null Sun 23 Dec 22:22:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ghs-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-3.2-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:50 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/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-3.2-parrot-hancs/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 207 and 0 Target number of residues in the AU: 207 Target solvent content: 0.6077 Checking the provided sequence file Detected sequence length: 326 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 326 Adjusted target solvent content: 0.38 Input MTZ file: 2ghs-3.2-parrot-hancs.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: 46.258 75.703 81.538 90.000 90.000 90.000 Input sequence file: 2ghs-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.55 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 Loops will be built when appropriate and at the last cycle Resolution range: 55.478 3.200 Wilson plot Bfac: 55.57 5039 reflections ( 99.47 % complete ) and 0 restraints for refining 2891 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3267 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3090 (Rfree = 0.000) for 2891 atoms. Found 25 (25 requested) and removed 37 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 2918 seeds are put forward Round 1: 134 peptides, 27 chains. Longest chain 8 peptides. Score 0.328 Round 2: 169 peptides, 27 chains. Longest chain 11 peptides. Score 0.513 Round 3: 180 peptides, 22 chains. Longest chain 19 peptides. Score 0.651 Round 4: 183 peptides, 25 chains. Longest chain 18 peptides. Score 0.612 Round 5: 190 peptides, 27 chains. Longest chain 14 peptides. Score 0.604 Taking the results from Round 3 Chains 23, Residues 158, Estimated correctness of the model 54.1 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5039 reflections ( 99.47 % complete ) and 5322 restraints for refining 2381 atoms. 4661 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2644 (Rfree = 0.000) for 2381 atoms. Found 17 (21 requested) and removed 25 (10 requested) atoms. Cycle 2: After refmac, R = 0.2639 (Rfree = 0.000) for 2330 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 3: After refmac, R = 0.2584 (Rfree = 0.000) for 2314 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 4: After refmac, R = 0.2140 (Rfree = 0.000) for 2312 atoms. Found 7 (20 requested) and removed 15 (10 requested) atoms. Cycle 5: After refmac, R = 0.2058 (Rfree = 0.000) for 2299 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.60 Search for helices and strands: 0 residues in 0 chains, 2376 seeds are put forward Round 1: 136 peptides, 23 chains. Longest chain 12 peptides. Score 0.433 Round 2: 165 peptides, 23 chains. Longest chain 14 peptides. Score 0.574 Round 3: 182 peptides, 21 chains. Longest chain 21 peptides. Score 0.675 Round 4: 178 peptides, 22 chains. Longest chain 17 peptides. Score 0.644 Round 5: 173 peptides, 20 chains. Longest chain 28 peptides. Score 0.659 Taking the results from Round 3 Chains 22, Residues 161, Estimated correctness of the model 59.7 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5039 reflections ( 99.47 % complete ) and 4979 restraints for refining 2257 atoms. 4315 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2557 (Rfree = 0.000) for 2257 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 7: After refmac, R = 0.2400 (Rfree = 0.000) for 2257 atoms. Found 9 (20 requested) and removed 17 (10 requested) atoms. Cycle 8: After refmac, R = 0.2285 (Rfree = 0.000) for 2243 atoms. Found 10 (20 requested) and removed 19 (10 requested) atoms. Cycle 9: After refmac, R = 0.2020 (Rfree = 0.000) for 2228 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2144 (Rfree = 0.000) for 2219 atoms. Found 11 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 2307 seeds are put forward Round 1: 168 peptides, 28 chains. Longest chain 16 peptides. Score 0.487 Round 2: 185 peptides, 25 chains. Longest chain 16 peptides. Score 0.619 Round 3: 195 peptides, 25 chains. Longest chain 21 peptides. Score 0.657 Round 4: 200 peptides, 27 chains. Longest chain 18 peptides. Score 0.643 Round 5: 201 peptides, 25 chains. Longest chain 16 peptides. Score 0.678 Taking the results from Round 5 Chains 28, Residues 176, Estimated correctness of the model 60.4 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 5039 reflections ( 99.47 % complete ) and 4736 restraints for refining 2261 atoms. 