null Mon 24 Dec 00:29:10 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 2o62-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-4.0-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/2o62-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-4.0-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 00:29:15 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/2o62-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-4.0-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 391 and 0 Target number of residues in the AU: 391 Target solvent content: 0.6373 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.50 Input MTZ file: 2o62-4.0-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: 19 Cell parameters: 61.210 71.880 132.610 90.000 90.000 90.000 Input sequence file: 2o62-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4320 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 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: 66.305 4.000 Wilson plot Bfac: 70.40 5176 reflections ( 97.73 % complete ) and 0 restraints for refining 4768 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3796 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3690 (Rfree = 0.000) for 4768 atoms. Found 9 (22 requested) and removed 90 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 4722 seeds are put forward NCS extension: 0 residues added, 4722 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 10 peptides. Score 0.234 Round 2: 139 peptides, 29 chains. Longest chain 9 peptides. Score 0.251 Round 3: 146 peptides, 29 chains. Longest chain 10 peptides. Score 0.274 Round 4: 155 peptides, 32 chains. Longest chain 8 peptides. Score 0.262 Round 5: 160 peptides, 33 chains. Longest chain 9 peptides. Score 0.264 Taking the results from Round 3 Chains 29, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 9685 restraints for refining 3900 atoms. 9246 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3393 (Rfree = 0.000) for 3900 atoms. Found 12 (18 requested) and removed 51 (9 requested) atoms. Cycle 2: After refmac, R = 0.3167 (Rfree = 0.000) for 3801 atoms. Found 15 (18 requested) and removed 31 (9 requested) atoms. Cycle 3: After refmac, R = 0.2769 (Rfree = 0.000) for 3744 atoms. Found 4 (17 requested) and removed 23 (8 requested) atoms. Cycle 4: After refmac, R = 0.3062 (Rfree = 0.000) for 3708 atoms. Found 14 (17 requested) and removed 21 (8 requested) atoms. Cycle 5: After refmac, R = 0.3229 (Rfree = 0.000) for 3690 atoms. Found 10 (17 requested) and removed 28 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.51 Search for helices and strands: 0 residues in 0 chains, 3721 seeds are put forward NCS extension: 0 residues added, 3721 seeds are put forward Round 1: 141 peptides, 32 chains. Longest chain 8 peptides. Score 0.214 Round 2: 163 peptides, 32 chains. Longest chain 10 peptides. Score 0.288 Round 3: 173 peptides, 34 chains. Longest chain 11 peptides. Score 0.293 Round 4: 175 peptides, 31 chains. Longest chain 11 peptides. Score 0.339 Round 5: 176 peptides, 32 chains. Longest chain 11 peptides. Score 0.329 Taking the results from Round 4 Chains 31, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7492 restraints for refining 3249 atoms. 6947 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3131 (Rfree = 0.000) for 3249 atoms. Found 11 (15 requested) and removed 35 (7 requested) atoms. Cycle 7: After refmac, R = 0.3096 (Rfree = 0.000) for 3205 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 8: After refmac, R = 0.2648 (Rfree = 0.000) for 3179 atoms. Found 11 (15 requested) and removed 14 (7 requested) atoms. Cycle 9: After refmac, R = 0.2927 (Rfree = 0.000) for 3158 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 10: After refmac, R = 0.2508 (Rfree = 0.000) for 3148 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.51 Search for helices and strands: 0 residues in 0 chains, 3200 seeds are put forward NCS extension: 0 residues added, 3200 seeds are put forward Round 1: 176 peptides, 38 chains. Longest chain 6 peptides. Score 0.248 Round 2: 204 peptides, 41 chains. Longest chain 13 peptides. Score 0.297 Round 3: 208 peptides, 43 chains. Longest chain 8 peptides. Score 0.283 Round 4: 215 peptides, 40 chains. Longest chain 10 peptides. Score 0.343 Round 5: 220 peptides, 40 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 5 Chains 40, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7787 restraints for refining 3439 atoms. 