Mon 24 Dec 01:12:55 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 1vlm-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-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/1vlm-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-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 01:13:00 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/1vlm-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-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 299 and 0 Target number of residues in the AU: 299 Target solvent content: 0.6290 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-3.6-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: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3504 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: 93.922 3.600 Wilson plot Bfac: 65.87 5411 reflections ( 99.69 % complete ) and 0 restraints for refining 3872 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3143 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3052 (Rfree = 0.000) for 3872 atoms. Found 24 (24 requested) and removed 64 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 3889 seeds are put forward NCS extension: 0 residues added, 3889 seeds are put forward Round 1: 153 peptides, 31 chains. Longest chain 8 peptides. Score 0.293 Round 2: 190 peptides, 32 chains. Longest chain 12 peptides. Score 0.419 Round 3: 229 peptides, 31 chains. Longest chain 20 peptides. Score 0.560 Round 4: 234 peptides, 33 chains. Longest chain 15 peptides. Score 0.549 Round 5: 239 peptides, 32 chains. Longest chain 23 peptides. Score 0.576 Taking the results from Round 5 Chains 33, Residues 207, Estimated correctness of the model 5.1 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7020 restraints for refining 3175 atoms. 6134 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2611 (Rfree = 0.000) for 3175 atoms. Found 8 (20 requested) and removed 30 (10 requested) atoms. Cycle 2: After refmac, R = 0.2374 (Rfree = 0.000) for 3105 atoms. Found 6 (20 requested) and removed 16 (10 requested) atoms. Cycle 3: After refmac, R = 0.2319 (Rfree = 0.000) for 3078 atoms. Found 3 (19 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2252 (Rfree = 0.000) for 3059 atoms. Found 4 (19 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.2231 (Rfree = 0.000) for 3044 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.55 Search for helices and strands: 0 residues in 0 chains, 3155 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3181 seeds are put forward Round 1: 194 peptides, 38 chains. Longest chain 10 peptides. Score 0.339 Round 2: 219 peptides, 33 chains. Longest chain 19 peptides. Score 0.502 Round 3: 245 peptides, 35 chains. Longest chain 18 peptides. Score 0.555 Round 4: 241 peptides, 33 chains. Longest chain 19 peptides. Score 0.569 Round 5: 247 peptides, 34 chains. Longest chain 21 peptides. Score 0.574 Taking the results from Round 5 Chains 34, Residues 213, Estimated correctness of the model 4.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 6978 restraints for refining 3086 atoms. 6160 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2688 (Rfree = 0.000) for 3086 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 7: After refmac, R = 0.2404 (Rfree = 0.000) for 3053 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 8: After refmac, R = 0.2229 (Rfree = 0.000) for 3037 atoms. Found 14 (19 requested) and removed 17 (9 requested) atoms. Cycle 9: After refmac, R = 0.2196 (Rfree = 0.000) for 3027 atoms. Found 10 (19 requested) and removed 18 (9 requested) atoms. Cycle 10: After refmac, R = 0.2143 (Rfree = 0.000) for 3012 atoms. Found 15 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 3138 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 3167 seeds are put forward Round 1: 194 peptides, 34 chains. Longest chain 13 peptides. Score 0.402 Round 2: 211 peptides, 30 chains. Longest chain 31 peptides. Score 0.519 Round 3: 238 peptides, 32 chains. Longest chain 30 peptides. Score 0.573 Round 4: 229 peptides, 31 chains. Longest chain 20 peptides. Score 0.560 Round 5: 234 peptides, 27 chains. Longest chain 29 peptides. Score 0.624 Taking the results from Round 5 Chains 27, Residues 207, Estimated correctness of the model 23.8 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 6905 restraints for refining 3176 atoms. 