null Sun 23 Dec 22:22:40 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 2p4o-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-3.4-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/2p4o-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-3.4-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 22:22:49 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/2p4o-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-3.4-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 200 and 0 Target number of residues in the AU: 200 Target solvent content: 0.6551 Checking the provided sequence file Detected sequence length: 306 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 306 Adjusted target solvent content: 0.47 Input MTZ file: 2p4o-3.4-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: 94 Cell parameters: 91.400 91.400 75.131 90.000 90.000 90.000 Input sequence file: 2p4o-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.65 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: 29.686 3.400 Wilson plot Bfac: 80.92 4696 reflections ( 99.77 % complete ) and 0 restraints for refining 2707 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3458 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3300 (Rfree = 0.000) for 2707 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.58 Search for helices and strands: 0 residues in 0 chains, 2737 seeds are put forward Round 1: 116 peptides, 23 chains. Longest chain 10 peptides. Score 0.310 Round 2: 170 peptides, 28 chains. Longest chain 12 peptides. Score 0.475 Round 3: 179 peptides, 25 chains. Longest chain 22 peptides. Score 0.569 Round 4: 177 peptides, 25 chains. Longest chain 23 peptides. Score 0.561 Round 5: 178 peptides, 20 chains. Longest chain 25 peptides. Score 0.649 Taking the results from Round 5 Chains 21, Residues 158, Estimated correctness of the model 43.8 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 4696 reflections ( 99.77 % complete ) and 4813 restraints for refining 2225 atoms. 4093 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2748 (Rfree = 0.000) for 2225 atoms. Found 11 (16 requested) and removed 30 (8 requested) atoms. Cycle 2: After refmac, R = 0.2523 (Rfree = 0.000) for 2176 atoms. Found 11 (16 requested) and removed 19 (8 requested) atoms. Cycle 3: After refmac, R = 0.2353 (Rfree = 0.000) for 2145 atoms. Found 7 (16 requested) and removed 14 (8 requested) atoms. Cycle 4: After refmac, R = 0.2327 (Rfree = 0.000) for 2127 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2108 (Rfree = 0.000) for 2118 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.58 Search for helices and strands: 0 residues in 0 chains, 2186 seeds are put forward Round 1: 149 peptides, 26 chains. Longest chain 12 peptides. Score 0.416 Round 2: 169 peptides, 26 chains. Longest chain 13 peptides. Score 0.509 Round 3: 174 peptides, 24 chains. Longest chain 14 peptides. Score 0.567 Round 4: 174 peptides, 25 chains. Longest chain 14 peptides. Score 0.549 Round 5: 187 peptides, 24 chains. Longest chain 19 peptides. Score 0.617 Taking the results from Round 5 Chains 27, Residues 163, Estimated correctness of the model 34.1 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 4696 reflections ( 99.77 % complete ) and 4741 restraints for refining 2226 atoms. 4001 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2515 (Rfree = 0.000) for 2226 atoms. Found 5 (16 requested) and removed 22 (8 requested) atoms. Cycle 7: After refmac, R = 0.2331 (Rfree = 0.000) for 2181 atoms. Found 5 (16 requested) and removed 20 (8 requested) atoms. Cycle 8: After refmac, R = 0.2214 (Rfree = 0.000) for 2156 atoms. Found 3 (16 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.2148 (Rfree = 0.000) for 2140 atoms. Found 4 (16 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.2246 (Rfree = 0.000) for 2129 atoms. Found 7 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.58 Search for helices and strands: 0 residues in 0 chains, 2203 seeds are put forward Round 1: 127 peptides, 24 chains. Longest chain 12 peptides. Score 0.347 Round 2: 178 peptides, 28 chains. Longest chain 12 peptides. Score 0.511 Round 3: 175 peptides, 27 chains. Longest chain 19 peptides. Score 0.517 Round 4: 178 peptides, 27 chains. Longest chain 13 peptides. Score 0.529 Round 5: 187 peptides, 29 chains. Longest chain 16 peptides. Score 0.531 Taking the results from Round 5 Chains 29, Residues 158, Estimated correctness of the model 4.