null Mon 24 Dec 00:53:59 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 2prv-1.3-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-1.3-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-1.3-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-1.3-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/2prv-1.3-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-1.3-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 ============================================================ Mon 24 Dec 00:54:04 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/2prv-1.3-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-1.3-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 321 and 0 Target number of residues in the AU: 321 Target solvent content: 0.4359 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-1.3-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: 1 Cell parameters: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-1.3-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2448 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 1 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: 44.420 1.300 Wilson plot Bfac: 12.49 69437 reflections ( 94.64 % complete ) and 0 restraints for refining 2710 atoms. Observations/parameters ratio is 6.41 ------------------------------------------------------ Starting model: R = 0.4252 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3877 (Rfree = 0.000) for 2710 atoms. Found 176 (316 requested) and removed 135 (158 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.55 1.64 Round 1: 114 peptides, 25 chains. Longest chain 9 peptides. Score 0.252 Round 2: 133 peptides, 28 chains. Longest chain 8 peptides. Score 0.290 Round 3: 131 peptides, 25 chains. Longest chain 9 peptides. Score 0.348 Round 4: 121 peptides, 22 chains. Longest chain 11 peptides. Score 0.363 Round 5: 139 peptides, 24 chains. Longest chain 17 peptides. Score 0.413 Taking the results from Round 5 Chains 24, Residues 115, Estimated correctness of the model 93.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 4771 restraints for refining 2592 atoms. 4335 conditional restraints added. Observations/parameters ratio is 6.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3896 (Rfree = 0.000) for 2592 atoms. Found 173 (303 requested) and removed 54 (151 requested) atoms. Cycle 2: After refmac, R = 0.3653 (Rfree = 0.000) for 2711 atoms. Found 128 (317 requested) and removed 25 (158 requested) atoms. Cycle 3: After refmac, R = 0.3462 (Rfree = 0.000) for 2812 atoms. Found 117 (329 requested) and removed 11 (164 requested) atoms. Cycle 4: After refmac, R = 0.3320 (Rfree = 0.000) for 2917 atoms. Found 115 (341 requested) and removed 5 (170 requested) atoms. Cycle 5: After refmac, R = 0.3207 (Rfree = 0.000) for 3023 atoms. Found 117 (353 requested) and removed 6 (176 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.48 1.56 Round 1: 120 peptides, 21 chains. Longest chain 12 peptides. Score 0.381 Round 2: 128 peptides, 20 chains. Longest chain 15 peptides. Score 0.445 Round 3: 123 peptides, 18 chains. Longest chain 16 peptides. Score 0.464 Round 4: 130 peptides, 19 chains. Longest chain 15 peptides. Score 0.476 Round 5: 143 peptides, 20 chains. Longest chain 16 peptides. Score 0.516 Taking the results from Round 5 Chains 20, Residues 123, Estimated correctness of the model 95.4 % 1 chains (4 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 6027 restraints for refining 3031 atoms. 5554 conditional restraints added. Observations/parameters ratio is 5.