6026 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2464 (Rfree = 0.000) for 3176 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 12: After refmac, R = 0.2270 (Rfree = 0.000) for 3155 atoms. Found 17 (20 requested) and removed 22 (10 requested) atoms. Cycle 13: After refmac, R = 0.2246 (Rfree = 0.000) for 3120 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 14: After refmac, R = 0.2103 (Rfree = 0.000) for 3105 atoms. Found 10 (20 requested) and removed 17 (10 requested) atoms. Cycle 15: After refmac, R = 0.2104 (Rfree = 0.000) for 3083 atoms. Found 17 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.53 Search for helices and strands: 0 residues in 0 chains, 3167 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 3195 seeds are put forward Round 1: 184 peptides, 36 chains. Longest chain 13 peptides. Score 0.333 Round 2: 218 peptides, 35 chains. Longest chain 16 peptides. Score 0.471 Round 3: 223 peptides, 37 chains. Longest chain 14 peptides. Score 0.458 Round 4: 233 peptides, 39 chains. Longest chain 15 peptides. Score 0.463 Round 5: 225 peptides, 35 chains. Longest chain 14 peptides. Score 0.494 Taking the results from Round 5 Chains 35, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7386 restraints for refining 3177 atoms. 6661 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2334 (Rfree = 0.000) for 3177 atoms. Found 17 (20 requested) and removed 46 (10 requested) atoms. Cycle 17: After refmac, R = 0.2058 (Rfree = 0.000) for 3121 atoms. Found 14 (20 requested) and removed 41 (10 requested) atoms. Cycle 18: After refmac, R = 0.1883 (Rfree = 0.000) for 3084 atoms. Found 14 (19 requested) and removed 24 (9 requested) atoms. Cycle 19: After refmac, R = 0.1925 (Rfree = 0.000) for 3073 atoms. Found 10 (19 requested) and removed 36 (9 requested) atoms. Cycle 20: After refmac, R = 0.1780 (Rfree = 0.000) for 3046 atoms. Found 8 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.55 Search for helices and strands: 0 residues in 0 chains, 3122 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3138 seeds are put forward Round 1: 199 peptides, 42 chains. Longest chain 10 peptides. Score 0.294 Round 2: 226 peptides, 39 chains. Longest chain 15 peptides. Score 0.440 Round 3: 217 peptides, 37 chains. Longest chain 16 peptides. Score 0.438 Round 4: 208 peptides, 34 chains. Longest chain 16 peptides. Score 0.451 Round 5: 207 peptides, 35 chains. Longest chain 15 peptides. Score 0.433 Taking the results from Round 4 Chains 37, Residues 174, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5411 reflections ( 99.69 % complete ) and 7179 restraints for refining 3177 atoms. 6424 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2231 (Rfree = 0.000) for 3177 atoms. Found 16 (20 requested) and removed 22 (10 requested) atoms. Cycle 22: After refmac, R = 0.2002 (Rfree = 0.000) for 3153 atoms. Found 17 (20 requested) and removed 28 (10 requested) atoms. Cycle 23: After refmac, R = 0.2029 (Rfree = 0.000) for 3132 atoms. Found 12 (20 requested) and removed 17 (10 requested) atoms. Cycle 24: After refmac, R = 0.1927 (Rfree = 0.000) for 3123 atoms. Found 9 (20 requested) and removed 16 (10 requested) atoms. Cycle 25: After refmac, R = 0.1918 (Rfree = 0.000) for 3113 atoms. Found 5 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3223 seeds are put forward Round 1: 169 peptides, 36 chains. Longest chain 9 peptides. Score 0.273 Round 2: 193 peptides, 36 chains. Longest chain 11 peptides. Score 0.367 Round 3: 187 peptides, 33 chains. Longest chain 11 peptides. Score 0.392 Round 4: 203 peptides, 31 chains. Longest chain 16 peptides. Score 0.479 Round 5: 210 peptides, 34 chains. Longest chain 12 peptides. Score 0.458 Taking the results from Round 4 Chains 31, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7279 restraints for refining 3177 atoms. 6622 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2127 (Rfree = 0.000) for 3177 atoms. Found 18 (20 requested) and removed 26 (10 requested) atoms. Cycle 27: After refmac, R = 0.2151 (Rfree = 0.000) for 3152 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 28: After refmac, R = 0.1871 (Rfree = 0.000) for 3139 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.1855 (Rfree = 0.000) for 3134 atoms. Found 9 (20 requested) and removed 14 (10 requested) atoms. Cycle 30: After refmac, R = 0.1760 (Rfree = 0.000) for 3128 atoms. Found 5 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 3213 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3236 seeds are put forward Round 1: 186 peptides, 36 chains. Longest chain 15 peptides. Score 0.340 Round 2: 203 peptides, 35 chains. Longest chain 13 peptides. Score 0.419 Round 3: 192 peptides, 34 chains. Longest chain 18 peptides. Score 0.395 Round 4: 181 peptides, 27 chains. Longest chain 18 peptides. Score 0.464 Round 5: 191 peptides, 31 chains. Longest chain 13 peptides. Score 0.438 Taking the results from Round 4 Chains 28, Residues 154, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7298 restraints for refining 3177 atoms. 