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4696 reflections ( 99.77 % complete ) and 5078 restraints for refining 2223 atoms. 4475 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2440 (Rfree = 0.000) for 2223 atoms. Found 11 (16 requested) and removed 21 (8 requested) atoms. Cycle 12: After refmac, R = 0.2216 (Rfree = 0.000) for 2200 atoms. Found 12 (16 requested) and removed 16 (8 requested) atoms. Cycle 13: After refmac, R = 0.2181 (Rfree = 0.000) for 2185 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 14: After refmac, R = 0.2166 (Rfree = 0.000) for 2174 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 15: After refmac, R = 0.2160 (Rfree = 0.000) for 2165 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.62 Search for helices and strands: 0 residues in 0 chains, 2226 seeds are put forward Round 1: 162 peptides, 32 chains. Longest chain 9 peptides. Score 0.354 Round 2: 154 peptides, 23 chains. Longest chain 18 peptides. Score 0.501 Round 3: 171 peptides, 29 chains. Longest chain 13 peptides. Score 0.460 Round 4: 168 peptides, 25 chains. Longest chain 14 peptides. Score 0.524 Round 5: 166 peptides, 27 chains. Longest chain 13 peptides. Score 0.477 Taking the results from Round 4 Chains 25, Residues 143, Estimated correctness of the model 1.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4696 reflections ( 99.77 % complete ) and 5215 restraints for refining 2226 atoms. 4668 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2253 (Rfree = 0.000) for 2226 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2222 (Rfree = 0.000) for 2214 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2249 (Rfree = 0.000) for 2207 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.2149 (Rfree = 0.000) for 2199 atoms. Found 14 (16 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.2219 (Rfree = 0.000) for 2200 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.61 Search for helices and strands: 0 residues in 0 chains, 2258 seeds are put forward Round 1: 149 peptides, 28 chains. Longest chain 12 peptides. Score 0.373 Round 2: 160 peptides, 25 chains. Longest chain 17 peptides. Score 0.489 Round 3: 135 peptides, 22 chains. Longest chain 13 peptides. Score 0.432 Round 4: 145 peptides, 20 chains. Longest chain 14 peptides. Score 0.520 Round 5: 147 peptides, 22 chains. Longest chain 17 peptides. Score 0.489 Taking the results from Round 4 Chains 20, Residues 125, Estimated correctness of the model 0.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4696 reflections ( 99.77 % complete ) and 5169 restraints for refining 2226 atoms. 4658 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2338 (Rfree = 0.000) for 2226 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 22: After refmac, R = 0.2319 (Rfree = 0.000) for 2217 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2598 (Rfree = 0.000) for 2212 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 24: After refmac, R = 0.2638 (Rfree = 0.000) for 2192 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 25: After refmac, R = 0.2390 (Rfree = 0.000) for 2187 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.57 Search for helices and strands: 0 residues in 0 chains, 2218 seeds are put forward Round 1: 121 peptides, 24 chains. Longest chain 11 peptides. Score 0.314 Round 2: 141 peptides, 24 chains. Longest chain 13 peptides. Score 0.419 Round 3: 147 peptides, 26 chains. Longest chain 10 peptides. Score 0.406 Round 4: 151 peptides, 23 chains. Longest chain 22 peptides. Score 0.487 Round 5: 145 peptides, 24 chains. Longest chain 11 peptides. Score 0.439 Taking the results from Round 4 Chains 23, Residues 128, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4696 reflections ( 99.77 % complete ) and 4837 restraints for refining 2140 atoms. 4330 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2829 (Rfree = 0.000) for 2140 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 27: After refmac, R = 0.2716 (Rfree = 0.000) for 2115 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 28: After refmac, R = 0.2600 (Rfree = 0.000) for 2105 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.2610 (Rfree = 0.000) for 2103 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 30: After refmac, R = 0.2499 (Rfree = 0.000) for 2101 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.52 Search for helices and strands: 0 residues in 0 chains, 2165 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 11 peptides. Score 0.299 Round 2: 115 peptides, 20 chains. Longest chain 12 peptides. Score 0.374 Round 3: 118 peptides, 21 chains. Longest chain 11 peptides. Score 0.367 Round 4: 128 peptides, 21 chains. Longest chain 14 peptides. Score 0.419 Round 5: 127 peptides, 23 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 4 Chains 21, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4696 reflections ( 99.77 % complete ) and 4759 restraints for refining 2097 atoms. 