Mon 24 Dec 01:00:38 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 2glz-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-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/2glz-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-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 01:00:43 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/2glz-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-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 288 and 0 Target number of residues in the AU: 288 Target solvent content: 0.6068 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.58 Input MTZ file: 2glz-3.4-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: 46.427 84.786 100.702 90.000 90.000 90.000 Input sequence file: 2glz-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.85 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: 29.894 3.400 Wilson plot Bfac: 55.20 5830 reflections ( 99.76 % complete ) and 0 restraints for refining 2709 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3273 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2777 (Rfree = 0.000) for 2709 atoms. Found 20 (20 requested) and removed 216 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 2.81 Search for helices and strands: 0 residues in 0 chains, 2540 seeds are put forward NCS extension: 0 residues added, 2540 seeds are put forward Round 1: 155 peptides, 30 chains. Longest chain 11 peptides. Score 0.329 Round 2: 181 peptides, 31 chains. Longest chain 12 peptides. Score 0.419 Round 3: 192 peptides, 28 chains. Longest chain 21 peptides. Score 0.508 Round 4: 202 peptides, 28 chains. Longest chain 17 peptides. Score 0.543 Round 5: 204 peptides, 27 chains. Longest chain 25 peptides. Score 0.564 Taking the results from Round 5 Chains 27, Residues 177, Estimated correctness of the model 16.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4758 restraints for refining 2225 atoms. 4077 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2859 (Rfree = 0.000) for 2225 atoms. Found 16 (16 requested) and removed 40 (8 requested) atoms. Cycle 2: After refmac, R = 0.2561 (Rfree = 0.000) for 2181 atoms. Found 14 (16 requested) and removed 22 (8 requested) atoms. Cycle 3: After refmac, R = 0.2408 (Rfree = 0.000) for 2164 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 4: After refmac, R = 0.2402 (Rfree = 0.000) for 2156 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 5: After refmac, R = 0.2291 (Rfree = 0.000) for 2151 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 2.79 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward NCS extension: 23 residues added (7 deleted due to clashes), 2265 seeds are put forward Round 1: 206 peptides, 29 chains. Longest chain 22 peptides. Score 0.541 Round 2: 227 peptides, 29 chains. Longest chain 22 peptides. Score 0.607 Round 3: 232 peptides, 28 chains. Longest chain 49 peptides. Score 0.634 Round 4: 224 peptides, 22 chains. Longest chain 47 peptides. Score 0.686 Round 5: 222 peptides, 24 chains. Longest chain 38 peptides. Score 0.657 Taking the results from Round 4 Chains 22, Residues 202, Estimated correctness of the model 54.2 % 1 chains (46 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4126 restraints for refining 2225 atoms. 3120 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2739 (Rfree = 0.000) for 2225 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 7: After refmac, R = 0.2518 (Rfree = 0.000) for 2200 atoms. Found 15 (16 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2390 (Rfree = 0.000) for 2197 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 9: After refmac, R = 0.2350 (Rfree = 0.000) for 2191 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.2320 (Rfree = 0.000) for 2182 atoms. Found 7 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 2.81 Search for helices and strands: 0 residues in 0 chains, 2263 seeds are put forward NCS extension: 68 residues added (6 deleted due to clashes), 2331 seeds are put forward Round 1: 203 peptides, 28 chains. Longest chain 19 peptides. Score 0.546 Round 2: 220 peptides, 25 chains. Longest chain 22 peptides. Score 0.639 Round 3: 216 peptides, 27 chains. Longest chain 31 peptides. Score 0.601 Round 4: 220 peptides, 27 chains. Longest chain 33 peptides. Score 0.613 Round 5: 235 peptides, 23 chains. Longest chain 51 peptides. Score 0.701 Taking the results from Round 5 Chains 25, Residues 212, Estimated correctness of the model 58.1 % 3 chains (94 residues) have been docked in sequence Building loops using Loopy2018 25 chains (212 residues) following loop building 3 chains (94 residues) in sequence following loop building ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 3675 restraints for refining 2226 atoms. 