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3413 (Rfree = 0.000) for 3031 atoms. Found 170 (354 requested) and removed 25 (177 requested) atoms. Cycle 7: After refmac, R = 0.3228 (Rfree = 0.000) for 3175 atoms. Found 134 (371 requested) and removed 9 (185 requested) atoms. Cycle 8: After refmac, R = 0.3114 (Rfree = 0.000) for 3300 atoms. Found 110 (385 requested) and removed 11 (192 requested) atoms. Cycle 9: After refmac, R = 0.3031 (Rfree = 0.000) for 3393 atoms. Found 106 (397 requested) and removed 4 (198 requested) atoms. Cycle 10: After refmac, R = 0.2960 (Rfree = 0.000) for 3489 atoms. Found 95 (408 requested) and removed 2 (204 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.44 1.52 Round 1: 128 peptides, 18 chains. Longest chain 14 peptides. Score 0.488 Round 2: 130 peptides, 16 chains. Longest chain 20 peptides. Score 0.539 Round 3: 139 peptides, 16 chains. Longest chain 15 peptides. Score 0.577 Round 4: 137 peptides, 17 chains. Longest chain 18 peptides. Score 0.549 Round 5: 144 peptides, 15 chains. Longest chain 20 peptides. Score 0.616 Taking the results from Round 5 Chains 15, Residues 129, Estimated correctness of the model 97.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 7056 restraints for refining 3455 atoms. 6484 conditional restraints added. Observations/parameters ratio is 5.02 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3135 (Rfree = 0.000) for 3455 atoms. Found 171 (404 requested) and removed 27 (202 requested) atoms. Cycle 12: After refmac, R = 0.3005 (Rfree = 0.000) for 3598 atoms. Found 120 (420 requested) and removed 9 (210 requested) atoms. Cycle 13: After refmac, R = 0.2899 (Rfree = 0.000) for 3707 atoms. Found 100 (433 requested) and removed 3 (216 requested) atoms. Cycle 14: After refmac, R = 0.2825 (Rfree = 0.000) for 3803 atoms. Found 93 (444 requested) and removed 7 (222 requested) atoms. Cycle 15: After refmac, R = 0.2765 (Rfree = 0.000) for 3885 atoms. Found 100 (454 requested) and removed 2 (227 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.42 1.50 Round 1: 112 peptides, 13 chains. Longest chain 20 peptides. Score 0.520 Round 2: 129 peptides, 16 chains. Longest chain 21 peptides. Score 0.534 Round 3: 115 peptides, 13 chains. Longest chain 18 peptides. Score 0.534 Round 4: 130 peptides, 16 chains. Longest chain 21 peptides. Score 0.539 Round 5: 131 peptides, 14 chains. Longest chain 20 peptides. Score 0.583 Taking the results from Round 5 Chains 14, Residues 117, Estimated correctness of the model 96.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 8560 restraints for refining 3812 atoms. 8106 conditional restraints added. Observations/parameters ratio is 4.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2879 (Rfree = 0.000) for 3812 atoms. Found 155 (445 requested) and removed 14 (222 requested) atoms. Cycle 17: After refmac, R = 0.2767 (Rfree = 0.000) for 3953 atoms. Found 107 (462 requested) and removed 3 (231 requested) atoms. Cycle 18: After refmac, R = 0.2697 (Rfree = 0.000) for 4052 atoms. Found 92 (474 requested) and removed 5 (237 requested) atoms. Cycle 19: After refmac, R = 0.2642 (Rfree = 0.000) for 4136 atoms. Found 78 (484 requested) and removed 3 (242 requested) atoms. Cycle 20: After refmac, R = 0.2610 (Rfree = 0.000) for 4208 atoms. Found 78 (492 requested) and removed 1 (246 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.42 1.50 Round 1: 116 peptides, 14 chains. Longest chain 19 peptides. Score 0.517 Round 2: 122 peptides, 15 chains. Longest chain 20 peptides. Score 0.524 Round 3: 127 peptides, 14 chains. Longest chain 20 peptides. Score 0.566 Round 4: 126 peptides, 15 chains. Longest chain 19 peptides. Score 0.541 Round 5: 133 peptides, 14 chains. Longest chain 20 peptides. Score 0.591 Taking the results from Round 5 Chains 14, Residues 119, Estimated correctness of the model 96.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 9694 restraints for refining 4134 atoms. 