7107 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2824 (Rfree = 0.000) for 3439 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. Cycle 12: After refmac, R = 0.2533 (Rfree = 0.000) for 3389 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 13: After refmac, R = 0.2589 (Rfree = 0.000) for 3354 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 14: After refmac, R = 0.2492 (Rfree = 0.000) for 3325 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 15: After refmac, R = 0.2632 (Rfree = 0.000) for 3306 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.52 Search for helices and strands: 0 residues in 0 chains, 3370 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3383 seeds are put forward Round 1: 182 peptides, 39 chains. Longest chain 7 peptides. Score 0.254 Round 2: 208 peptides, 40 chains. Longest chain 10 peptides. Score 0.322 Round 3: 215 peptides, 37 chains. Longest chain 12 peptides. Score 0.380 Round 4: 213 peptides, 34 chains. Longest chain 14 peptides. Score 0.411 Round 5: 199 peptides, 34 chains. Longest chain 15 peptides. Score 0.371 Taking the results from Round 4 Chains 34, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7815 restraints for refining 3468 atoms. 7133 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2568 (Rfree = 0.000) for 3468 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 17: After refmac, R = 0.2688 (Rfree = 0.000) for 3425 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 18: After refmac, R = 0.2607 (Rfree = 0.000) for 3386 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 19: After refmac, R = 0.2556 (Rfree = 0.000) for 3361 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 20: After refmac, R = 0.2477 (Rfree = 0.000) for 3341 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.46 Search for helices and strands: 0 residues in 0 chains, 3411 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3429 seeds are put forward Round 1: 171 peptides, 36 chains. Longest chain 9 peptides. Score 0.259 Round 2: 214 peptides, 40 chains. Longest chain 13 peptides. Score 0.340 Round 3: 211 peptides, 38 chains. Longest chain 11 peptides. Score 0.356 Round 4: 214 peptides, 35 chains. Longest chain 12 peptides. Score 0.402 Round 5: 218 peptides, 35 chains. Longest chain 11 peptides. Score 0.413 Taking the results from Round 5 Chains 35, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 8087 restraints for refining 3568 atoms. 7390 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2864 (Rfree = 0.000) for 3568 atoms. Found 16 (16 requested) and removed 34 (8 requested) atoms. Cycle 22: After refmac, R = 0.2692 (Rfree = 0.000) for 3519 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 23: After refmac, R = 0.2559 (Rfree = 0.000) for 3490 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 24: After refmac, R = 0.2581 (Rfree = 0.000) for 3456 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.1950 (Rfree = 0.000) for 3443 atoms. Found 7 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.53 Search for helices and strands: 0 residues in 0 chains, 3485 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3497 seeds are put forward Round 1: 180 peptides, 38 chains. Longest chain 9 peptides. Score 0.261 Round 2: 224 peptides, 43 chains. Longest chain 11 peptides. Score 0.331 Round 3: 211 peptides, 40 chains. Longest chain 8 peptides. Score 0.331 Round 4: 218 peptides, 42 chains. Longest chain 10 peptides. Score 0.326 Round 5: 198 peptides, 35 chains. Longest chain 12 peptides. Score 0.356 Taking the results from Round 5 Chains 35, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 8087 restraints for refining 3519 atoms. 7470 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2719 (Rfree = 0.000) for 3519 atoms. Found 16 (16 requested) and removed 37 (8 requested) atoms. Cycle 27: After refmac, R = 0.2580 (Rfree = 0.000) for 3475 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 28: After refmac, R = 0.2562 (Rfree = 0.000) for 3445 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 29: After refmac, R = 0.2606 (Rfree = 0.000) for 3421 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 30: After refmac, R = 0.2527 (Rfree = 0.000) for 3408 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.48 Search for helices and strands: 0 residues in 0 chains, 3474 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3491 seeds are put forward Round 1: 179 peptides, 41 chains. Longest chain 7 peptides. Score 0.217 Round 2: 198 peptides, 36 chains. Longest chain 14 peptides. Score 0.343 Round 3: 202 peptides, 37 chains. Longest chain 11 peptides. Score 0.342 Round 4: 203 peptides, 36 chains. Longest chain 16 peptides. Score 0.358 Round 5: 193 peptides, 35 chains. Longest chain 12 peptides. Score 0.341 Taking the results from Round 4 Chains 36, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7991 restraints for refining 3574 atoms. 