6679 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2129 (Rfree = 0.000) for 3177 atoms. Found 17 (20 requested) and removed 18 (10 requested) atoms. Cycle 32: After refmac, R = 0.1984 (Rfree = 0.000) for 3162 atoms. Found 14 (20 requested) and removed 17 (10 requested) atoms. Cycle 33: After refmac, R = 0.1979 (Rfree = 0.000) for 3154 atoms. Found 12 (20 requested) and removed 15 (10 requested) atoms. Cycle 34: After refmac, R = 0.1876 (Rfree = 0.000) for 3142 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1621 (Rfree = 0.000) for 3132 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 3221 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3237 seeds are put forward Round 1: 156 peptides, 34 chains. Longest chain 8 peptides. Score 0.254 Round 2: 191 peptides, 37 chains. Longest chain 11 peptides. Score 0.343 Round 3: 185 peptides, 34 chains. Longest chain 10 peptides. Score 0.369 Round 4: 192 peptides, 33 chains. Longest chain 13 peptides. Score 0.410 Round 5: 200 peptides, 34 chains. Longest chain 11 peptides. Score 0.423 Taking the results from Round 5 Chains 35, Residues 166, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7293 restraints for refining 3177 atoms. 6639 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2226 (Rfree = 0.000) for 3177 atoms. Found 14 (20 requested) and removed 22 (10 requested) atoms. Cycle 37: After refmac, R = 0.2064 (Rfree = 0.000) for 3144 atoms. Found 11 (20 requested) and removed 17 (10 requested) atoms. Cycle 38: After refmac, R = 0.1976 (Rfree = 0.000) for 3127 atoms. Found 14 (20 requested) and removed 16 (10 requested) atoms. Cycle 39: After refmac, R = 0.1940 (Rfree = 0.000) for 3117 atoms. Found 17 (20 requested) and removed 14 (10 requested) atoms. Cycle 40: After refmac, R = 0.1902 (Rfree = 0.000) for 3118 atoms. Found 14 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.51 Search for helices and strands: 0 residues in 0 chains, 3195 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3206 seeds are put forward Round 1: 155 peptides, 33 chains. Longest chain 8 peptides. Score 0.267 Round 2: 180 peptides, 32 chains. Longest chain 12 peptides. Score 0.382 Round 3: 184 peptides, 32 chains. Longest chain 9 peptides. Score 0.397 Round 4: 167 peptides, 27 chains. Longest chain 13 peptides. Score 0.414 Round 5: 174 peptides, 29 chains. Longest chain 9 peptides. Score 0.408 Taking the results from Round 4 Chains 27, Residues 140, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7400 restraints for refining 3177 atoms. 6822 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2154 (Rfree = 0.000) for 3177 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 42: After refmac, R = 0.2000 (Rfree = 0.000) for 3171 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 43: After refmac, R = 0.1968 (Rfree = 0.000) for 3170 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 44: After refmac, R = 0.1986 (Rfree = 0.000) for 3172 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 45: After refmac, R = 0.1790 (Rfree = 0.000) for 3174 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.59 Search for helices and strands: 0 residues in 0 chains, 3250 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3270 seeds are put forward Round 1: 136 peptides, 30 chains. Longest chain 7 peptides. Score 0.239 Round 2: 151 peptides, 29 chains. Longest chain 9 peptides. Score 0.319 Round 3: 147 peptides, 29 chains. Longest chain 7 peptides. Score 0.303 Round 4: 138 peptides, 23 chains. Longest chain 10 peptides. Score 0.371 Round 5: 145 peptides, 25 chains. Longest chain 9 peptides. Score 0.364 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 115, 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 1vlm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5411 reflections ( 99.69 % complete ) and 7769 restraints for refining 3177 atoms. 7332 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2056 (Rfree = 0.000) for 3177 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1884 (Rfree = 0.000) for 3161 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1847 (Rfree = 0.000) for 3145 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1857 (Rfree = 0.000) for 3133 atoms. TimeTaking 41.22