Mon 24 Dec 00:52:36 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 2a9v-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.2-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/2a9v-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.2-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 00:52:41 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/2a9v-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.2-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 527 and 0 Target number of residues in the AU: 527 Target solvent content: 0.6117 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 848 Adjusted target solvent content: 0.38 Input MTZ file: 2a9v-3.2-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6784 target number of atoms Had to go as low as 0.45 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: 137.806 3.200 Wilson plot Bfac: 57.34 12968 reflections ( 99.99 % complete ) and 0 restraints for refining 7479 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3694 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3421 (Rfree = 0.000) for 7479 atoms. Found 42 (67 requested) and removed 145 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.65 Search for helices and strands: 0 residues in 0 chains, 7467 seeds are put forward NCS extension: 0 residues added, 7467 seeds are put forward Round 1: 198 peptides, 45 chains. Longest chain 9 peptides. Score 0.217 Round 2: 248 peptides, 52 chains. Longest chain 10 peptides. Score 0.271 Round 3: 277 peptides, 57 chains. Longest chain 8 peptides. Score 0.291 Round 4: 280 peptides, 54 chains. Longest chain 10 peptides. Score 0.328 Round 5: 305 peptides, 55 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 5 Chains 55, Residues 250, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 15084 restraints for refining 6193 atoms. 14139 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2868 (Rfree = 0.000) for 6193 atoms. Found 18 (55 requested) and removed 119 (27 requested) atoms. Cycle 2: After refmac, R = 0.2694 (Rfree = 0.000) for 6023 atoms. Found 20 (54 requested) and removed 53 (27 requested) atoms. Cycle 3: After refmac, R = 0.2569 (Rfree = 0.000) for 5969 atoms. Found 14 (53 requested) and removed 39 (26 requested) atoms. Cycle 4: After refmac, R = 0.2477 (Rfree = 0.000) for 5933 atoms. Found 7 (53 requested) and removed 33 (26 requested) atoms. Cycle 5: After refmac, R = 0.2470 (Rfree = 0.000) for 5901 atoms. Found 9 (53 requested) and removed 41 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 6076 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6089 seeds are put forward Round 1: 254 peptides, 55 chains. Longest chain 8 peptides. Score 0.255 Round 2: 320 peptides, 63 chains. Longest chain 13 peptides. Score 0.333 Round 3: 307 peptides, 57 chains. Longest chain 12 peptides. Score 0.361 Round 4: 308 peptides, 56 chains. Longest chain 12 peptides. Score 0.373 Round 5: 328 peptides, 58 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 5 Chains 58, Residues 270, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 13709 restraints for refining 5845 atoms. 12643 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2486 (Rfree = 0.000) for 5845 atoms. Found 27 (52 requested) and removed 63 (26 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2544 (Rfree = 0.000) for 5796 atoms. Found 31 (52 requested) and removed 44 (26 requested) atoms. Cycle 8: After refmac, R = 0.2299 (Rfree = 0.000) for 5766 atoms. Found 18 (51 requested) and removed 37 (25 requested) atoms. Cycle 9: After refmac, R = 0.2294 (Rfree = 0.000) for 5739 atoms. Found 20 (51 requested) and removed 30 (25 requested) atoms. Cycle 10: After refmac, R = 0.2297 (Rfree = 0.000) for 5723 atoms. Found 17 (51 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.00 3.53 Search for helices and strands: 0 residues in 0 chains, 5860 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5874 seeds are put forward Round 1: 295 peptides, 59 chains. Longest chain 11 peptides. Score 0.314 Round 2: 325 peptides, 58 chains. Longest chain 13 peptides. Score 0.392 Round 3: 345 peptides, 61 chains. Longest chain 15 peptides. Score 0.407 Round 4: 370 peptides, 63 chains. Longest chain 15 peptides. Score 0.441 Round 5: 355 peptides, 59 chains. Longest chain 15 peptides. Score 0.446 Taking the results from Round 5 Chains 59, Residues 296, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 13575 restraints for refining 5986 atoms. 