: After refmac, R = 0.2450 (Rfree = 0.000) for 3230 atoms. Found 15 (21 requested) and removed 19 (14 requested) atoms. Cycle 15: After refmac, R = 0.2477 (Rfree = 0.000) for 3217 atoms. Found 20 (20 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.02 2.64 Search for helices and strands: 0 residues in 0 chains, 3315 seeds are put forward Round 1: 336 peptides, 29 chains. Longest chain 36 peptides. Score 0.710 Round 2: 356 peptides, 27 chains. Longest chain 37 peptides. Score 0.753 Round 3: 349 peptides, 26 chains. Longest chain 51 peptides. Score 0.750 Round 4: 338 peptides, 28 chains. Longest chain 32 peptides. Score 0.721 Round 5: 346 peptides, 26 chains. Longest chain 70 peptides. Score 0.746 Taking the results from Round 2 Chains 30, Residues 329, Estimated correctness of the model 75.6 % 6 chains (149 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 182 A 28 chains (331 residues) following loop building 5 chains (152 residues) in sequence following loop building ------------------------------------------------------ 10285 reflections ( 99.08 % complete ) and 5451 restraints for refining 3293 atoms. 3535 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2625 (Rfree = 0.000) for 3293 atoms. Found 16 (20 requested) and removed 19 (14 requested) atoms. Cycle 17: After refmac, R = 0.2708 (Rfree = 0.000) for 3281 atoms. Found 18 (20 requested) and removed 20 (14 requested) atoms. Cycle 18: After refmac, R = 0.2265 (Rfree = 0.000) for 3274 atoms. Found 7 (19 requested) and removed 17 (14 requested) atoms. Cycle 19: After refmac, R = 0.2249 (Rfree = 0.000) for 3255 atoms. Found 3 (19 requested) and removed 16 (14 requested) atoms. Cycle 20: After refmac, R = 0.2184 (Rfree = 0.000) for 3240 atoms. Found 4 (18 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 2.65 Search for helices and strands: 0 residues in 0 chains, 3291 seeds are put forward Round 1: 324 peptides, 34 chains. Longest chain 40 peptides. Score 0.651 Round 2: 351 peptides, 21 chains. Longest chain 51 peptides. Score 0.785 Round 3: 344 peptides, 23 chains. Longest chain 56 peptides. Score 0.764 Round 4: 357 peptides, 27 chains. Longest chain 44 peptides. Score 0.754 Round 5: 345 peptides, 26 chains. Longest chain 39 peptides. Score 0.745 Taking the results from Round 2 Chains 21, Residues 330, Estimated correctness of the model 81.1 % 7 chains (225 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 119 A and 124 A 20 chains (334 residues) following loop building 6 chains (229 residues) in sequence following loop building ------------------------------------------------------ 10285 reflections ( 99.08 % complete ) and 4609 restraints for refining 3293 atoms. 2374 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2553 (Rfree = 0.000) for 3293 atoms. Found 16 (17 requested) and removed 29 (14 requested) atoms. Cycle 22: After refmac, R = 0.2444 (Rfree = 0.000) for 3257 atoms. Found 17 (17 requested) and removed 25 (14 requested) atoms. Cycle 23: After refmac, R = 0.2310 (Rfree = 0.000) for 3234 atoms. Found 15 (16 requested) and removed 21 (14 requested) atoms. Cycle 24: After refmac, R = 0.2240 (Rfree = 0.000) for 3219 atoms. Found 15 (15 requested) and removed 18 (14 requested) atoms. Cycle 25: After refmac, R = 0.2227 (Rfree = 0.000) for 3208 atoms. Found 15 (15 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 2.66 Search for helices and strands: 0 residues in 0 chains, 3275 seeds are put forward Round 1: 346 peptides, 34 chains. Longest chain 36 peptides. Score 0.689 Round 2: 350 peptides, 25 chains. Longest chain 54 peptides. Score 0.758 Round 3: 344 peptides, 24 chains. Longest chain 37 peptides. Score 0.757 Round 4: 348 peptides, 26 chains. Longest chain 34 peptides. Score 0.749 Round 5: 360 peptides, 23 chains. Longest chain 49 peptides. Score 0.784 Taking the results from Round 5 Chains 24, Residues 337, Estimated correctness of the model 80.9 % 7 chains (195 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 345 A and 349 A 23 chains (340 residues) following loop building 6 chains (198 residues) in sequence following loop building ------------------------------------------------------ 10285 reflections ( 99.08 % complete ) and 4971 restraints for refining 3294 atoms. 2855 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2604 (Rfree = 0.000) for 3294 atoms. Found 14 (14 requested) and removed 27 (14 requested) atoms. Cycle 27: After refmac, R = 0.2545 (Rfree = 0.000) for 3251 atoms. Found 14 (14 requested) and removed 20 (14 requested) atoms. Cycle 28: After refmac, R = 0.2157 (Rfree = 0.000) for 3237 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. Cycle 29: After refmac, R = 0.2029 (Rfree = 0.000) for 3228 atoms. Found 12 (14 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.1950 (Rfree = 0.000) for 3218 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.04 2.66 Search for helices and strands: 0 residues in 0 chains, 3308 seeds are put forward Round 1: 342 peptides, 29 chains. Longest chain 38 peptides. Score 0.719 Round 2: 353 peptides, 27 chains. Longest chain 33 peptides. Score 0.749 Round 3: 354 peptides, 27 chains. Longest chain 37 peptides. Score 0.750 Round 4: 362 peptides, 26 chains. Longest chain 46 peptides. Score 0.767 Round 5: 357 peptides, 25 chains. Longest chain 41 peptides. Score 0.767 Taking the results from Round 5 Chains 25, Residues 332, Estimated correctness of the model 78.1 % 6 chains (170 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 57 A 24 chains (334 residues) following loop building 5 chains (173 residues) in sequence following loop building ------------------------------------------------------ 10285 reflections ( 99.08 % complete ) and 5206 restraints for refining 3294 atoms. 