9212 conditional restraints added. Observations/parameters ratio is 4.20 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2745 (Rfree = 0.000) for 4134 atoms. Found 151 (483 requested) and removed 17 (241 requested) atoms. Cycle 22: After refmac, R = 0.2648 (Rfree = 0.000) for 4268 atoms. Found 106 (499 requested) and removed 6 (249 requested) atoms. Cycle 23: After refmac, R = 0.2584 (Rfree = 0.000) for 4367 atoms. Found 79 (510 requested) and removed 5 (255 requested) atoms. Cycle 24: After refmac, R = 0.2540 (Rfree = 0.000) for 4438 atoms. Found 70 (519 requested) and removed 1 (259 requested) atoms. Cycle 25: After refmac, R = 0.2500 (Rfree = 0.000) for 4505 atoms. Found 75 (527 requested) and removed 0 (263 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.42 1.50 Round 1: 123 peptides, 16 chains. Longest chain 18 peptides. Score 0.507 Round 2: 115 peptides, 12 chains. Longest chain 19 peptides. Score 0.555 Round 3: 120 peptides, 12 chains. Longest chain 19 peptides. Score 0.577 Round 4: 111 peptides, 12 chains. Longest chain 19 peptides. Score 0.537 Round 5: 112 peptides, 12 chains. Longest chain 19 peptides. Score 0.542 Taking the results from Round 3 Chains 12, Residues 108, Estimated correctness of the model 96.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 11107 restraints for refining 4403 atoms. 10687 conditional restraints added. Observations/parameters ratio is 3.94 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2604 (Rfree = 0.000) for 4403 atoms. Found 153 (514 requested) and removed 6 (257 requested) atoms. Cycle 27: After refmac, R = 0.2524 (Rfree = 0.000) for 4550 atoms. Found 113 (532 requested) and removed 6 (266 requested) atoms. Cycle 28: After refmac, R = 0.2459 (Rfree = 0.000) for 4655 atoms. Found 95 (544 requested) and removed 2 (272 requested) atoms. Cycle 29: After refmac, R = 0.2415 (Rfree = 0.000) for 4744 atoms. Found 74 (555 requested) and removed 3 (277 requested) atoms. Cycle 30: After refmac, R = 0.2379 (Rfree = 0.000) for 4812 atoms. Found 61 (563 requested) and removed 3 (281 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.41 1.49 Round 1: 119 peptides, 16 chains. Longest chain 18 peptides. Score 0.488 Round 2: 123 peptides, 15 chains. Longest chain 19 peptides. Score 0.528 Round 3: 121 peptides, 16 chains. Longest chain 19 peptides. Score 0.498 Round 4: 121 peptides, 16 chains. Longest chain 17 peptides. Score 0.498 Round 5: 123 peptides, 16 chains. Longest chain 19 peptides. Score 0.507 Taking the results from Round 2 Chains 15, Residues 108, Estimated correctness of the model 95.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 12179 restraints for refining 4681 atoms. 11762 conditional restraints added. Observations/parameters ratio is 3.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2497 (Rfree = 0.000) for 4681 atoms. Found 164 (547 requested) and removed 7 (273 requested) atoms. Cycle 32: After refmac, R = 0.2429 (Rfree = 0.000) for 4838 atoms. Found 112 (565 requested) and removed 4 (282 requested) atoms. Cycle 33: After refmac, R = 0.2377 (Rfree = 0.000) for 4944 atoms. Found 106 (578 requested) and removed 7 (289 requested) atoms. Cycle 34: After refmac, R = 0.2346 (Rfree = 0.000) for 5039 atoms. Found 83 (589 requested) and removed 4 (294 requested) atoms. Cycle 35: After refmac, R = 0.2319 (Rfree = 0.000) for 5114 atoms. Found 58 (598 requested) and removed 8 (299 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.41 1.49 Round 1: 122 peptides, 18 chains. Longest chain 18 peptides. Score 0.459 Round 2: 136 peptides, 17 chains. Longest chain 19 peptides. Score 0.545 Round 3: 137 peptides, 20 chains. Longest chain 19 peptides. Score 0.489 Round 4: 132 peptides, 17 chains. Longest chain 19 peptides. Score 0.527 Round 5: 130 peptides, 19 chains. Longest chain 19 peptides. Score 0.476 Taking the results from Round 2 Chains 17, Residues 119, Estimated correctness of the model 95.