null Mon 24 Dec 07:58:44 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2otm-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2otm-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2otm-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.6-parrot-noncs ############### 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 07:58:49 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/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.6-parrot-noncs/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 378 and 0 Target number of residues in the AU: 378 Target solvent content: 0.6303 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-3.6-parrot-noncs.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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3696 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 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: 78.536 3.600 Wilson plot Bfac: 66.47 6456 reflections ( 99.77 % complete ) and 0 restraints for refining 4072 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3169 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2868 (Rfree = 0.000) for 4072 atoms. Found 26 (26 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 4140 seeds are put forward NCS extension: 0 residues added, 4140 seeds are put forward Round 1: 215 peptides, 39 chains. Longest chain 13 peptides. Score 0.363 Round 2: 277 peptides, 39 chains. Longest chain 17 peptides. Score 0.532 Round 3: 277 peptides, 36 chains. Longest chain 23 peptides. Score 0.563 Round 4: 306 peptides, 35 chains. Longest chain 26 peptides. Score 0.636 Round 5: 307 peptides, 35 chains. Longest chain 20 peptides. Score 0.638 Taking the results from Round 5 Chains 37, Residues 272, Estimated correctness of the model 28.9 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 6882 restraints for refining 3350 atoms. 5719 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2476 (Rfree = 0.000) for 3350 atoms. Found 15 (21 requested) and removed 28 (10 requested) atoms. Cycle 2: After refmac, R = 0.2339 (Rfree = 0.000) for 3290 atoms. Found 8 (21 requested) and removed 13 (10 requested) atoms. Cycle 3: After refmac, R = 0.2257 (Rfree = 0.000) for 3267 atoms. Found 4 (21 requested) and removed 17 (10 requested) atoms. Cycle 4: After refmac, R = 0.2232 (Rfree = 0.000) for 3239 atoms. Found 7 (20 requested) and removed 16 (10 requested) atoms. Cycle 5: After refmac, R = 0.2129 (Rfree = 0.000) for 3220 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 3309 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3320 seeds are put forward Round 1: 280 peptides, 36 chains. Longest chain 23 peptides. Score 0.570 Round 2: 302 peptides, 34 chains. Longest chain 24 peptides. Score 0.637 Round 3: 296 peptides, 32 chains. Longest chain 24 peptides. Score 0.643 Round 4: 291 peptides, 34 chains. Longest chain 27 peptides. Score 0.614 Round 5: 298 peptides, 33 chains. Longest chain 26 peptides. Score 0.638 Taking the results from Round 3 Chains 39, Residues 264, Estimated correctness of the model 30.7 % 6 chains (56 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 6702 restraints for refining 3350 atoms. 5509 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2297 (Rfree = 0.000) for 3350 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 7: After refmac, R = 0.2135 (Rfree = 0.000) for 3324 atoms. Found 5 (21 requested) and removed 20 (10 requested) atoms. Cycle 8: After refmac, R = 0.2039 (Rfree = 0.000) for 3299 atoms. Found 5 (21 requested) and removed 16 (10 requested) atoms. Cycle 9: After refmac, R = 0.2003 (Rfree = 0.000) for 3279 atoms. Found 2 (21 requested) and removed 13 (10 requested) atoms. Cycle 10: After refmac, R = 0.2005 (Rfree = 0.000) for 3261 atoms. Found 4 (20 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 3353 seeds are put forward NCS extension: 31 residues added (11 deleted due to clashes), 3384 seeds are put forward Round 1: 268 peptides, 38 chains. Longest chain 26 peptides. Score 0.520 Round 2: 281 peptides, 37 chains. Longest chain 16 peptides. Score 0.562 Round 3: 273 peptides, 34 chains. Longest chain 17 peptides. Score 0.575 Round 4: 277 peptides, 35 chains. Longest chain 25 peptides. Score 0.574 Round 5: 295 peptides, 35 chains. Longest chain 28 peptides. Score 0.613 Taking the results from Round 5 Chains 38, Residues 260, Estimated correctness of the model 19.7 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7184 restraints for refining 3350 atoms. 