2426 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2665 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 12: After refmac, R = 0.2459 (Rfree = 0.000) for 2202 atoms. Found 14 (16 requested) and removed 17 (8 requested) atoms. Cycle 13: After refmac, R = 0.2282 (Rfree = 0.000) for 2196 atoms. Found 3 (15 requested) and removed 20 (8 requested) atoms. Cycle 14: After refmac, R = 0.2265 (Rfree = 0.000) for 2176 atoms. Found 5 (15 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.2235 (Rfree = 0.000) for 2171 atoms. Found 7 (15 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 2.80 Search for helices and strands: 0 residues in 0 chains, 2258 seeds are put forward NCS extension: 73 residues added (29 deleted due to clashes), 2331 seeds are put forward Round 1: 209 peptides, 28 chains. Longest chain 25 peptides. Score 0.565 Round 2: 229 peptides, 25 chains. Longest chain 29 peptides. Score 0.663 Round 3: 217 peptides, 20 chains. Longest chain 54 peptides. Score 0.692 Round 4: 218 peptides, 23 chains. Longest chain 39 peptides. Score 0.659 Round 5: 230 peptides, 24 chains. Longest chain 31 peptides. Score 0.678 Taking the results from Round 3 Chains 21, Residues 197, Estimated correctness of the model 55.8 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4290 restraints for refining 2226 atoms. 3340 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2636 (Rfree = 0.000) for 2226 atoms. Found 14 (14 requested) and removed 29 (8 requested) atoms. Cycle 17: After refmac, R = 0.2397 (Rfree = 0.000) for 2203 atoms. Found 13 (14 requested) and removed 14 (8 requested) atoms. Cycle 18: After refmac, R = 0.2353 (Rfree = 0.000) for 2199 atoms. Found 6 (14 requested) and removed 15 (8 requested) atoms. Cycle 19: After refmac, R = 0.2216 (Rfree = 0.000) for 2186 atoms. Found 7 (14 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.2171 (Rfree = 0.000) for 2180 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 2.79 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward NCS extension: 36 residues added (5 deleted due to clashes), 2278 seeds are put forward Round 1: 190 peptides, 25 chains. Longest chain 20 peptides. Score 0.547 Round 2: 209 peptides, 23 chains. Longest chain 35 peptides. Score 0.634 Round 3: 203 peptides, 22 chains. Longest chain 31 peptides. Score 0.630 Round 4: 199 peptides, 23 chains. Longest chain 45 peptides. Score 0.605 Round 5: 213 peptides, 24 chains. Longest chain 42 peptides. Score 0.632 Taking the results from Round 2 Chains 25, Residues 186, Estimated correctness of the model 39.4 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4458 restraints for refining 2225 atoms. 3625 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2383 (Rfree = 0.000) for 2225 atoms. Found 14 (14 requested) and removed 14 (8 requested) atoms. Cycle 22: After refmac, R = 0.2190 (Rfree = 0.000) for 2217 atoms. Found 4 (14 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2106 (Rfree = 0.000) for 2208 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2066 (Rfree = 0.000) for 2205 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2039 (Rfree = 0.000) for 2201 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 2.78 Search for helices and strands: 0 residues in 0 chains, 2278 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 2319 seeds are put forward Round 1: 190 peptides, 29 chains. Longest chain 20 peptides. Score 0.486 Round 2: 202 peptides, 23 chains. Longest chain 25 peptides. Score 0.614 Round 3: 195 peptides, 22 chains. Longest chain 34 peptides. Score 0.607 Round 4: 216 peptides, 26 chains. Longest chain 22 peptides. Score 0.614 Round 5: 212 peptides, 24 chains. Longest chain 30 peptides. Score 0.629 Taking the results from Round 5 Chains 26, Residues 188, Estimated correctness of the model 37.9 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4404 restraints for refining 2225 atoms. 3594 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2397 (Rfree = 0.000) for 2225 atoms. Found 14 (14 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2184 (Rfree = 0.000) for 2222 atoms. Found 14 (14 requested) and removed 14 (8 requested) atoms. Cycle 28: After refmac, R = 0.2109 (Rfree = 0.000) for 2221 atoms. Found 6 (14 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2082 (Rfree = 0.000) for 2217 atoms. Found 9 (14 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2057 (Rfree = 0.000) for 2216 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 2.81 Search for helices and strands: 0 residues in 0 chains, 2283 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 2314 seeds are put forward Round 1: 188 peptides, 28 chains. Longest chain 21 peptides. Score 0.494 Round 2: 211 peptides, 23 chains. Longest chain 27 peptides. Score 0.640 Round 3: 226 peptides, 24 chains. Longest chain 22 peptides. Score 0.667 Round 4: 212 peptides, 27 chains. Longest chain 23 peptides. Score 0.589 Round 5: 208 peptides, 28 chains. Longest chain 17 peptides. Score 0.562 Taking the results from Round 3 Chains 25, Residues 202, Estimated correctness of the model 49.