Mon 24 Dec 00:36:47 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-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/2a9v-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-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 00:36:51 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-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 492 and 0 Target number of residues in the AU: 492 Target solvent content: 0.6375 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-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6784 target number of atoms Had to go as low as 0.50 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 4.001 Wilson plot Bfac: 70.41 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 6772 reflections ( 99.99 % complete ) and 0 restraints for refining 7506 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3802 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3558 (Rfree = 0.000) for 7506 atoms. Found 35 (35 requested) and removed 179 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 4.24 Search for helices and strands: 0 residues in 0 chains, 7453 seeds are put forward NCS extension: 0 residues added, 7453 seeds are put forward Round 1: 114 peptides, 26 chains. Longest chain 10 peptides. Score 0.201 Round 2: 136 peptides, 30 chains. Longest chain 6 peptides. Score 0.217 Round 3: 175 peptides, 37 chains. Longest chain 10 peptides. Score 0.245 Round 4: 201 peptides, 44 chains. Longest chain 7 peptides. Score 0.236 Round 5: 221 peptides, 44 chains. Longest chain 10 peptides. Score 0.288 Taking the results from Round 5 Chains 44, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 15693 restraints for refining 6126 atoms. 15029 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2872 (Rfree = 0.000) for 6126 atoms. Found 17 (29 requested) and removed 116 (14 requested) atoms. Cycle 2: After refmac, R = 0.2741 (Rfree = 0.000) for 5918 atoms. Found 20 (28 requested) and removed 94 (14 requested) atoms. Cycle 3: After refmac, R = 0.2580 (Rfree = 0.000) for 5784 atoms. Found 13 (27 requested) and removed 78 (13 requested) atoms. Cycle 4: After refmac, R = 0.2678 (Rfree = 0.000) for 5680 atoms. Found 27 (27 requested) and removed 63 (13 requested) atoms. Cycle 5: After refmac, R = 0.2457 (Rfree = 0.000) for 5602 atoms. Found 20 (26 requested) and removed 61 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 4.24 Search for helices and strands: 0 residues in 0 chains, 5720 seeds are put forward NCS extension: 0 residues added, 5720 seeds are put forward Round 1: 212 peptides, 50 chains. Longest chain 6 peptides. Score 0.200 Round 2: 264 peptides, 56 chains. Longest chain 9 peptides. Score 0.270 Round 3: 260 peptides, 52 chains. Longest chain 8 peptides. Score 0.301 Round 4: 271 peptides, 50 chains. Longest chain 10 peptides. Score 0.347 Round 5: 265 peptides, 45 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 5 Chains 45, Residues 220, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 12757 restraints for refining 5459 atoms. 11901 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2374 (Rfree = 0.000) for 5459 atoms. Found 24 (25 requested) and removed 89 (12 requested) atoms. Cycle 7: After refmac, R = 0.2282 (Rfree = 0.000) for 5361 atoms. Found 24 (25 requested) and removed 63 (12 requested) atoms. Cycle 8: After refmac, R = 0.2098 (Rfree = 0.000) for 5300 atoms. Found 25 (25 requested) and removed 45 (12 requested) atoms. Cycle 9: After refmac, R = 0.2078 (Rfree = 0.000) for 5261 atoms. Found 25 (25 requested) and removed 32 (12 requested) atoms. Cycle 10: After refmac, R = 0.1881 (Rfree = 0.000) for 5243 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 5385 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5398 seeds are put forward Round 1: 259 peptides, 55 chains. Longest chain 9 peptides. Score 0.268 Round 2: 275 peptides, 50 chains. Longest chain 12 peptides. Score 0.356 Round 3: 275 peptides, 48 chains. Longest chain 12 peptides. Score 0.376 Round 4: 271 peptides, 48 chains. Longest chain 10 peptides. Score 0.367 Round 5: 267 peptides, 45 chains. Longest chain 12 peptides. Score 0.387 Taking the results from Round 5 Chains 45, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 13091 restraints for refining 5593 atoms. 