null Tue 25 Dec 19:27:55 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 2ghr-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-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/2ghr-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-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 ============================================================ Tue 25 Dec 19:28:04 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/2ghr-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-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 250 and 0 Target number of residues in the AU: 250 Target solvent content: 0.6089 Checking the provided sequence file Detected sequence length: 302 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 302 Adjusted target solvent content: 0.53 Input MTZ file: 2ghr-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: 91 Cell parameters: 95.828 95.828 75.339 90.000 90.000 90.000 Input sequence file: 2ghr-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2416 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: 95.828 3.401 Wilson plot Bfac: 55.80 5135 reflections ( 99.11 % complete ) and 0 restraints for refining 2668 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3424 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3094 (Rfree = 0.000) for 2668 atoms. Found 16 (20 requested) and removed 25 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 2.96 Search for helices and strands: 0 residues in 0 chains, 2705 seeds are put forward Round 1: 128 peptides, 26 chains. Longest chain 8 peptides. Score 0.297 Round 2: 150 peptides, 23 chains. Longest chain 16 peptides. Score 0.461 Round 3: 163 peptides, 24 chains. Longest chain 16 peptides. Score 0.498 Round 4: 168 peptides, 26 chains. Longest chain 16 peptides. Score 0.482 Round 5: 175 peptides, 18 chains. Longest chain 25 peptides. Score 0.641 Taking the results from Round 5 Chains 19, Residues 157, Estimated correctness of the model 41.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5135 reflections ( 99.11 % complete ) and 4646 restraints for refining 2154 atoms. 4010 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3144 (Rfree = 0.000) for 2154 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 2: After refmac, R = 0.2924 (Rfree = 0.000) for 2126 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.2848 (Rfree = 0.000) for 2125 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.2815 (Rfree = 0.000) for 2110 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2828 (Rfree = 0.000) for 2099 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 2170 seeds are put forward Round 1: 164 peptides, 25 chains. Longest chain 14 peptides. Score 0.484 Round 2: 184 peptides, 23 chains. Longest chain 18 peptides. Score 0.594 Round 3: 186 peptides, 20 chains. Longest chain 25 peptides. Score 0.647 Round 4: 188 peptides, 21 chains. Longest chain 21 peptides. Score 0.638 Round 5: 184 peptides, 19 chains. Longest chain 34 peptides. Score 0.655 Taking the results from Round 5 Chains 19, Residues 165, Estimated correctness of the model 45.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5135 reflections ( 99.11 % complete ) and 4914 restraints for refining 2161 atoms. 4273 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2943 (Rfree = 0.000) for 2161 atoms. Found 16 (16 requested) and removed 43 (8 requested) atoms. Cycle 7: After refmac, R = 0.2826 (Rfree = 0.000) for 2122 atoms. Found 9 (16 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2724 (Rfree = 0.000) for 2111 atoms. Found 9 (15 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.2549 (Rfree = 0.000) for 2097 atoms. Found 10 (15 requested) and removed 16 (7 requested) atoms. Cycle 10: After refmac, R = 0.2563 (Rfree = 0.000) for 2081 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 2.98 Search for helices and strands: 0 residues in 0 chains, 2158 seeds are put forward Round 1: 147 peptides, 27 chains. Longest chain 9 peptides. Score 0.369 Round 2: 165 peptides, 25 chains. Longest chain 13 peptides. Score 0.488 Round 3: 175 peptides, 23 chains. Longest chain 16 peptides. Score 0.562 Round 4: 173 peptides, 25 chains. Longest chain 13 peptides. Score 0.520 Round 5: 172 peptides, 23 chains. Longest chain 17 peptides. Score 0.551 Taking the results from Round 3 Chains 23, Residues 152, Estimated correctness of the model 15.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5135 reflections ( 99.11 % complete ) and 4975 restraints for refining 2186 atoms. 4390 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2879 (Rfree = 0.000) for 2186 atoms. Found 15 (16 requested) and removed 41 (8 requested) atoms. Cycle 12: After refmac, R = 0.2565 (Rfree = 0.000) for 2141 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2502 (Rfree = 0.000) for 2127 atoms. Found 10 (16 requested) and removed 13 (8 requested) atoms. Cycle 14: After refmac, R = 0.2509 (Rfree = 0.000) for 2113 atoms. Found 8 (16 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.2223 (Rfree = 0.000) for 2099 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.03 Search for helices and strands: 0 residues in 0 chains, 2163 seeds are put forward Round 1: 155 peptides, 27 chains. Longest chain 12 peptides. Score 0.406 Round 2: 165 peptides, 26 chains. Longest chain 19 peptides. Score 0.469 Round 3: 168 peptides, 24 chains. Longest chain 16 peptides. Score 0.518 Round 4: 173 peptides, 23 chains. Longest chain 23 peptides. Score 0.554 Round 5: 178 peptides, 24 chains. Longest chain 28 peptides. Score 0.556 Taking the results from Round 5 Chains 26, Residues 154, Estimated correctness of the model 13.6 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5135 reflections ( 99.11 % complete ) and 4669 restraints for refining 2196 atoms. 3982 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3042 (Rfree = 0.000) for 2196 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 17: After refmac, R = 0.2792 (Rfree = 0.000) for 2181 atoms. Found 12 (16 requested) and removed 23 (8 requested) atoms. Cycle 18: After refmac, R = 0.2445 (Rfree = 0.000) for 2153 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2565 (Rfree = 0.000) for 2141 atoms. Found 3 (16 requested) and removed 16 (8 requested) atoms. Cycle 20: After refmac, R = 0.2715 (Rfree = 0.000) for 2123 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 2188 seeds are put forward Round 1: 139 peptides, 28 chains. Longest chain 12 peptides. Score 0.310 Round 2: 148 peptides, 21 chains. Longest chain 17 peptides. Score 0.491 Round 3: 149 peptides, 22 chains. Longest chain 18 peptides. Score 0.476 Round 4: 153 peptides, 22 chains. Longest chain 21 peptides. Score 0.493 Round 5: 168 peptides, 22 chains. Longest chain 17 peptides. Score 0.552 Taking the results from Round 5 Chains 22, Residues 146, Estimated correctness of the model 12.