7359 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2730 (Rfree = 0.000) for 3574 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 32: After refmac, R = 0.2454 (Rfree = 0.000) for 3544 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 33: After refmac, R = 0.2418 (Rfree = 0.000) for 3521 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 34: After refmac, R = 0.2247 (Rfree = 0.000) for 3504 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 35: After refmac, R = 0.2335 (Rfree = 0.000) for 3495 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.57 Search for helices and strands: 0 residues in 0 chains, 3537 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 3565 seeds are put forward Round 1: 152 peptides, 36 chains. Longest chain 6 peptides. Score 0.195 Round 2: 180 peptides, 35 chains. Longest chain 9 peptides. Score 0.301 Round 3: 176 peptides, 35 chains. Longest chain 9 peptides. Score 0.289 Round 4: 184 peptides, 34 chains. Longest chain 9 peptides. Score 0.327 Round 5: 177 peptides, 33 chains. Longest chain 10 peptides. Score 0.319 Taking the results from Round 4 Chains 34, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 8570 restraints for refining 3663 atoms. 8004 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2484 (Rfree = 0.000) for 3663 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 37: After refmac, R = 0.2557 (Rfree = 0.000) for 3624 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 38: After refmac, R = 0.2512 (Rfree = 0.000) for 3594 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 39: After refmac, R = 0.2352 (Rfree = 0.000) for 3565 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 40: After refmac, R = 0.1775 (Rfree = 0.000) for 3557 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.56 Search for helices and strands: 0 residues in 0 chains, 3597 seeds are put forward NCS extension: 0 residues added, 3597 seeds are put forward Round 1: 144 peptides, 33 chains. Longest chain 6 peptides. Score 0.210 Round 2: 166 peptides, 33 chains. Longest chain 10 peptides. Score 0.284 Round 3: 175 peptides, 34 chains. Longest chain 15 peptides. Score 0.299 Round 4: 174 peptides, 33 chains. Longest chain 9 peptides. Score 0.309 Round 5: 162 peptides, 33 chains. Longest chain 10 peptides. Score 0.271 Taking the results from Round 4 Chains 33, Residues 141, Estimated correctness of the model 0.0 % 5 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 8123 restraints for refining 3608 atoms. 7544 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2642 (Rfree = 0.000) for 3608 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 42: After refmac, R = 0.2513 (Rfree = 0.000) for 3585 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 43: After refmac, R = 0.1945 (Rfree = 0.000) for 3563 atoms. Found 10 (17 requested) and removed 13 (8 requested) atoms. Cycle 44: After refmac, R = 0.1851 (Rfree = 0.000) for 3549 atoms. Found 11 (16 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1922 (Rfree = 0.000) for 3541 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 3585 seeds are put forward NCS extension: 0 residues added, 3585 seeds are put forward Round 1: 123 peptides, 26 chains. Longest chain 8 peptides. Score 0.239 Round 2: 147 peptides, 30 chains. Longest chain 9 peptides. Score 0.263 Round 3: 168 peptides, 31 chains. Longest chain 13 peptides. Score 0.317 Round 4: 157 peptides, 28 chains. Longest chain 9 peptides. Score 0.324 Round 5: 163 peptides, 30 chains. Longest chain 10 peptides. Score 0.315 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 129, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2o62-4_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (129 residues) following loop building 4 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5176 reflections ( 97.73 % complete ) and 7991 restraints for refining 3543 atoms. 7467 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2611 (Rfree = 0.000) for 3543 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2649 (Rfree = 0.000) for 3521 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2313 (Rfree = 0.000) for 3496 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2603 (Rfree = 0.000) for 3475 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:13:09 GMT 2018 Job finished. TimeTaking 43.99 Used memory is bytes: 14940776