12248 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2240 (Rfree = 0.000) for 5593 atoms. Found 26 (26 requested) and removed 95 (13 requested) atoms. Cycle 12: After refmac, R = 0.1919 (Rfree = 0.000) for 5494 atoms. Found 26 (26 requested) and removed 47 (13 requested) atoms. Cycle 13: After refmac, R = 0.1997 (Rfree = 0.000) for 5454 atoms. Found 25 (25 requested) and removed 45 (12 requested) atoms. Cycle 14: After refmac, R = 0.1931 (Rfree = 0.000) for 5418 atoms. Found 23 (25 requested) and removed 44 (12 requested) atoms. Cycle 15: After refmac, R = 0.1838 (Rfree = 0.000) for 5378 atoms. Found 25 (25 requested) and removed 39 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 4.11 Search for helices and strands: 0 residues in 0 chains, 5481 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5501 seeds are put forward Round 1: 228 peptides, 51 chains. Longest chain 7 peptides. Score 0.231 Round 2: 261 peptides, 51 chains. Longest chain 8 peptides. Score 0.313 Round 3: 267 peptides, 47 chains. Longest chain 12 peptides. Score 0.367 Round 4: 273 peptides, 47 chains. Longest chain 12 peptides. Score 0.381 Round 5: 286 peptides, 51 chains. Longest chain 12 peptides. Score 0.372 Taking the results from Round 4 Chains 47, Residues 226, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 13068 restraints for refining 5650 atoms. 12182 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1944 (Rfree = 0.000) for 5650 atoms. Found 25 (26 requested) and removed 65 (13 requested) atoms. Cycle 17: After refmac, R = 0.1977 (Rfree = 0.000) for 5592 atoms. Found 26 (26 requested) and removed 46 (13 requested) atoms. Cycle 18: After refmac, R = 0.2007 (Rfree = 0.000) for 5552 atoms. Found 26 (26 requested) and removed 40 (13 requested) atoms. Cycle 19: After refmac, R = 0.1948 (Rfree = 0.000) for 5522 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 20: After refmac, R = 0.1402 (Rfree = 0.000) for 5487 atoms. Found 8 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 4.10 Search for helices and strands: 0 residues in 0 chains, 5657 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5670 seeds are put forward Round 1: 204 peptides, 44 chains. Longest chain 7 peptides. Score 0.244 Round 2: 223 peptides, 45 chains. Longest chain 7 peptides. Score 0.282 Round 3: 244 peptides, 47 chains. Longest chain 8 peptides. Score 0.313 Round 4: 251 peptides, 47 chains. Longest chain 12 peptides. Score 0.330 Round 5: 245 peptides, 48 chains. Longest chain 10 peptides. Score 0.305 Taking the results from Round 4 Chains 47, Residues 204, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 13012 restraints for refining 5635 atoms. 12210 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1990 (Rfree = 0.000) for 5635 atoms. Found 26 (26 requested) and removed 64 (13 requested) atoms. Cycle 22: After refmac, R = 0.2138 (Rfree = 0.000) for 5579 atoms. Found 26 (26 requested) and removed 44 (13 requested) atoms. Cycle 23: After refmac, R = 0.2029 (Rfree = 0.000) for 5544 atoms. Found 26 (26 requested) and removed 40 (13 requested) atoms. Cycle 24: After refmac, R = 0.1959 (Rfree = 0.000) for 5517 atoms. Found 26 (26 requested) and removed 33 (13 requested) atoms. Cycle 25: After refmac, R = 0.1963 (Rfree = 0.000) for 5497 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 4.13 Search for helices and strands: 0 residues in 0 chains, 5673 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5693 seeds are put forward Round 1: 210 peptides, 48 chains. Longest chain 7 peptides. Score 0.216 Round 2: 244 peptides, 52 chains. Longest chain 10 peptides. Score 0.261 Round 3: 229 peptides, 44 chains. Longest chain 9 peptides. Score 0.308 Round 4: 240 peptides, 47 chains. Longest chain 9 peptides. Score 0.303 Round 5: 249 peptides, 47 chains. Longest chain 11 peptides. Score 0.325 Taking the results from Round 5 Chains 47, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 13206 restraints for refining 5649 atoms. 12445 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2005 (Rfree = 0.000) for 5649 atoms. Found 26 (26 requested) and removed 62 (13 requested) atoms. Cycle 27: After refmac, R = 0.2022 (Rfree = 0.000) for 5584 atoms. Found 26 (26 requested) and removed 37 (13 requested) atoms. Cycle 28: After refmac, R = 0.1936 (Rfree = 0.000) for 5559 atoms. Found 26 (26 requested) and removed 44 (13 requested) atoms. Cycle 29: After refmac, R = 0.2019 (Rfree = 0.000) for 5531 atoms. Found 26 (26 requested) and removed 31 (13 requested) atoms. Cycle 30: After refmac, R = 0.1784 (Rfree = 0.000) for 5517 atoms. Found 26 (26 requested) and removed 43 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 4.12 Search for helices and strands: 0 residues in 0 chains, 5652 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 5659 seeds are put forward Round 1: 202 peptides, 44 chains. Longest chain 9 peptides. Score 0.239 Round 2: 223 peptides, 45 chains. Longest chain 9 peptides. Score 0.282 Round 3: 237 peptides, 47 chains. Longest chain 11 peptides. Score 0.296 Round 4: 251 peptides, 50 chains. Longest chain 10 peptides. Score 0.299 Round 5: 229 peptides, 45 chains. Longest chain 15 peptides. Score 0.297 Taking the results from Round 4 Chains 50, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 13651 restraints for refining 5745 atoms. 