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5135 reflections ( 99.11 % complete ) and 5035 restraints for refining 2195 atoms. 4473 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2943 (Rfree = 0.000) for 2195 atoms. Found 11 (16 requested) and removed 26 (8 requested) atoms. Cycle 22: After refmac, R = 0.2570 (Rfree = 0.000) for 2173 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.2553 (Rfree = 0.000) for 2162 atoms. Found 11 (16 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.2374 (Rfree = 0.000) for 2156 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2268 (Rfree = 0.000) for 2152 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 2200 seeds are put forward Round 1: 152 peptides, 27 chains. Longest chain 12 peptides. Score 0.393 Round 2: 167 peptides, 24 chains. Longest chain 18 peptides. Score 0.514 Round 3: 158 peptides, 21 chains. Longest chain 17 peptides. Score 0.531 Round 4: 155 peptides, 23 chains. Longest chain 13 peptides. Score 0.483 Round 5: 156 peptides, 23 chains. Longest chain 13 peptides. Score 0.487 Taking the results from Round 3 Chains 21, Residues 137, Estimated correctness of the model 4.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5135 reflections ( 99.11 % complete ) and 5095 restraints for refining 2196 atoms. 4568 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2601 (Rfree = 0.000) for 2196 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 27: After refmac, R = 0.2566 (Rfree = 0.000) for 2185 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2418 (Rfree = 0.000) for 2184 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2269 (Rfree = 0.000) for 2178 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2069 (Rfree = 0.000) for 2168 atoms. Found 0 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 2219 seeds are put forward Round 1: 148 peptides, 27 chains. Longest chain 11 peptides. Score 0.374 Round 2: 155 peptides, 23 chains. Longest chain 14 peptides. Score 0.483 Round 3: 165 peptides, 24 chains. Longest chain 15 peptides. Score 0.506 Round 4: 164 peptides, 25 chains. Longest chain 22 peptides. Score 0.484 Round 5: 164 peptides, 24 chains. Longest chain 14 peptides. Score 0.502 Taking the results from Round 3 Chains 24, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5135 reflections ( 99.11 % complete ) and 5005 restraints for refining 2196 atoms. 4465 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2632 (Rfree = 0.000) for 2196 atoms. Found 14 (16 requested) and removed 9 (8 requested) atoms. Cycle 32: After refmac, R = 0.2602 (Rfree = 0.000) for 2193 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2452 (Rfree = 0.000) for 2183 atoms. Found 15 (16 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.2333 (Rfree = 0.000) for 2183 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.2169 (Rfree = 0.000) for 2178 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.00 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward Round 1: 145 peptides, 27 chains. Longest chain 15 peptides. Score 0.360 Round 2: 143 peptides, 26 chains. Longest chain 14 peptides. Score 0.371 Round 3: 145 peptides, 26 chains. Longest chain 10 peptides. Score 0.380 Round 4: 138 peptides, 24 chains. Longest chain 11 peptides. Score 0.387 Round 5: 134 peptides, 22 chains. Longest chain 15 peptides. Score 0.409 Taking the results from Round 5 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5135 reflections ( 99.11 % complete ) and 5300 restraints for refining 2194 atoms. 4874 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2532 (Rfree = 0.000) for 2194 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. Cycle 37: After refmac, R = 0.2619 (Rfree = 0.000) for 2188 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.2406 (Rfree = 0.000) for 2191 atoms. Found 14 (16 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.2349 (Rfree = 0.000) for 2190 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2367 (Rfree = 0.000) for 2187 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 2251 seeds are put forward Round 1: 115 peptides, 23 chains. Longest chain 7 peptides. Score 0.295 Round 2: 124 peptides, 21 chains. Longest chain 15 peptides. Score 0.383 Round 3: 133 peptides, 22 chains. Longest chain 15 peptides. Score 0.405 Round 4: 110 peptides, 19 chains. Longest chain 12 peptides. Score 0.357 Round 5: 116 peptides, 20 chains. Longest chain 12 peptides. Score 0.365 Taking the results from Round 3 Chains 22, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5135 reflections ( 99.11 % complete ) and 5142 restraints for refining 2194 atoms. 4720 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2674 (Rfree = 0.000) for 2194 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.2724 (Rfree = 0.000) for 2194 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2497 (Rfree = 0.000) for 2194 atoms. Found 14 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.2453 (Rfree = 0.000) for 2193 atoms. Found 12 (16 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.2338 (Rfree = 0.000) for 2192 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 2255 seeds are put forward Round 1: 113 peptides, 26 chains. Longest chain 7 peptides. Score 0.217 Round 2: 139 peptides, 26 chains. Longest chain 12 peptides. Score 0.351 Round 3: 128 peptides, 24 chains. Longest chain 10 peptides. Score 0.339 Round 4: 132 peptides, 23 chains. Longest chain 11 peptides. Score 0.380 Round 5: 126 peptides, 22 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 109, 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 2ghr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5135 reflections ( 99.11 % complete ) and 5131 restraints for refining 2196 atoms. 4718 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2398 (Rfree = 0.000) for 2196 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2297 (Rfree = 0.000) for 2182 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2286 (Rfree = 0.000) for 2169 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2271 (Rfree = 0.000) for 2156 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:14:27 GMT 2018 Job finished. TimeTaking 46.53 Used memory is bytes: 14717360