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4408 restraints for refining 2225 atoms. 3562 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2492 (Rfree = 0.000) for 2225 atoms. Found 14 (14 requested) and removed 17 (8 requested) atoms. Cycle 32: After refmac, R = 0.2321 (Rfree = 0.000) for 2220 atoms. Found 7 (14 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.2234 (Rfree = 0.000) for 2212 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2181 (Rfree = 0.000) for 2206 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.2128 (Rfree = 0.000) for 2202 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 2268 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 2288 seeds are put forward Round 1: 182 peptides, 30 chains. Longest chain 20 peptides. Score 0.439 Round 2: 205 peptides, 24 chains. Longest chain 27 peptides. Score 0.609 Round 3: 197 peptides, 23 chains. Longest chain 20 peptides. Score 0.599 Round 4: 197 peptides, 26 chains. Longest chain 24 peptides. Score 0.556 Round 5: 207 peptides, 26 chains. Longest chain 24 peptides. Score 0.587 Taking the results from Round 2 Chains 25, Residues 181, Estimated correctness of the model 31.6 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4612 restraints for refining 2226 atoms. 3846 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2343 (Rfree = 0.000) for 2226 atoms. Found 14 (14 requested) and removed 11 (8 requested) atoms. Cycle 37: After refmac, R = 0.2197 (Rfree = 0.000) for 2228 atoms. Found 9 (14 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.2093 (Rfree = 0.000) for 2226 atoms. Found 7 (14 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.2042 (Rfree = 0.000) for 2224 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2047 (Rfree = 0.000) for 2219 atoms. Found 5 (14 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 2.83 Search for helices and strands: 0 residues in 0 chains, 2274 seeds are put forward NCS extension: 29 residues added (15 deleted due to clashes), 2303 seeds are put forward Round 1: 175 peptides, 24 chains. Longest chain 20 peptides. Score 0.511 Round 2: 189 peptides, 23 chains. Longest chain 20 peptides. Score 0.574 Round 3: 195 peptides, 24 chains. Longest chain 23 peptides. Score 0.578 Round 4: 192 peptides, 24 chains. Longest chain 26 peptides. Score 0.569 Round 5: 197 peptides, 21 chains. Longest chain 29 peptides. Score 0.626 Taking the results from Round 5 Chains 21, Residues 176, Estimated correctness of the model 36.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4768 restraints for refining 2226 atoms. 4085 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2299 (Rfree = 0.000) for 2226 atoms. Found 14 (14 requested) and removed 12 (8 requested) atoms. Cycle 42: After refmac, R = 0.2203 (Rfree = 0.000) for 2222 atoms. Found 8 (14 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2113 (Rfree = 0.000) for 2219 atoms. Found 9 (14 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.2047 (Rfree = 0.000) for 2216 atoms. Found 8 (14 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1942 (Rfree = 0.000) for 2215 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 2.80 Search for helices and strands: 0 residues in 0 chains, 2276 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 2296 seeds are put forward Round 1: 190 peptides, 29 chains. Longest chain 21 peptides. Score 0.486 Round 2: 202 peptides, 25 chains. Longest chain 33 peptides. Score 0.586 Round 3: 195 peptides, 22 chains. Longest chain 34 peptides. Score 0.607 Round 4: 196 peptides, 24 chains. Longest chain 32 peptides. Score 0.581 Round 5: 187 peptides, 23 chains. Longest chain 28 peptides. Score 0.567 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 173, Estimated correctness of the model 30.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2glz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5830 reflections ( 99.76 % complete ) and 4685 restraints for refining 2226 atoms. 4015 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2197 (Rfree = 0.000) for 2226 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2106 (Rfree = 0.000) for 2217 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2090 (Rfree = 0.000) for 2209 atoms. Found 0 (14 requested) and removed 4 (8 requested) atoms. Cycle 49: After refmac, R = 0.2057 (Rfree = 0.000) for 2205 atoms. TimeTaking 34.82