Mon 24 Dec 00:57:56 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 1z85-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-4.0-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/1z85-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-4.0-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 00:58:00 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/1z85-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-4.0-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 356 and 0 Target number of residues in the AU: 356 Target solvent content: 0.6657 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 468 Adjusted target solvent content: 0.56 Input MTZ file: 1z85-4.0-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: 65.676 82.546 106.310 90.000 90.000 90.000 Input sequence file: 1z85-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3744 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: 65.199 4.000 Wilson plot Bfac: 88.57 5207 reflections ( 99.64 % complete ) and 0 restraints for refining 4136 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3344 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3093 (Rfree = 0.000) for 4136 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.51 Search for helices and strands: 0 residues in 0 chains, 4204 seeds are put forward NCS extension: 0 residues added, 4204 seeds are put forward Round 1: 207 peptides, 35 chains. Longest chain 10 peptides. Score 0.384 Round 2: 253 peptides, 31 chains. Longest chain 19 peptides. Score 0.550 Round 3: 260 peptides, 32 chains. Longest chain 20 peptides. Score 0.555 Round 4: 276 peptides, 32 chains. Longest chain 23 peptides. Score 0.591 Round 5: 274 peptides, 30 chains. Longest chain 20 peptides. Score 0.606 Taking the results from Round 5 Chains 30, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7849 restraints for refining 3379 atoms. 6903 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2440 (Rfree = 0.000) for 3379 atoms. Found 13 (16 requested) and removed 18 (8 requested) atoms. Cycle 2: After refmac, R = 0.2251 (Rfree = 0.000) for 3318 atoms. Found 9 (16 requested) and removed 17 (8 requested) atoms. Cycle 3: After refmac, R = 0.2129 (Rfree = 0.000) for 3279 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 4: After refmac, R = 0.2066 (Rfree = 0.000) for 3246 atoms. Found 7 (15 requested) and removed 18 (7 requested) atoms. Cycle 5: After refmac, R = 0.1965 (Rfree = 0.000) for 3217 atoms. Found 5 (15 requested) and removed 20 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.43 Search for helices and strands: 0 residues in 0 chains, 3308 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 3336 seeds are put forward Round 1: 233 peptides, 35 chains. Longest chain 20 peptides. Score 0.456 Round 2: 253 peptides, 31 chains. Longest chain 19 peptides. Score 0.550 Round 3: 253 peptides, 29 chains. Longest chain 28 peptides. Score 0.571 Round 4: 260 peptides, 29 chains. Longest chain 22 peptides. Score 0.586 Round 5: 255 peptides, 30 chains. Longest chain 22 peptides. Score 0.565 Taking the results from Round 4 Chains 29, Residues 231, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7588 restraints for refining 3361 atoms. 6673 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2337 (Rfree = 0.000) for 3361 atoms. Found 13 (15 requested) and removed 28 (7 requested) atoms. Cycle 7: After refmac, R = 0.2212 (Rfree = 0.000) for 3299 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.2200 (Rfree = 0.000) for 3264 atoms. Found 14 (15 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.2102 (Rfree = 0.000) for 3246 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 10: After refmac, R = 0.2021 (Rfree = 0.000) for 3233 atoms. Found 13 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 3359 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3371 seeds are put forward Round 1: 212 peptides, 34 chains. Longest chain 13 peptides. Score 0.411 Round 2: 248 peptides, 34 chains. Longest chain 15 peptides. Score 0.505 Round 3: 245 peptides, 34 chains. Longest chain 22 peptides. Score 0.498 Round 4: 241 peptides, 29 chains. Longest chain 21 peptides. Score 0.543 Round 5: 255 peptides, 31 chains. Longest chain 23 peptides. Score 0.554 Taking the results from Round 5 Chains 33, Residues 224, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7473 restraints for refining 3379 atoms. 