12897 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1874 (Rfree = 0.000) for 5745 atoms. Found 27 (27 requested) and removed 60 (13 requested) atoms. Cycle 32: After refmac, R = 0.1928 (Rfree = 0.000) for 5694 atoms. Found 27 (27 requested) and removed 48 (13 requested) atoms. Cycle 33: After refmac, R = 0.1904 (Rfree = 0.000) for 5659 atoms. Found 26 (26 requested) and removed 38 (13 requested) atoms. Cycle 34: After refmac, R = 0.1965 (Rfree = 0.000) for 5637 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. Cycle 35: After refmac, R = 0.1881 (Rfree = 0.000) for 5615 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 4.12 Search for helices and strands: 0 residues in 0 chains, 5768 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 5771 seeds are put forward Round 1: 182 peptides, 43 chains. Longest chain 6 peptides. Score 0.195 Round 2: 212 peptides, 42 chains. Longest chain 9 peptides. Score 0.287 Round 3: 193 peptides, 38 chains. Longest chain 8 peptides. Score 0.282 Round 4: 202 peptides, 38 chains. Longest chain 11 peptides. Score 0.305 Round 5: 203 peptides, 39 chains. Longest chain 9 peptides. Score 0.296 Taking the results from Round 4 Chains 38, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 13500 restraints for refining 5680 atoms. 12882 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1981 (Rfree = 0.000) for 5680 atoms. Found 26 (26 requested) and removed 40 (13 requested) atoms. Cycle 37: After refmac, R = 0.2057 (Rfree = 0.000) for 5654 atoms. Found 26 (26 requested) and removed 46 (13 requested) atoms. Cycle 38: After refmac, R = 0.1942 (Rfree = 0.000) for 5622 atoms. Found 26 (26 requested) and removed 38 (13 requested) atoms. Cycle 39: After refmac, R = 0.1931 (Rfree = 0.000) for 5598 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. Cycle 40: After refmac, R = 0.1888 (Rfree = 0.000) for 5583 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 4.19 Search for helices and strands: 0 residues in 0 chains, 5730 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5742 seeds are put forward Round 1: 193 peptides, 46 chains. Longest chain 5 peptides. Score 0.192 Round 2: 234 peptides, 48 chains. Longest chain 8 peptides. Score 0.278 Round 3: 242 peptides, 48 chains. Longest chain 9 peptides. Score 0.298 Round 4: 222 peptides, 45 chains. Longest chain 10 peptides. Score 0.280 Round 5: 222 peptides, 43 chains. Longest chain 9 peptides. Score 0.301 Taking the results from Round 5 Chains 43, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6772 reflections ( 99.99 % complete ) and 13137 restraints for refining 5608 atoms. 12464 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2004 (Rfree = 0.000) for 5608 atoms. Found 26 (26 requested) and removed 61 (13 requested) atoms. Cycle 42: After refmac, R = 0.1984 (Rfree = 0.000) for 5559 atoms. Found 26 (26 requested) and removed 53 (13 requested) atoms. Cycle 43: After refmac, R = 0.1856 (Rfree = 0.000) for 5522 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 44: After refmac, R = 0.1286 (Rfree = 0.000) for 5504 atoms. Found 18 (26 requested) and removed 23 (13 requested) atoms. Cycle 45: After refmac, R = 0.1121 (Rfree = 0.000) for 5493 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 4.13 Search for helices and strands: 0 residues in 0 chains, 5630 seeds are put forward NCS extension: 0 residues added, 5630 seeds are put forward Round 1: 159 peptides, 37 chains. Longest chain 6 peptides. Score 0.200 Round 2: 177 peptides, 38 chains. Longest chain 8 peptides. Score 0.239 Round 3: 195 peptides, 38 chains. Longest chain 9 peptides. Score 0.287 Round 4: 191 peptides, 39 chains. Longest chain 8 peptides. Score 0.265 Round 5: 195 peptides, 35 chains. Longest chain 10 peptides. Score 0.320 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 160, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2a9v-4_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (160 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6772 reflections ( 99.99 % complete ) and 12801 restraints for refining 5564 atoms. 12170 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1753 (Rfree = 0.000) for 5564 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1961 (Rfree = 0.000) for 5533 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1818 (Rfree = 0.000) for 5518 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1922 (Rfree = 0.000) for 5492 atoms. TimeTaking 59.93