null Tue 25 Dec 19:27:57 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-3.6-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 19:28:05 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-3.6-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 195 and 0 Target number of residues in the AU: 195 Target solvent content: 0.6637 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-3.6-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-3.6-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 3.601 Wilson plot Bfac: 86.67 3985 reflections ( 99.72 % complete ) and 0 restraints for refining 2732 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3438 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3298 (Rfree = 0.000) for 2732 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.72 Search for helices and strands: 0 residues in 0 chains, 2761 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.315 Round 2: 142 peptides, 25 chains. Longest chain 14 peptides. Score 0.403 Round 3: 153 peptides, 24 chains. Longest chain 18 peptides. Score 0.477 Round 4: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.499 Round 5: 170 peptides, 25 chains. Longest chain 21 peptides. Score 0.532 Taking the results from Round 5 Chains 25, Residues 145, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3985 reflections ( 99.72 % complete ) and 5118 restraints for refining 2219 atoms. 4548 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2869 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 2: After refmac, R = 0.2612 (Rfree = 0.000) for 2190 atoms. Found 11 (14 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.2579 (Rfree = 0.000) for 2177 atoms. Found 13 (14 requested) and removed 14 (7 requested) atoms. Cycle 4: After refmac, R = 0.2484 (Rfree = 0.000) for 2163 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 5: After refmac, R = 0.2504 (Rfree = 0.000) for 2160 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.74 Search for helices and strands: 0 residues in 0 chains, 2240 seeds are put forward Round 1: 137 peptides, 27 chains. Longest chain 14 peptides. Score 0.333 Round 2: 163 peptides, 24 chains. Longest chain 17 peptides. Score 0.521 Round 3: 169 peptides, 23 chains. Longest chain 23 peptides. Score 0.565 Round 4: 175 peptides, 24 chains. Longest chain 19 peptides. Score 0.571 Round 5: 185 peptides, 24 chains. Longest chain 24 peptides. Score 0.609 Taking the results from Round 5 Chains 27, Residues 161, Estimated correctness of the model 18.1 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 3985 reflections ( 99.72 % complete ) and 4837 restraints for refining 2218 atoms. 4104 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2639 (Rfree = 0.000) for 2218 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 7: After refmac, R = 0.2426 (Rfree = 0.000) for 2189 atoms. Found 13 (14 requested) and removed 18 (7 requested) atoms. Cycle 8: After refmac, R = 0.2395 (Rfree = 0.000) for 2166 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.2399 (Rfree = 0.000) for 2161 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 10: After refmac, R = 0.2287 (Rfree = 0.000) for 2155 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.74 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward Round 1: 131 peptides, 23 chains. Longest chain 9 peptides. Score 0.390 Round 2: 150 peptides, 22 chains. Longest chain 15 peptides. Score 0.503 Round 3: 156 peptides, 19 chains. Longest chain 21 peptides. Score 0.585 Round 4: 160 peptides, 24 chains. Longest chain 17 peptides. Score 0.508 Round 5: 162 peptides, 22 chains. Longest chain 19 peptides. Score 0.554 Taking the results from Round 3 Chains 19, Residues 137, Estimated correctness of the model 8.6 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 3985 reflections ( 99.72 % complete ) and 4841 restraints for refining 2202 atoms. 4225 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2578 (Rfree = 0.000) for 2202 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 12: After refmac, R = 0.2291 (Rfree = 0.000) for 2170 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2176 (Rfree = 0.000) for 2163 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 14: After refmac, R = 0.2087 (Rfree = 0.000) for 2157 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.1861 (Rfree = 0.000) for 2152 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.74 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 14 peptides. Score 0.361 Round 2: 147 peptides, 21 chains. Longest chain 21 peptides. Score 0.509 Round 3: 157 peptides, 21 chains. Longest chain 16 peptides. Score 0.552 Round 4: 162 peptides, 22 chains. Longest chain 16 peptides. Score 0.554 Round 5: 167 peptides, 22 chains. Longest chain 20 peptides. Score 0.575 Taking the results from Round 5 Chains 23, Residues 145, Estimated correctness of the model 4.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3985 reflections ( 99.72 % complete ) and 5063 restraints for refining 2217 atoms. 4476 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2228 (Rfree = 0.000) for 2217 atoms. Found 12 (14 requested) and removed 16 (7 requested) atoms. Cycle 17: After refmac, R = 0.2150 (Rfree = 0.000) for 2199 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 18: After refmac, R = 0.2100 (Rfree = 0.000) for 2184 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.1982 (Rfree = 0.000) for 2182 atoms. Found 10 (13 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1984 (Rfree = 0.000) for 2183 atoms. Found 6 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.75 Search for helices and strands: 0 residues in 0 chains, 2216 seeds are put forward Round 1: 122 peptides, 22 chains. Longest chain 10 peptides. Score 0.366 Round 2: 143 peptides, 22 chains. Longest chain 16 peptides. Score 0.471 Round 3: 129 peptides, 21 chains. Longest chain 15 peptides. Score 0.424 Round 4: 141 peptides, 19 chains. Longest chain 14 peptides. Score 0.522 Round 5: 143 peptides, 19 chains. Longest chain 14 peptides. Score 0.531 Taking the results from Round 5 Chains 20, Residues 124, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3985 reflections ( 99.72 % complete ) and 5194 restraints for refining 2219 atoms. 