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 13002 restraints for refining 4934 atoms. 12543 conditional restraints added. Observations/parameters ratio is 3.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2484 (Rfree = 0.000) for 4934 atoms. Found 192 (576 requested) and removed 11 (288 requested) atoms. Cycle 37: After refmac, R = 0.2410 (Rfree = 0.000) for 5115 atoms. Found 110 (598 requested) and removed 5 (299 requested) atoms. Cycle 38: After refmac, R = 0.2343 (Rfree = 0.000) for 5219 atoms. Found 103 (610 requested) and removed 5 (305 requested) atoms. Cycle 39: After refmac, R = 0.2298 (Rfree = 0.000) for 5313 atoms. Found 83 (621 requested) and removed 9 (310 requested) atoms. Cycle 40: After refmac, R = 0.2259 (Rfree = 0.000) for 5382 atoms. Found 92 (629 requested) and removed 5 (314 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.41 1.49 Round 1: 108 peptides, 14 chains. Longest chain 18 peptides. Score 0.479 Round 2: 115 peptides, 14 chains. Longest chain 19 peptides. Score 0.513 Round 3: 116 peptides, 15 chains. Longest chain 19 peptides. Score 0.496 Round 4: 112 peptides, 14 chains. Longest chain 19 peptides. Score 0.498 Round 5: 118 peptides, 14 chains. Longest chain 19 peptides. Score 0.526 Taking the results from Round 5 Chains 14, Residues 104, Estimated correctness of the model 95.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 14126 restraints for refining 5150 atoms. 13724 conditional restraints added. Observations/parameters ratio is 3.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2402 (Rfree = 0.000) for 5150 atoms. Found 191 (602 requested) and removed 1 (301 requested) atoms. Cycle 42: After refmac, R = 0.2328 (Rfree = 0.000) for 5339 atoms. Found 117 (624 requested) and removed 9 (312 requested) atoms. Cycle 43: After refmac, R = 0.2277 (Rfree = 0.000) for 5446 atoms. Found 79 (636 requested) and removed 5 (318 requested) atoms. Cycle 44: After refmac, R = 0.2248 (Rfree = 0.000) for 5520 atoms. Found 75 (645 requested) and removed 11 (322 requested) atoms. Cycle 45: After refmac, R = 0.2235 (Rfree = 0.000) for 5582 atoms. Found 67 (652 requested) and removed 9 (326 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.41 1.49 Round 1: 106 peptides, 15 chains. Longest chain 18 peptides. Score 0.446 Round 2: 108 peptides, 14 chains. Longest chain 19 peptides. Score 0.479 Round 3: 109 peptides, 15 chains. Longest chain 19 peptides. Score 0.461 Round 4: 111 peptides, 15 chains. Longest chain 19 peptides. Score 0.471 Round 5: 107 peptides, 15 chains. Longest chain 19 peptides. Score 0.451 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 94.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2prv-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 69437 reflections ( 94.64 % complete ) and 14825 restraints for refining 5346 atoms. 14463 conditional restraints added. Observations/parameters ratio is 3.25 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2355 (Rfree = 0.000) for 5346 atoms. Found 0 (625 requested) and removed 1 (312 requested) atoms. Cycle 47: After refmac, R = 0.2316 (Rfree = 0.000) for 5345 atoms. Found 0 (625 requested) and removed 0 (312 requested) atoms. Cycle 48: After refmac, R = 0.2299 (Rfree = 0.000) for 5345 atoms. Found 0 (625 requested) and removed 0 (312 requested) atoms. Cycle 49: After refmac, R = 0.2291 (Rfree = 0.000) for 5345 atoms. Found 0 (625 requested) and removed 0 (312 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:50:58 GMT 2018 Job finished. TimeTaking 56.98 Used memory is bytes: 14836432