6542 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2229 (Rfree = 0.000) for 3379 atoms. Found 13 (16 requested) and removed 19 (8 requested) atoms. Cycle 12: After refmac, R = 0.2136 (Rfree = 0.000) for 3346 atoms. Found 3 (16 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2101 (Rfree = 0.000) for 3330 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. Cycle 14: After refmac, R = 0.2068 (Rfree = 0.000) for 3321 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 15: After refmac, R = 0.2053 (Rfree = 0.000) for 3315 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 3.51 Search for helices and strands: 0 residues in 0 chains, 3416 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3433 seeds are put forward Round 1: 236 peptides, 42 chains. Longest chain 13 peptides. Score 0.380 Round 2: 255 peptides, 34 chains. Longest chain 22 peptides. Score 0.522 Round 3: 237 peptides, 34 chains. Longest chain 17 peptides. Score 0.478 Round 4: 251 peptides, 34 chains. Longest chain 18 peptides. Score 0.513 Round 5: 257 peptides, 34 chains. Longest chain 23 peptides. Score 0.527 Taking the results from Round 5 Chains 36, Residues 223, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7534 restraints for refining 3381 atoms. 6596 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2325 (Rfree = 0.000) for 3381 atoms. Found 12 (16 requested) and removed 21 (8 requested) atoms. Cycle 17: After refmac, R = 0.2316 (Rfree = 0.000) for 3332 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.2224 (Rfree = 0.000) for 3314 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 19: After refmac, R = 0.1959 (Rfree = 0.000) for 3299 atoms. Found 3 (15 requested) and removed 11 (7 requested) atoms. Cycle 20: After refmac, R = 0.2013 (Rfree = 0.000) for 3287 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.52 Search for helices and strands: 0 residues in 0 chains, 3377 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 3411 seeds are put forward Round 1: 207 peptides, 39 chains. Longest chain 12 peptides. Score 0.333 Round 2: 228 peptides, 34 chains. Longest chain 21 peptides. Score 0.454 Round 3: 230 peptides, 37 chains. Longest chain 16 peptides. Score 0.424 Round 4: 241 peptides, 32 chains. Longest chain 17 peptides. Score 0.510 Round 5: 236 peptides, 33 chains. Longest chain 16 peptides. Score 0.487 Taking the results from Round 4 Chains 32, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7957 restraints for refining 3380 atoms. 7153 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2449 (Rfree = 0.000) for 3380 atoms. Found 14 (16 requested) and removed 14 (8 requested) atoms. Cycle 22: After refmac, R = 0.2394 (Rfree = 0.000) for 3344 atoms. Found 10 (16 requested) and removed 16 (8 requested) atoms. Cycle 23: After refmac, R = 0.2333 (Rfree = 0.000) for 3320 atoms. Found 12 (15 requested) and removed 12 (7 requested) atoms. Cycle 24: After refmac, R = 0.2255 (Rfree = 0.000) for 3293 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.2268 (Rfree = 0.000) for 3268 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 3383 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3414 seeds are put forward Round 1: 186 peptides, 38 chains. Longest chain 8 peptides. Score 0.281 Round 2: 218 peptides, 40 chains. Longest chain 12 peptides. Score 0.353 Round 3: 230 peptides, 38 chains. Longest chain 18 peptides. Score 0.412 Round 4: 237 peptides, 37 chains. Longest chain 14 peptides. Score 0.443 Round 5: 240 peptides, 36 chains. Longest chain 15 peptides. Score 0.462 Taking the results from Round 5 Chains 36, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7858 restraints for refining 3381 atoms. 7078 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2389 (Rfree = 0.000) for 3381 atoms. Found 12 (16 requested) and removed 99 (8 requested) atoms. Cycle 27: After refmac, R = 0.2132 (Rfree = 0.000) for 3269 atoms. Found 7 (15 requested) and removed 51 (7 requested) atoms. Cycle 28: After refmac, R = 0.2010 (Rfree = 0.000) for 3211 atoms. Found 7 (15 requested) and removed 38 (7 requested) atoms. Cycle 29: After refmac, R = 0.1979 (Rfree = 0.000) for 3170 atoms. Found 2 (15 requested) and removed 19 (7 requested) atoms. Cycle 30: After refmac, R = 0.1992 (Rfree = 0.000) for 3146 atoms. Found 6 (14 requested) and removed 20 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 3259 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3283 seeds are put forward Round 1: 168 peptides, 34 chains. Longest chain 12 peptides. Score 0.278 Round 2: 206 peptides, 36 chains. Longest chain 12 peptides. Score 0.368 Round 3: 188 peptides, 33 chains. Longest chain 12 peptides. Score 0.354 Round 4: 182 peptides, 31 chains. Longest chain 12 peptides. Score 0.362 Round 5: 173 peptides, 31 chains. Longest chain 12 peptides. Score 0.334 Taking the results from Round 2 Chains 36, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7089 restraints for refining 3162 atoms. 