4677 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2460 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 22: After refmac, R = 0.2420 (Rfree = 0.000) for 2200 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.2473 (Rfree = 0.000) for 2190 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.2070 (Rfree = 0.000) for 2189 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 25: After refmac, R = 0.2002 (Rfree = 0.000) for 2179 atoms. Found 6 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.83 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 8 peptides. Score 0.292 Round 2: 132 peptides, 22 chains. Longest chain 14 peptides. Score 0.417 Round 3: 139 peptides, 22 chains. Longest chain 13 peptides. Score 0.452 Round 4: 138 peptides, 22 chains. Longest chain 12 peptides. Score 0.447 Round 5: 138 peptides, 21 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 5 Chains 21, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3985 reflections ( 99.72 % complete ) and 5152 restraints for refining 2170 atoms. 4705 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2904 (Rfree = 0.000) for 2170 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 27: After refmac, R = 0.2639 (Rfree = 0.000) for 2142 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 28: After refmac, R = 0.2539 (Rfree = 0.000) for 2126 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.2537 (Rfree = 0.000) for 2118 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.2398 (Rfree = 0.000) for 2114 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.73 Search for helices and strands: 0 residues in 0 chains, 2173 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 7 peptides. Score 0.224 Round 2: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.285 Round 3: 134 peptides, 24 chains. Longest chain 12 peptides. Score 0.384 Round 4: 122 peptides, 21 chains. Longest chain 9 peptides. Score 0.388 Round 5: 113 peptides, 21 chains. Longest chain 9 peptides. Score 0.340 Taking the results from Round 4 Chains 21, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3985 reflections ( 99.72 % complete ) and 4928 restraints for refining 2114 atoms. 4545 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2280 (Rfree = 0.000) for 2114 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2409 (Rfree = 0.000) for 2107 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 33: After refmac, R = 0.2316 (Rfree = 0.000) for 2098 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.2207 (Rfree = 0.000) for 2095 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1913 (Rfree = 0.000) for 2095 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.68 Search for helices and strands: 0 residues in 0 chains, 2147 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 9 peptides. Score 0.261 Round 2: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.315 Round 3: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.310 Round 4: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.315 Round 5: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.297 Taking the results from Round 4 Chains 19, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3985 reflections ( 99.72 % complete ) and 5089 restraints for refining 2136 atoms. 4784 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2510 (Rfree = 0.000) for 2136 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 37: After refmac, R = 0.2276 (Rfree = 0.000) for 2122 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.2202 (Rfree = 0.000) for 2121 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2275 (Rfree = 0.000) for 2122 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.2270 (Rfree = 0.000) for 2123 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.78 Search for helices and strands: 0 residues in 0 chains, 2176 seeds are put forward Round 1: 89 peptides, 19 chains. Longest chain 9 peptides. Score 0.250 Round 2: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.327 Round 3: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.332 Round 4: 94 peptides, 16 chains. Longest chain 13 peptides. Score 0.355 Round 5: 94 peptides, 18 chains. Longest chain 11 peptides. Score 0.305 Taking the results from Round 4 Chains 16, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3985 reflections ( 99.72 % complete ) and 5048 restraints for refining 2150 atoms. 4752 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2356 (Rfree = 0.000) for 2150 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 42: After refmac, R = 0.2395 (Rfree = 0.000) for 2140 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.2478 (Rfree = 0.000) for 2136 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 44: After refmac, R = 0.2384 (Rfree = 0.000) for 2122 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.2391 (Rfree = 0.000) for 2122 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.71 Search for helices and strands: 0 residues in 0 chains, 2163 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 6 peptides. Score 0.189 Round 2: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.239 Round 3: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.288 Round 4: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.281 Round 5: 54 peptides, 10 chains. Longest chain 10 peptides. Score 0.274 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 53, 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 2p4o-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3985 reflections ( 99.72 % complete ) and 4779 restraints for refining 2031 atoms. 4579 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2259 (Rfree = 0.000) for 2031 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2251 (Rfree = 0.000) for 2022 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2234 (Rfree = 0.000) for 2016 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2269 (Rfree = 0.000) for 2008 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:12:47 GMT 2018 Job finished. TimeTaking 44.85 Used memory is bytes: -71608