3314 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2704 (Rfree = 0.000) for 3294 atoms. Found 14 (14 requested) and removed 27 (14 requested) atoms. Cycle 32: After refmac, R = 0.2366 (Rfree = 0.000) for 3261 atoms. Found 14 (14 requested) and removed 17 (14 requested) atoms. Cycle 33: After refmac, R = 0.2288 (Rfree = 0.000) for 3248 atoms. Found 14 (14 requested) and removed 17 (14 requested) atoms. Cycle 34: After refmac, R = 0.2232 (Rfree = 0.000) for 3240 atoms. Found 11 (14 requested) and removed 17 (14 requested) atoms. Cycle 35: After refmac, R = 0.2211 (Rfree = 0.000) for 3230 atoms. Found 6 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 2.70 Search for helices and strands: 0 residues in 0 chains, 3300 seeds are put forward Round 1: 319 peptides, 39 chains. Longest chain 28 peptides. Score 0.599 Round 2: 339 peptides, 32 chains. Longest chain 29 peptides. Score 0.693 Round 3: 328 peptides, 32 chains. Longest chain 42 peptides. Score 0.675 Round 4: 341 peptides, 31 chains. Longest chain 39 peptides. Score 0.703 Round 5: 336 peptides, 29 chains. Longest chain 51 peptides. Score 0.710 Taking the results from Round 5 Chains 33, Residues 307, Estimated correctness of the model 67.3 % 7 chains (142 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 56 A 31 chains (309 residues) following loop building 6 chains (145 residues) in sequence following loop building ------------------------------------------------------ 10285 reflections ( 99.08 % complete ) and 5574 restraints for refining 3293 atoms. 3861 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2791 (Rfree = 0.000) for 3293 atoms. Found 14 (14 requested) and removed 26 (14 requested) atoms. Cycle 37: After refmac, R = 0.2538 (Rfree = 0.000) for 3267 atoms. Found 12 (14 requested) and removed 21 (14 requested) atoms. Cycle 38: After refmac, R = 0.2470 (Rfree = 0.000) for 3243 atoms. Found 14 (14 requested) and removed 22 (14 requested) atoms. Cycle 39: After refmac, R = 0.2440 (Rfree = 0.000) for 3226 atoms. Found 9 (14 requested) and removed 19 (14 requested) atoms. Cycle 40: After refmac, R = 0.2296 (Rfree = 0.000) for 3210 atoms. Found 9 (14 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 2.66 Search for helices and strands: 0 residues in 0 chains, 3265 seeds are put forward Round 1: 303 peptides, 38 chains. Longest chain 22 peptides. Score 0.576 Round 2: 334 peptides, 30 chains. Longest chain 24 peptides. Score 0.700 Round 3: 339 peptides, 30 chains. Longest chain 23 peptides. Score 0.708 Round 4: 338 peptides, 30 chains. Longest chain 45 peptides. Score 0.706 Round 5: 335 peptides, 31 chains. Longest chain 21 peptides. Score 0.694 Taking the results from Round 3 Chains 36, Residues 309, Estimated correctness of the model 66.9 % 8 chains (125 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 181 A 35 chains (310 residues) following loop building 7 chains (127 residues) in sequence following loop building ------------------------------------------------------ 10285 reflections ( 99.08 % complete ) and 5667 restraints for refining 3294 atoms. 3975 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2910 (Rfree = 0.000) for 3294 atoms. Found 14 (14 requested) and removed 33 (14 requested) atoms. Cycle 42: After refmac, R = 0.2734 (Rfree = 0.000) for 3263 atoms. Found 14 (14 requested) and removed 22 (14 requested) atoms. Cycle 43: After refmac, R = 0.2744 (Rfree = 0.000) for 3240 atoms. Found 14 (14 requested) and removed 19 (14 requested) atoms. Cycle 44: After refmac, R = 0.2432 (Rfree = 0.000) for 3221 atoms. Found 9 (14 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.2362 (Rfree = 0.000) for 3206 atoms. Found 6 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 2.65 Search for helices and strands: 0 residues in 0 chains, 3284 seeds are put forward Round 1: 299 peptides, 33 chains. Longest chain 23 peptides. Score 0.614 Round 2: 335 peptides, 29 chains. Longest chain 44 peptides. Score 0.709 Round 3: 326 peptides, 29 chains. Longest chain 37 peptides. Score 0.695 Round 4: 340 peptides, 28 chains. Longest chain 39 peptides. Score 0.724 Round 5: 337 peptides, 30 chains. Longest chain 47 peptides. Score 0.705 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 312, Estimated correctness of the model 70.1 % 7 chains (162 residues) have been docked in sequence Sequence coverage is 51 % Consider running further cycles of model building using 1vpb-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 52 A and 58 A 31 chains (316 residues) following loop building 6 chains (167 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10285 reflections ( 99.08 % complete ) and 5329 restraints for refining 3294 atoms. 3461 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2615 (Rfree = 0.000) for 3294 atoms. Found 0 (14 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2431 (Rfree = 0.000) for 3272 atoms. Found 0 (14 requested) and removed 12 (14 requested) atoms. Cycle 48: After refmac, R = 0.2392 (Rfree = 0.000) for 3258 atoms. Found 0 (14 requested) and removed 2 (14 requested) atoms. Cycle 49: After refmac, R = 0.2327 (Rfree = 0.000) for 3255 atoms. TimeTaking 64.45