4352 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2512 (Rfree = 0.000) for 2097 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 32: After refmac, R = 0.2332 (Rfree = 0.000) for 2086 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.2382 (Rfree = 0.000) for 2083 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 34: After refmac, R = 0.2356 (Rfree = 0.000) for 2080 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.2330 (Rfree = 0.000) for 2080 atoms. Found 14 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.50 Search for helices and strands: 0 residues in 0 chains, 2150 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 14 peptides. Score 0.267 Round 2: 120 peptides, 21 chains. Longest chain 14 peptides. Score 0.378 Round 3: 131 peptides, 23 chains. Longest chain 14 peptides. Score 0.390 Round 4: 116 peptides, 19 chains. Longest chain 13 peptides. Score 0.402 Round 5: 122 peptides, 20 chains. Longest chain 14 peptides. Score 0.411 Taking the results from Round 5 Chains 21, Residues 102, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4696 reflections ( 99.77 % complete ) and 4790 restraints for refining 2127 atoms. 4366 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2621 (Rfree = 0.000) for 2127 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 37: After refmac, R = 0.2676 (Rfree = 0.000) for 2119 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 38: After refmac, R = 0.2626 (Rfree = 0.000) for 2112 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 39: After refmac, R = 0.2504 (Rfree = 0.000) for 2108 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.2217 (Rfree = 0.000) for 2110 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.49 Search for helices and strands: 0 residues in 0 chains, 2159 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 7 peptides. Score 0.253 Round 2: 104 peptides, 20 chains. Longest chain 11 peptides. Score 0.314 Round 3: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.332 Round 4: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.347 Round 5: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.330 Taking the results from Round 4 Chains 18, Residues 80, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4696 reflections ( 99.77 % complete ) and 4619 restraints for refining 2038 atoms. 4287 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2500 (Rfree = 0.000) for 2038 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 42: After refmac, R = 0.2696 (Rfree = 0.000) for 2030 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 43: After refmac, R = 0.2540 (Rfree = 0.000) for 2021 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 44: After refmac, R = 0.2461 (Rfree = 0.000) for 2017 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 45: After refmac, R = 0.3013 (Rfree = 0.000) for 2019 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.48 Search for helices and strands: 0 residues in 0 chains, 2056 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 11 peptides. Score 0.235 Round 2: 105 peptides, 21 chains. Longest chain 8 peptides. Score 0.295 Round 3: 99 peptides, 19 chains. Longest chain 8 peptides. Score 0.310 Round 4: 103 peptides, 19 chains. Longest chain 13 peptides. Score 0.332 Round 5: 100 peptides, 16 chains. Longest chain 14 peptides. Score 0.388 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 84, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2p4o-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4696 reflections ( 99.77 % complete ) and 4017 restraints for refining 1908 atoms. 3660 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2983 (Rfree = 0.000) for 1908 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2582 (Rfree = 0.000) for 1893 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2435 (Rfree = 0.000) for 1879 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2368 (Rfree = 0.000) for 1867 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:07:20 GMT 2018 Job finished. TimeTaking 44.67 Used memory is bytes: 20295984