6094 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2409 (Rfree = 0.000) for 3350 atoms. Found 9 (21 requested) and removed 27 (10 requested) atoms. Cycle 12: After refmac, R = 0.2231 (Rfree = 0.000) for 3321 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. Cycle 13: After refmac, R = 0.2150 (Rfree = 0.000) for 3311 atoms. Found 2 (21 requested) and removed 17 (10 requested) atoms. Cycle 14: After refmac, R = 0.2135 (Rfree = 0.000) for 3294 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.2145 (Rfree = 0.000) for 3279 atoms. Found 4 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 3357 seeds are put forward NCS extension: 30 residues added (8 deleted due to clashes), 3387 seeds are put forward Round 1: 257 peptides, 40 chains. Longest chain 17 peptides. Score 0.469 Round 2: 276 peptides, 38 chains. Longest chain 23 peptides. Score 0.540 Round 3: 269 peptides, 36 chains. Longest chain 31 peptides. Score 0.544 Round 4: 289 peptides, 40 chains. Longest chain 28 peptides. Score 0.550 Round 5: 281 peptides, 37 chains. Longest chain 25 peptides. Score 0.562 Taking the results from Round 5 Chains 37, Residues 244, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7447 restraints for refining 3350 atoms. 6490 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2273 (Rfree = 0.000) for 3350 atoms. Found 8 (21 requested) and removed 18 (10 requested) atoms. Cycle 17: After refmac, R = 0.2088 (Rfree = 0.000) for 3329 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. Cycle 18: After refmac, R = 0.2006 (Rfree = 0.000) for 3312 atoms. Found 3 (21 requested) and removed 15 (10 requested) atoms. Cycle 19: After refmac, R = 0.1959 (Rfree = 0.000) for 3297 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.2072 (Rfree = 0.000) for 3287 atoms. Found 6 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 3379 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3402 seeds are put forward Round 1: 227 peptides, 40 chains. Longest chain 16 peptides. Score 0.386 Round 2: 265 peptides, 39 chains. Longest chain 17 peptides. Score 0.502 Round 3: 285 peptides, 40 chains. Longest chain 16 peptides. Score 0.540 Round 4: 278 peptides, 38 chains. Longest chain 17 peptides. Score 0.545 Round 5: 272 peptides, 37 chains. Longest chain 20 peptides. Score 0.541 Taking the results from Round 4 Chains 39, Residues 240, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7322 restraints for refining 3350 atoms. 6359 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2181 (Rfree = 0.000) for 3350 atoms. Found 10 (21 requested) and removed 22 (10 requested) atoms. Cycle 22: After refmac, R = 0.2066 (Rfree = 0.000) for 3324 atoms. Found 3 (21 requested) and removed 14 (10 requested) atoms. Cycle 23: After refmac, R = 0.2088 (Rfree = 0.000) for 3305 atoms. Found 5 (21 requested) and removed 14 (10 requested) atoms. Cycle 24: After refmac, R = 0.2006 (Rfree = 0.000) for 3290 atoms. Found 0 (21 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.2065 (Rfree = 0.000) for 3275 atoms. Found 11 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 3365 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3384 seeds are put forward Round 1: 214 peptides, 42 chains. Longest chain 10 peptides. Score 0.320 Round 2: 240 peptides, 34 chains. Longest chain 23 peptides. Score 0.494 Round 3: 240 peptides, 33 chains. Longest chain 17 peptides. Score 0.506 Round 4: 234 peptides, 32 chains. Longest chain 23 peptides. Score 0.502 Round 5: 248 peptides, 36 chains. Longest chain 21 peptides. Score 0.492 Taking the results from Round 3 Chains 33, Residues 207, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7439 restraints for refining 3349 atoms. 6616 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2076 (Rfree = 0.000) for 3349 atoms. Found 10 (21 requested) and removed 22 (10 requested) atoms. Cycle 27: After refmac, R = 0.1985 (Rfree = 0.000) for 3328 atoms. Found 4 (21 requested) and removed 14 (10 requested) atoms. Cycle 28: After refmac, R = 0.1978 (Rfree = 0.000) for 3316 atoms. Found 1 (21 requested) and removed 12 (10 requested) atoms. Cycle 29: After refmac, R = 0.2221 (Rfree = 0.000) for 3295 atoms. Found 15 (21 requested) and removed 21 (10 requested) atoms. Cycle 30: After refmac, R = 0.1944 (Rfree = 0.000) for 3286 atoms. Found 1 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 3367 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3391 seeds are put forward Round 1: 226 peptides, 42 chains. Longest chain 11 peptides. Score 0.357 Round 2: 254 peptides, 40 chains. Longest chain 14 peptides. Score 0.461 Round 3: 254 peptides, 38 chains. Longest chain 17 peptides. Score 0.485 Round 4: 245 peptides, 35 chains. Longest chain 21 peptides. Score 0.496 Round 5: 260 peptides, 37 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 5 Chains 37, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7299 restraints for refining 3350 atoms. 