Mon 24 Dec 00:46:31 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 2fea-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-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/2fea-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-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 00:46:36 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/2fea-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.6600 Checking the provided sequence file Detected sequence length: 236 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 472 Adjusted target solvent content: 0.54 Input MTZ file: 2fea-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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3776 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: 22.949 4.000 Wilson plot Bfac: 84.85 4735 reflections ( 98.16 % complete ) and 0 restraints for refining 4197 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3451 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3412 (Rfree = 0.000) for 4197 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 4252 seeds are put forward NCS extension: 0 residues added, 4252 seeds are put forward Round 1: 137 peptides, 26 chains. Longest chain 17 peptides. Score 0.292 Round 2: 161 peptides, 27 chains. Longest chain 17 peptides. Score 0.358 Round 3: 186 peptides, 30 chains. Longest chain 19 peptides. Score 0.394 Round 4: 190 peptides, 31 chains. Longest chain 20 peptides. Score 0.393 Round 5: 200 peptides, 32 chains. Longest chain 22 peptides. Score 0.409 Taking the results from Round 5 Chains 32, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 8255 restraints for refining 3407 atoms. 7615 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2624 (Rfree = 0.000) for 3407 atoms. Found 14 (16 requested) and removed 19 (8 requested) atoms. Cycle 2: After refmac, R = 0.2514 (Rfree = 0.000) for 3331 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2581 (Rfree = 0.000) for 3277 atoms. Found 15 (15 requested) and removed 166 (7 requested) atoms. Cycle 4: After refmac, R = 0.2402 (Rfree = 0.000) for 3106 atoms. Found 12 (14 requested) and removed 17 (7 requested) atoms. Cycle 5: After refmac, R = 0.2322 (Rfree = 0.000) for 3088 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 3236 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 3271 seeds are put forward Round 1: 179 peptides, 35 chains. Longest chain 12 peptides. Score 0.304 Round 2: 215 peptides, 32 chains. Longest chain 25 peptides. Score 0.452 Round 3: 217 peptides, 35 chains. Longest chain 14 peptides. Score 0.420 Round 4: 228 peptides, 32 chains. Longest chain 15 peptides. Score 0.488 Round 5: 226 peptides, 32 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 4 Chains 32, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7350 restraints for refining 3180 atoms. 6598 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2448 (Rfree = 0.000) for 3180 atoms. Found 15 (15 requested) and removed 45 (7 requested) atoms. Cycle 7: After refmac, R = 0.2329 (Rfree = 0.000) for 3118 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 8: After refmac, R = 0.2334 (Rfree = 0.000) for 3103 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 9: After refmac, R = 0.2302 (Rfree = 0.000) for 3077 atoms. Found 12 (14 requested) and removed 100 (7 requested) atoms. Cycle 10: After refmac, R = 0.2196 (Rfree = 0.000) for 2973 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 3063 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3080 seeds are put forward Round 1: 183 peptides, 36 chains. Longest chain 8 peptides. Score 0.303 Round 2: 214 peptides, 34 chains. Longest chain 14 peptides. Score 0.424 Round 3: 228 peptides, 37 chains. Longest chain 13 peptides. Score 0.427 Round 4: 215 peptides, 31 chains. Longest chain 15 peptides. Score 0.465 Round 5: 224 peptides, 35 chains. Longest chain 16 peptides. Score 0.440 Taking the results from Round 4 Chains 32, Residues 184, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7269 restraints for refining 3188 atoms. 