12412 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2379 (Rfree = 0.000) for 5986 atoms. Found 32 (53 requested) and removed 75 (26 requested) atoms. Cycle 12: After refmac, R = 0.2277 (Rfree = 0.000) for 5927 atoms. Found 23 (53 requested) and removed 46 (26 requested) atoms. Cycle 13: After refmac, R = 0.2247 (Rfree = 0.000) for 5882 atoms. Found 22 (52 requested) and removed 34 (26 requested) atoms. Cycle 14: After refmac, R = 0.2191 (Rfree = 0.000) for 5867 atoms. Found 16 (52 requested) and removed 32 (26 requested) atoms. Cycle 15: After refmac, R = 0.2129 (Rfree = 0.000) for 5845 atoms. Found 13 (52 requested) and removed 32 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.03 3.57 Search for helices and strands: 0 residues in 0 chains, 5988 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 6012 seeds are put forward Round 1: 275 peptides, 57 chains. Longest chain 9 peptides. Score 0.286 Round 2: 298 peptides, 52 chains. Longest chain 10 peptides. Score 0.389 Round 3: 314 peptides, 52 chains. Longest chain 16 peptides. Score 0.423 Round 4: 318 peptides, 52 chains. Longest chain 16 peptides. Score 0.432 Round 5: 307 peptides, 57 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 4 Chains 52, Residues 266, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 13773 restraints for refining 5994 atoms. 12761 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2306 (Rfree = 0.000) for 5994 atoms. Found 27 (53 requested) and removed 57 (26 requested) atoms. Cycle 17: After refmac, R = 0.2454 (Rfree = 0.000) for 5954 atoms. Found 33 (53 requested) and removed 56 (26 requested) atoms. Cycle 18: After refmac, R = 0.2107 (Rfree = 0.000) for 5924 atoms. Found 20 (53 requested) and removed 44 (26 requested) atoms. Cycle 19: After refmac, R = 0.2067 (Rfree = 0.000) for 5890 atoms. Found 32 (52 requested) and removed 38 (26 requested) atoms. Cycle 20: After refmac, R = 0.1983 (Rfree = 0.000) for 5880 atoms. Found 16 (52 requested) and removed 40 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.97 3.50 Search for helices and strands: 0 residues in 0 chains, 6039 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 6069 seeds are put forward Round 1: 266 peptides, 56 chains. Longest chain 9 peptides. Score 0.275 Round 2: 311 peptides, 55 chains. Longest chain 16 peptides. Score 0.389 Round 3: 308 peptides, 57 chains. Longest chain 13 peptides. Score 0.363 Round 4: 292 peptides, 53 chains. Longest chain 14 peptides. Score 0.366 Round 5: 292 peptides, 51 chains. Longest chain 13 peptides. Score 0.385 Taking the results from Round 2 Chains 55, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 13639 restraints for refining 5952 atoms. 12670 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2163 (Rfree = 0.000) for 5952 atoms. Found 22 (53 requested) and removed 55 (26 requested) atoms. Cycle 22: After refmac, R = 0.2106 (Rfree = 0.000) for 5904 atoms. Found 23 (53 requested) and removed 41 (26 requested) atoms. Cycle 23: After refmac, R = 0.2147 (Rfree = 0.000) for 5881 atoms. Found 19 (52 requested) and removed 41 (26 requested) atoms. Cycle 24: After refmac, R = 0.2121 (Rfree = 0.000) for 5846 atoms. Found 25 (52 requested) and removed 37 (26 requested) atoms. Cycle 25: After refmac, R = 0.2523 (Rfree = 0.000) for 5832 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 3.55 Search for helices and strands: 0 residues in 0 chains, 6002 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6020 seeds are put forward Round 1: 251 peptides, 54 chains. Longest chain 7 peptides. Score 0.258 Round 2: 284 peptides, 57 chains. Longest chain 11 peptides. Score 0.308 Round 3: 310 peptides, 57 chains. Longest chain 14 peptides. Score 0.368 Round 4: 320 peptides, 57 chains. Longest chain 12 peptides. Score 0.390 Round 5: 314 peptides, 55 chains. Longest chain 16 peptides. Score 0.396 Taking the results from Round 5 Chains 55, Residues 259, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 13600 restraints for refining 6017 atoms. 12560 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2200 (Rfree = 0.000) for 6017 atoms. Found 27 (54 requested) and removed 61 (27 requested) atoms. Cycle 27: After refmac, R = 0.2559 (Rfree = 0.000) for 5978 atoms. Found 53 (53 requested) and removed 56 (26 requested) atoms. Cycle 28: After refmac, R = 0.1986 (Rfree = 0.000) for 5969 atoms. Found 17 (53 requested) and removed 46 (26 requested) atoms. Cycle 29: After refmac, R = 0.1944 (Rfree = 0.000) for 5935 atoms. Found 16 (53 requested) and removed 31 (26 requested) atoms. Cycle 30: After refmac, R = 0.1849 (Rfree = 0.000) for 5916 atoms. Found 20 (53 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.99 3.52 Search for helices and strands: 0 residues in 0 chains, 6047 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 6072 seeds are put forward Round 1: 274 peptides, 61 chains. Longest chain 9 peptides. Score 0.243 Round 2: 322 peptides, 62 chains. Longest chain 12 peptides. Score 0.347 Round 3: 299 peptides, 52 chains. Longest chain 19 peptides. Score 0.391 Round 4: 305 peptides, 52 chains. Longest chain 20 peptides. Score 0.404 Round 5: 318 peptides, 58 chains. Longest chain 15 peptides. Score 0.376 Taking the results from Round 4 Chains 54, Residues 253, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 13589 restraints for refining 6150 atoms. 