6445 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2147 (Rfree = 0.000) for 3162 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 32: After refmac, R = 0.2095 (Rfree = 0.000) for 3143 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 33: After refmac, R = 0.1996 (Rfree = 0.000) for 3129 atoms. Found 6 (14 requested) and removed 20 (7 requested) atoms. Cycle 34: After refmac, R = 0.2119 (Rfree = 0.000) for 3110 atoms. Found 12 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1858 (Rfree = 0.000) for 3107 atoms. Found 1 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.44 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 3197 seeds are put forward Round 1: 165 peptides, 35 chains. Longest chain 14 peptides. Score 0.254 Round 2: 187 peptides, 35 chains. Longest chain 15 peptides. Score 0.324 Round 3: 197 peptides, 34 chains. Longest chain 14 peptides. Score 0.367 Round 4: 188 peptides, 32 chains. Longest chain 11 peptides. Score 0.367 Round 5: 193 peptides, 30 chains. Longest chain 16 peptides. Score 0.407 Taking the results from Round 5 Chains 30, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7512 restraints for refining 3292 atoms. 6890 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2320 (Rfree = 0.000) for 3292 atoms. Found 15 (15 requested) and removed 37 (7 requested) atoms. Cycle 37: After refmac, R = 0.2253 (Rfree = 0.000) for 3255 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 38: After refmac, R = 0.2068 (Rfree = 0.000) for 3227 atoms. Found 15 (15 requested) and removed 29 (7 requested) atoms. Cycle 39: After refmac, R = 0.2072 (Rfree = 0.000) for 3198 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 40: After refmac, R = 0.1978 (Rfree = 0.000) for 3181 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 3282 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3303 seeds are put forward Round 1: 159 peptides, 32 chains. Longest chain 12 peptides. Score 0.276 Round 2: 182 peptides, 31 chains. Longest chain 15 peptides. Score 0.362 Round 3: 168 peptides, 27 chains. Longest chain 18 peptides. Score 0.373 Round 4: 185 peptides, 31 chains. Longest chain 14 peptides. Score 0.371 Round 5: 197 peptides, 32 chains. Longest chain 17 peptides. Score 0.393 Taking the results from Round 5 Chains 32, Residues 165, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7135 restraints for refining 3204 atoms. 6492 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1898 (Rfree = 0.000) for 3204 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. Cycle 42: After refmac, R = 0.1788 (Rfree = 0.000) for 3178 atoms. Found 4 (15 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.1768 (Rfree = 0.000) for 3167 atoms. Found 2 (15 requested) and removed 12 (7 requested) atoms. Cycle 44: After refmac, R = 0.1721 (Rfree = 0.000) for 3150 atoms. Found 3 (15 requested) and removed 14 (7 requested) atoms. Cycle 45: After refmac, R = 0.1703 (Rfree = 0.000) for 3132 atoms. Found 3 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.43 Search for helices and strands: 0 residues in 0 chains, 3211 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3233 seeds are put forward Round 1: 162 peptides, 35 chains. Longest chain 9 peptides. Score 0.244 Round 2: 187 peptides, 36 chains. Longest chain 10 peptides. Score 0.311 Round 3: 181 peptides, 30 chains. Longest chain 16 peptides. Score 0.372 Round 4: 177 peptides, 33 chains. Longest chain 10 peptides. Score 0.320 Round 5: 177 peptides, 33 chains. Longest chain 11 peptides. Score 0.320 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 151, 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 1z85-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5207 reflections ( 99.64 % complete ) and 7314 restraints for refining 3242 atoms. 6740 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1909 (Rfree = 0.000) for 3242 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2471 (Rfree = 0.000) for 3217 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2546 (Rfree = 0.000) for 3187 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2285 (Rfree = 0.000) for 3148 atoms. TimeTaking 37.57