6524 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2560 (Rfree = 0.000) for 3188 atoms. Found 15 (15 requested) and removed 37 (7 requested) atoms. Cycle 12: After refmac, R = 0.2268 (Rfree = 0.000) for 3145 atoms. Found 11 (15 requested) and removed 27 (7 requested) atoms. Cycle 13: After refmac, R = 0.2194 (Rfree = 0.000) for 3113 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 14: After refmac, R = 0.2087 (Rfree = 0.000) for 3102 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 15: After refmac, R = 0.2033 (Rfree = 0.000) for 3093 atoms. Found 12 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 3209 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3226 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 9 peptides. Score 0.275 Round 2: 207 peptides, 34 chains. Longest chain 20 peptides. Score 0.404 Round 3: 208 peptides, 33 chains. Longest chain 15 peptides. Score 0.420 Round 4: 214 peptides, 32 chains. Longest chain 15 peptides. Score 0.450 Round 5: 219 peptides, 33 chains. Longest chain 15 peptides. Score 0.451 Taking the results from Round 5 Chains 33, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4735 reflections ( 98.16 % complete ) and 7543 restraints for refining 3279 atoms. 6832 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2328 (Rfree = 0.000) for 3279 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 17: After refmac, R = 0.2216 (Rfree = 0.000) for 3243 atoms. Found 15 (15 requested) and removed 28 (7 requested) atoms. Cycle 18: After refmac, R = 0.2204 (Rfree = 0.000) for 3215 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 19: After refmac, R = 0.2124 (Rfree = 0.000) for 3204 atoms. Found 12 (15 requested) and removed 16 (7 requested) atoms. Cycle 20: After refmac, R = 0.2249 (Rfree = 0.000) for 3190 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 3329 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3348 seeds are put forward Round 1: 181 peptides, 39 chains. Longest chain 10 peptides. Score 0.255 Round 2: 201 peptides, 37 chains. Longest chain 9 peptides. Score 0.347 Round 3: 193 peptides, 30 chains. Longest chain 11 peptides. Score 0.415 Round 4: 191 peptides, 32 chains. Longest chain 10 peptides. Score 0.382 Round 5: 195 peptides, 31 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 3 Chains 30, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7543 restraints for refining 3220 atoms. 6921 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2623 (Rfree = 0.000) for 3220 atoms. Found 15 (15 requested) and removed 134 (7 requested) atoms. Cycle 22: After refmac, R = 0.2338 (Rfree = 0.000) for 3081 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. Cycle 23: After refmac, R = 0.2466 (Rfree = 0.000) for 3058 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 24: After refmac, R = 0.2148 (Rfree = 0.000) for 3043 atoms. Found 14 (14 requested) and removed 63 (7 requested) atoms. Cycle 25: After refmac, R = 0.2174 (Rfree = 0.000) for 2989 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.57 Search for helices and strands: 0 residues in 0 chains, 3116 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3122 seeds are put forward Round 1: 185 peptides, 39 chains. Longest chain 12 peptides. Score 0.268 Round 2: 202 peptides, 39 chains. Longest chain 12 peptides. Score 0.323 Round 3: 219 peptides, 37 chains. Longest chain 12 peptides. Score 0.401 Round 4: 204 peptides, 33 chains. Longest chain 14 peptides. Score 0.408 Round 5: 201 peptides, 33 chains. Longest chain 14 peptides. Score 0.399 Taking the results from Round 4 Chains 33, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7554 restraints for refining 3269 atoms. 6903 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2522 (Rfree = 0.000) for 3269 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. Cycle 27: After refmac, R = 0.2191 (Rfree = 0.000) for 3238 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 28: After refmac, R = 0.2226 (Rfree = 0.000) for 3210 atoms. Found 14 (15 requested) and removed 15 (7 requested) atoms. Cycle 29: After refmac, R = 0.1763 (Rfree = 0.000) for 3203 atoms. Found 1 (15 requested) and removed 12 (7 requested) atoms. Cycle 30: After refmac, R = 0.1588 (Rfree = 0.000) for 3188 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 3309 seeds are put forward NCS extension: 0 residues added, 3309 seeds are put forward Round 1: 177 peptides, 38 chains. Longest chain 8 peptides. Score 0.255 Round 2: 197 peptides, 35 chains. Longest chain 14 peptides. Score 0.361 Round 3: 199 peptides, 34 chains. Longest chain 12 peptides. Score 0.380 Round 4: 197 peptides, 33 chains. Longest chain 13 peptides. Score 0.387 Round 5: 201 peptides, 33 chains. Longest chain 11 peptides. Score 0.399 Taking the results from Round 5 Chains 33, Residues 168, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7747 restraints for refining 3327 atoms. 