3969 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2504 (Rfree = 0.000) for 2261 atoms. Found 10 (20 requested) and removed 27 (10 requested) atoms. Cycle 12: After refmac, R = 0.2566 (Rfree = 0.000) for 2235 atoms. Found 17 (20 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.2239 (Rfree = 0.000) for 2233 atoms. Found 5 (20 requested) and removed 13 (10 requested) atoms. Cycle 14: After refmac, R = 0.2214 (Rfree = 0.000) for 2219 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.1987 (Rfree = 0.000) for 2212 atoms. Found 4 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.63 Search for helices and strands: 0 residues in 0 chains, 2283 seeds are put forward Round 1: 182 peptides, 27 chains. Longest chain 13 peptides. Score 0.571 Round 2: 192 peptides, 24 chains. Longest chain 21 peptides. Score 0.662 Round 3: 192 peptides, 26 chains. Longest chain 21 peptides. Score 0.629 Round 4: 199 peptides, 26 chains. Longest chain 16 peptides. Score 0.655 Round 5: 189 peptides, 23 chains. Longest chain 21 peptides. Score 0.667 Taking the results from Round 5 Chains 28, Residues 166, Estimated correctness of the model 57.9 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 5039 reflections ( 99.47 % complete ) and 4944 restraints for refining 2290 atoms. 4205 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2595 (Rfree = 0.000) for 2290 atoms. Found 13 (20 requested) and removed 29 (10 requested) atoms. Cycle 17: After refmac, R = 0.2497 (Rfree = 0.000) for 2269 atoms. Found 15 (20 requested) and removed 16 (10 requested) atoms. Cycle 18: After refmac, R = 0.2107 (Rfree = 0.000) for 2263 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.2094 (Rfree = 0.000) for 2257 atoms. Found 2 (20 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.2100 (Rfree = 0.000) for 2244 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 3.68 Search for helices and strands: 0 residues in 0 chains, 2291 seeds are put forward Round 1: 157 peptides, 23 chains. Longest chain 19 peptides. Score 0.538 Round 2: 170 peptides, 25 chains. Longest chain 13 peptides. Score 0.557 Round 3: 170 peptides, 23 chains. Longest chain 14 peptides. Score 0.595 Round 4: 175 peptides, 24 chains. Longest chain 23 peptides. Score 0.597 Round 5: 187 peptides, 24 chains. Longest chain 22 peptides. Score 0.644 Taking the results from Round 5 Chains 26, Residues 163, Estimated correctness of the model 52.4 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5039 reflections ( 99.47 % complete ) and 5018 restraints for refining 2287 atoms. 4327 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2528 (Rfree = 0.000) for 2287 atoms. Found 16 (20 requested) and removed 18 (10 requested) atoms. Cycle 22: After refmac, R = 0.2315 (Rfree = 0.000) for 2278 atoms. Found 11 (20 requested) and removed 12 (10 requested) atoms. Cycle 23: After refmac, R = 0.2139 (Rfree = 0.000) for 2274 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.2138 (Rfree = 0.000) for 2262 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.2098 (Rfree = 0.000) for 2255 atoms. Found 2 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 2309 seeds are put forward Round 1: 166 peptides, 26 chains. Longest chain 13 peptides. Score 0.519 Round 2: 167 peptides, 20 chains. Longest chain 20 peptides. Score 0.636 Round 3: 167 peptides, 22 chains. Longest chain 19 peptides. Score 0.601 Round 4: 180 peptides, 22 chains. Longest chain 20 peptides. Score 0.651 Round 5: 183 peptides, 20 chains. Longest chain 25 peptides. Score 0.693 Taking the results from Round 5 Chains 24, Residues 163, Estimated correctness of the model 63.7 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5039 reflections ( 99.47 % complete ) and 5144 restraints for refining 2334 atoms. 4456 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2733 (Rfree = 0.000) for 2334 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 27: After refmac, R = 0.2620 (Rfree = 0.000) for 2325 atoms. Found 19 (20 requested) and removed 14 (10 requested) atoms. Cycle 28: After refmac, R = 0.2481 (Rfree = 0.000) for 2322 atoms. Found 17 (20 requested) and removed 16 (10 requested) atoms. Cycle 29: After refmac, R = 0.2513 (Rfree = 0.000) for 2319 atoms. Found 18 (20 requested) and removed 13 (10 requested) atoms. Cycle 30: After refmac, R = 0.2328 (Rfree = 0.000) for 2322 atoms. Found 9 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 3.64 Search for helices and strands: 0 residues in 0 chains, 2377 seeds are put forward Round 1: 130 peptides, 25 chains. Longest chain 11 peptides. Score 0.353 Round 2: 158 peptides, 23 chains. Longest chain 15 peptides. Score 0.542 Round 3: 161 peptides, 23 chains. Longest chain 17 peptides. Score 0.556 Round 4: 149 peptides, 21 chains. Longest chain 20 peptides. Score 0.541 Round 5: 166 peptides, 21 chains. Longest chain 21 peptides. Score 0.615 Taking the results from Round 5 Chains 23, Residues 145, Estimated correctness of the model 45.