12533 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2080 (Rfree = 0.000) for 6150 atoms. Found 23 (55 requested) and removed 69 (27 requested) atoms. Cycle 32: After refmac, R = 0.1908 (Rfree = 0.000) for 6093 atoms. Found 20 (54 requested) and removed 35 (27 requested) atoms. Cycle 33: After refmac, R = 0.1904 (Rfree = 0.000) for 6072 atoms. Found 16 (54 requested) and removed 32 (27 requested) atoms. Cycle 34: After refmac, R = 0.1845 (Rfree = 0.000) for 6049 atoms. Found 13 (54 requested) and removed 27 (27 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1884 (Rfree = 0.000) for 6032 atoms. Found 16 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 3.55 Search for helices and strands: 0 residues in 0 chains, 6129 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6146 seeds are put forward Round 1: 250 peptides, 55 chains. Longest chain 9 peptides. Score 0.245 Round 2: 288 peptides, 53 chains. Longest chain 11 peptides. Score 0.357 Round 3: 290 peptides, 53 chains. Longest chain 12 peptides. Score 0.361 Round 4: 285 peptides, 47 chains. Longest chain 15 peptides. Score 0.408 Round 5: 281 peptides, 51 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 4 Chains 47, Residues 238, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 13832 restraints for refining 6123 atoms. 12895 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2110 (Rfree = 0.000) for 6123 atoms. Found 32 (54 requested) and removed 44 (27 requested) atoms. Cycle 37: After refmac, R = 0.2035 (Rfree = 0.000) for 6100 atoms. Found 24 (54 requested) and removed 33 (27 requested) atoms. Cycle 38: After refmac, R = 0.1981 (Rfree = 0.000) for 6086 atoms. Found 20 (54 requested) and removed 32 (27 requested) atoms. Cycle 39: After refmac, R = 0.1974 (Rfree = 0.000) for 6067 atoms. Found 11 (54 requested) and removed 32 (27 requested) atoms. Cycle 40: After refmac, R = 0.1953 (Rfree = 0.000) for 6036 atoms. Found 16 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.00 3.53 Search for helices and strands: 0 residues in 0 chains, 6148 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 6174 seeds are put forward Round 1: 237 peptides, 50 chains. Longest chain 11 peptides. Score 0.265 Round 2: 283 peptides, 52 chains. Longest chain 14 peptides. Score 0.355 Round 3: 294 peptides, 55 chains. Longest chain 13 peptides. Score 0.351 Round 4: 281 peptides, 51 chains. Longest chain 12 peptides. Score 0.360 Round 5: 275 peptides, 49 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 5 Chains 49, Residues 226, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14015 restraints for refining 6175 atoms. 13096 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2116 (Rfree = 0.000) for 6175 atoms. Found 44 (55 requested) and removed 38 (27 requested) atoms. Cycle 42: After refmac, R = 0.1934 (Rfree = 0.000) for 6169 atoms. Found 14 (55 requested) and removed 31 (27 requested) atoms. Cycle 43: After refmac, R = 0.1864 (Rfree = 0.000) for 6144 atoms. Found 16 (55 requested) and removed 30 (27 requested) atoms. Cycle 44: After refmac, R = 0.1786 (Rfree = 0.000) for 6125 atoms. Found 9 (55 requested) and removed 28 (27 requested) atoms. Cycle 45: After refmac, R = 0.1793 (Rfree = 0.000) for 6102 atoms. Found 3 (54 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.61 Search for helices and strands: 0 residues in 0 chains, 6223 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6234 seeds are put forward Round 1: 228 peptides, 50 chains. Longest chain 10 peptides. Score 0.242 Round 2: 268 peptides, 49 chains. Longest chain 18 peptides. Score 0.350 Round 3: 271 peptides, 50 chains. Longest chain 20 peptides. Score 0.347 Round 4: 266 peptides, 49 chains. Longest chain 10 peptides. Score 0.345 Round 5: 270 peptides, 48 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 222, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2a9v-3_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (222 residues) following loop building 2 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12968 reflections ( 99.99 % complete ) and 14534 restraints for refining 6193 atoms. 13660 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1996 (Rfree = 0.000) for 6193 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1871 (Rfree = 0.000) for 6162 atoms. Found 0 (55 requested) and removed 9 (27 requested) atoms. Cycle 48: After refmac, R = 0.1843 (Rfree = 0.000) for 6150 atoms. Found 0 (55 requested) and removed 5 (27 requested) atoms. Cycle 49: After refmac, R = 0.1828 (Rfree = 0.000) for 6143 atoms. TimeTaking 63.03