7089 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2415 (Rfree = 0.000) for 3327 atoms. Found 8 (15 requested) and removed 183 (7 requested) atoms. Cycle 32: After refmac, R = 0.2284 (Rfree = 0.000) for 3129 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. Cycle 33: After refmac, R = 0.2121 (Rfree = 0.000) for 3096 atoms. Found 10 (14 requested) and removed 19 (7 requested) atoms. Cycle 34: After refmac, R = 0.2048 (Rfree = 0.000) for 3077 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.2012 (Rfree = 0.000) for 3071 atoms. Found 12 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 3176 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3188 seeds are put forward Round 1: 163 peptides, 33 chains. Longest chain 8 peptides. Score 0.279 Round 2: 174 peptides, 32 chains. Longest chain 10 peptides. Score 0.329 Round 3: 185 peptides, 35 chains. Longest chain 11 peptides. Score 0.323 Round 4: 188 peptides, 33 chains. Longest chain 11 peptides. Score 0.360 Round 5: 191 peptides, 31 chains. Longest chain 14 peptides. Score 0.396 Taking the results from Round 5 Chains 31, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7536 restraints for refining 3283 atoms. 6927 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2378 (Rfree = 0.000) for 3283 atoms. Found 14 (15 requested) and removed 27 (7 requested) atoms. Cycle 37: After refmac, R = 0.2092 (Rfree = 0.000) for 3256 atoms. Found 12 (15 requested) and removed 19 (7 requested) atoms. Cycle 38: After refmac, R = 0.2091 (Rfree = 0.000) for 3243 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 39: After refmac, R = 0.1945 (Rfree = 0.000) for 3231 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 40: After refmac, R = 0.1524 (Rfree = 0.000) for 3230 atoms. Found 4 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 3334 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3354 seeds are put forward Round 1: 154 peptides, 35 chains. Longest chain 8 peptides. Score 0.218 Round 2: 187 peptides, 38 chains. Longest chain 13 peptides. Score 0.288 Round 3: 200 peptides, 37 chains. Longest chain 11 peptides. Score 0.344 Round 4: 184 peptides, 32 chains. Longest chain 12 peptides. Score 0.361 Round 5: 180 peptides, 32 chains. Longest chain 13 peptides. Score 0.348 Taking the results from Round 4 Chains 32, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 8011 restraints for refining 3409 atoms. 7435 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2025 (Rfree = 0.000) for 3409 atoms. Found 10 (16 requested) and removed 28 (8 requested) atoms. Cycle 42: After refmac, R = 0.1864 (Rfree = 0.000) for 3381 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 43: After refmac, R = 0.1945 (Rfree = 0.000) for 3377 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 44: After refmac, R = 0.1919 (Rfree = 0.000) for 3366 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 45: After refmac, R = 0.1883 (Rfree = 0.000) for 3364 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 3468 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3484 seeds are put forward Round 1: 124 peptides, 27 chains. Longest chain 8 peptides. Score 0.230 Round 2: 127 peptides, 26 chains. Longest chain 9 peptides. Score 0.257 Round 3: 133 peptides, 25 chains. Longest chain 12 peptides. Score 0.294 Round 4: 122 peptides, 23 chains. Longest chain 12 peptides. Score 0.285 Round 5: 118 peptides, 22 chains. Longest chain 8 peptides. Score 0.287 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2fea-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4735 reflections ( 98.16 % complete ) and 8195 restraints for refining 3409 atoms. 7788 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1881 (Rfree = 0.000) for 3409 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2134 (Rfree = 0.000) for 3390 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2042 (Rfree = 0.000) for 3373 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2075 (Rfree = 0.000) for 3357 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 41.25