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 5039 reflections ( 99.47 % complete ) and 4948 restraints for refining 2362 atoms. 4257 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2877 (Rfree = 0.000) for 2362 atoms. Found 21 (21 requested) and removed 38 (10 requested) atoms. Cycle 32: After refmac, R = 0.2415 (Rfree = 0.000) for 2330 atoms. Found 13 (21 requested) and removed 17 (10 requested) atoms. Cycle 33: After refmac, R = 0.2341 (Rfree = 0.000) for 2319 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 34: After refmac, R = 0.2179 (Rfree = 0.000) for 2312 atoms. Found 10 (20 requested) and removed 12 (10 requested) atoms. Cycle 35: After refmac, R = 0.2187 (Rfree = 0.000) for 2306 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.04 3.58 Search for helices and strands: 0 residues in 0 chains, 2354 seeds are put forward Round 1: 130 peptides, 21 chains. Longest chain 13 peptides. Score 0.447 Round 2: 144 peptides, 19 chains. Longest chain 18 peptides. Score 0.559 Round 3: 149 peptides, 23 chains. Longest chain 13 peptides. Score 0.500 Round 4: 148 peptides, 18 chains. Longest chain 17 peptides. Score 0.597 Round 5: 148 peptides, 21 chains. Longest chain 14 peptides. Score 0.537 Taking the results from Round 4 Chains 18, Residues 130, Estimated correctness of the model 40.2 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5039 reflections ( 99.47 % complete ) and 5134 restraints for refining 2307 atoms. 4611 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2874 (Rfree = 0.000) for 2307 atoms. Found 18 (20 requested) and removed 24 (10 requested) atoms. Cycle 37: After refmac, R = 0.2792 (Rfree = 0.000) for 2293 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 38: After refmac, R = 0.2432 (Rfree = 0.000) for 2280 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 39: After refmac, R = 0.1922 (Rfree = 0.000) for 2283 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1992 (Rfree = 0.000) for 2279 atoms. Found 13 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 2322 seeds are put forward Round 1: 113 peptides, 19 chains. Longest chain 11 peptides. Score 0.402 Round 2: 120 peptides, 20 chains. Longest chain 16 peptides. Score 0.417 Round 3: 113 peptides, 17 chains. Longest chain 14 peptides. Score 0.450 Round 4: 117 peptides, 17 chains. Longest chain 12 peptides. Score 0.472 Round 5: 126 peptides, 18 chains. Longest chain 16 peptides. Score 0.495 Taking the results from Round 5 Chains 18, Residues 108, Estimated correctness of the model 9.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5039 reflections ( 99.47 % complete ) and 5154 restraints for refining 2237 atoms. 4740 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2451 (Rfree = 0.000) for 2237 atoms. Found 16 (20 requested) and removed 14 (10 requested) atoms. Cycle 42: After refmac, R = 0.2031 (Rfree = 0.000) for 2233 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2025 (Rfree = 0.000) for 2229 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.2014 (Rfree = 0.000) for 2227 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.1969 (Rfree = 0.000) for 2228 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 3.57 Search for helices and strands: 0 residues in 0 chains, 2287 seeds are put forward Round 1: 98 peptides, 19 chains. Longest chain 16 peptides. Score 0.313 Round 2: 114 peptides, 19 chains. Longest chain 16 peptides. Score 0.408 Round 3: 101 peptides, 16 chains. Longest chain 16 peptides. Score 0.409 Round 4: 99 peptides, 15 chains. Longest chain 16 peptides. Score 0.422 Round 5: 102 peptides, 16 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 84, 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 2ghs-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5039 reflections ( 99.47 % complete ) and 5386 restraints for refining 2276 atoms. 5065 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2149 (Rfree = 0.000) for 2276 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2710 (Rfree = 0.000) for 2265 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2177 (Rfree = 0.000) for 2250 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1873 (Rfree = 0.000) for 2237 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:09:07 GMT 2018 Job finished. TimeTaking 46.43 Used memory is bytes: 19117528