6444 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2251 (Rfree = 0.000) for 3350 atoms. Found 12 (21 requested) and removed 23 (10 requested) atoms. Cycle 32: After refmac, R = 0.2154 (Rfree = 0.000) for 3324 atoms. Found 10 (21 requested) and removed 24 (10 requested) atoms. Cycle 33: After refmac, R = 0.2216 (Rfree = 0.000) for 3305 atoms. Found 9 (21 requested) and removed 24 (10 requested) atoms. Cycle 34: After refmac, R = 0.2102 (Rfree = 0.000) for 3286 atoms. Found 9 (21 requested) and removed 15 (10 requested) atoms. Cycle 35: After refmac, R = 0.1943 (Rfree = 0.000) for 3275 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 3363 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3377 seeds are put forward Round 1: 216 peptides, 39 chains. Longest chain 11 peptides. Score 0.366 Round 2: 229 peptides, 35 chains. Longest chain 20 peptides. Score 0.453 Round 3: 249 peptides, 38 chains. Longest chain 20 peptides. Score 0.471 Round 4: 242 peptides, 36 chains. Longest chain 17 peptides. Score 0.476 Round 5: 238 peptides, 36 chains. Longest chain 21 peptides. Score 0.466 Taking the results from Round 4 Chains 36, Residues 206, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7295 restraints for refining 3350 atoms. 6437 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2263 (Rfree = 0.000) for 3350 atoms. Found 13 (21 requested) and removed 22 (10 requested) atoms. Cycle 37: After refmac, R = 0.2089 (Rfree = 0.000) for 3336 atoms. Found 3 (21 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.2011 (Rfree = 0.000) for 3315 atoms. Found 11 (21 requested) and removed 14 (10 requested) atoms. Cycle 39: After refmac, R = 0.1930 (Rfree = 0.000) for 3312 atoms. Found 4 (21 requested) and removed 13 (10 requested) atoms. Cycle 40: After refmac, R = 0.1866 (Rfree = 0.000) for 3299 atoms. Found 4 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3356 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3371 seeds are put forward Round 1: 226 peptides, 42 chains. Longest chain 15 peptides. Score 0.357 Round 2: 242 peptides, 39 chains. Longest chain 13 peptides. Score 0.441 Round 3: 252 peptides, 40 chains. Longest chain 13 peptides. Score 0.456 Round 4: 249 peptides, 42 chains. Longest chain 14 peptides. Score 0.424 Round 5: 249 peptides, 41 chains. Longest chain 12 peptides. Score 0.436 Taking the results from Round 3 Chains 40, Residues 212, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7231 restraints for refining 3349 atoms. 6357 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2042 (Rfree = 0.000) for 3349 atoms. Found 6 (21 requested) and removed 18 (10 requested) atoms. Cycle 42: After refmac, R = 0.1912 (Rfree = 0.000) for 3316 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. Cycle 43: After refmac, R = 0.1867 (Rfree = 0.000) for 3301 atoms. Found 0 (21 requested) and removed 15 (10 requested) atoms. Cycle 44: After refmac, R = 0.1851 (Rfree = 0.000) for 3284 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1838 (Rfree = 0.000) for 3273 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3342 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 3356 seeds are put forward Round 1: 198 peptides, 36 chains. Longest chain 12 peptides. Score 0.350 Round 2: 238 peptides, 38 chains. Longest chain 29 peptides. Score 0.442 Round 3: 228 peptides, 37 chains. Longest chain 12 peptides. Score 0.426 Round 4: 211 peptides, 33 chains. Longest chain 14 peptides. Score 0.427 Round 5: 213 peptides, 35 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 200, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 38 chains (200 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6456 reflections ( 99.77 % complete ) and 7395 restraints for refining 3314 atoms. 6614 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2029 (Rfree = 0.000) for 3314 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1943 (Rfree = 0.000) for 3297 atoms. Found 0 (21 requested) and removed 6 (10 requested) atoms. Cycle 48: After refmac, R = 0.1923 (Rfree = 0.000) for 3289 atoms. Found 0 (21 requested) and removed 9 (10 requested) atoms. Cycle 49: After refmac, R = 0.1978 (Rfree = 0.000) for 3277 atoms. Found 0 (21 requested) and removed 9 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:39:34 GMT 2018 Job finished. TimeTaking 40.83 Used memory is bytes: 12630496