null Sun 23 Dec 22:22:49 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 1vmi-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-4.0-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/1vmi-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-4.0-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 22:22:59 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/1vmi-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-4.0-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 273 and 0 Target number of residues in the AU: 273 Target solvent content: 0.6725 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.57 Input MTZ file: 1vmi-4.0-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: 182 Cell parameters: 94.674 94.674 174.359 90.000 90.000 120.000 Input sequence file: 1vmi-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 target number of atoms Had to go as low as 0.75 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: 87.180 4.001 Wilson plot Bfac: 94.16 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4287 reflections ( 99.51 % complete ) and 0 restraints for refining 3142 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3492 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3298 (Rfree = 0.000) for 3142 atoms. Found 14 (14 requested) and removed 68 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.87 3.52 Search for helices and strands: 0 residues in 0 chains, 3132 seeds are put forward Round 1: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.327 Round 2: 161 peptides, 26 chains. Longest chain 12 peptides. Score 0.402 Round 3: 177 peptides, 22 chains. Longest chain 18 peptides. Score 0.517 Round 4: 176 peptides, 21 chains. Longest chain 21 peptides. Score 0.529 Round 5: 198 peptides, 21 chains. Longest chain 23 peptides. Score 0.593 Taking the results from Round 5 Chains 25, Residues 177, Estimated correctness of the model 0.0 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 4287 reflections ( 99.51 % complete ) and 4922 restraints for refining 2386 atoms. 4072 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2933 (Rfree = 0.000) for 2386 atoms. Found 7 (11 requested) and removed 43 (5 requested) atoms. Cycle 2: After refmac, R = 0.2663 (Rfree = 0.000) for 2303 atoms. Found 5 (11 requested) and removed 18 (5 requested) atoms. Cycle 3: After refmac, R = 0.2567 (Rfree = 0.000) for 2265 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2459 (Rfree = 0.000) for 2258 atoms. Found 1 (10 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.2429 (Rfree = 0.000) for 2246 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward Round 1: 161 peptides, 22 chains. Longest chain 16 peptides. Score 0.465 Round 2: 186 peptides, 18 chains. Longest chain 27 peptides. Score 0.599 Round 3: 195 peptides, 22 chains. Longest chain 20 peptides. Score 0.571 Round 4: 192 peptides, 21 chains. Longest chain 19 peptides. Score 0.576 Round 5: 185 peptides, 19 chains. Longest chain 21 peptides. Score 0.583 Taking the results from Round 2 Chains 22, Residues 168, Estimated correctness of the model 0.0 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 4287 reflections ( 99.51 % complete ) and 5076 restraints for refining 2378 atoms. 4303 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2452 (Rfree = 0.000) for 2378 atoms. Found 10 (11 requested) and removed 31 (5 requested) atoms. Cycle 7: After refmac, R = 0.2293 (Rfree = 0.000) for 2335 atoms. Found 3 (11 requested) and removed 14 (5 requested) atoms. Cycle 8: After refmac, R = 0.2203 (Rfree = 0.000) for 2318 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.2157 (Rfree = 0.000) for 2308 atoms. Found 1 (10 requested) and removed 11 (5 requested) atoms. Cycle 10: After refmac, R = 0.2125 (Rfree = 0.000) for 2295 atoms. Found 0 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 2381 seeds are put forward Round 1: 174 peptides, 26 chains. Longest chain 20 peptides. Score 0.448 Round 2: 181 peptides, 20 chains. Longest chain 29 peptides. Score 0.558 Round 3: 179 peptides, 20 chains. Longest chain 23 peptides. Score 0.552 Round 4: 180 peptides, 18 chains. Longest chain 24 peptides. Score 0.582 Round 5: 183 peptides, 18 chains. Longest chain 32 peptides. Score 0.591 Taking the results from Round 5 Chains 18, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4287 reflections ( 99.51 % complete ) and 5617 restraints for refining 2437 atoms. 4975 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2388 (Rfree = 0.000) for 2437 atoms. Found 8 (11 requested) and removed 30 (5 requested) atoms. Cycle 12: After refmac, R = 0.2105 (Rfree = 0.000) for 2405 atoms. Found 2 (11 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2069 (Rfree = 0.000) for 2386 atoms. Found 1 (11 requested) and removed 16 (5 requested) atoms. Cycle 14: After refmac, R = 0.2392 (Rfree = 0.000) for 2366 atoms. Found 7 (11 requested) and removed 23 (5 requested) atoms. Cycle 15: After refmac, R = 0.2245 (Rfree = 0.000) for 2336 atoms. Found 11 (11 requested) and removed 27 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.47 Search for helices and strands: 0 residues in 0 chains, 2455 seeds are put forward Round 1: 152 peptides, 27 chains. Longest chain 9 peptides. Score 0.353 Round 2: 171 peptides, 24 chains. Longest chain 15 peptides. Score 0.468 Round 3: 179 peptides, 25 chains. Longest chain 17 peptides. Score 0.480 Round 4: 197 peptides, 23 chains. Longest chain 22 peptides. Score 0.564 Round 5: 191 peptides, 22 chains. Longest chain 24 peptides. Score 0.560 Taking the results from Round 4 Chains 24, Residues 174, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 4287 reflections ( 99.51 % complete ) and 5401 restraints for refining 2501 atoms. 4659 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2643 (Rfree = 0.000) for 2501 atoms. Found 11 (11 requested) and removed 181 (5 requested) atoms. Cycle 17: After refmac, R = 0.2365 (Rfree = 0.000) for 2306 atoms. Found 11 (11 requested) and removed 75 (5 requested) atoms. Cycle 18: After refmac, R = 0.2175 (Rfree = 0.000) for 2231 atoms. Found 6 (10 requested) and removed 26 (5 requested) atoms. Cycle 19: After refmac, R = 0.1992 (Rfree = 0.000) for 2204 atoms. Found 4 (10 requested) and removed 25 (5 requested) atoms. Cycle 20: After refmac, R = 0.2013 (Rfree = 0.000) for 2176 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.44 Search for helices and strands: 0 residues in 0 chains, 2278 seeds are put forward Round 1: 160 peptides, 27 chains. Longest chain 15 peptides. Score 0.383 Round 2: 184 peptides, 23 chains. Longest chain 31 peptides. Score 0.525 Round 3: 181 peptides, 22 chains. Longest chain 20 peptides. Score 0.530 Round 4: 199 peptides, 22 chains. Longest chain 17 peptides. Score 0.583 Round 5: 200 peptides, 22 chains. Longest chain 17 peptides. Score 0.585 Taking the results from Round 5 Chains 23, Residues 178, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4287 reflections ( 99.51 % complete ) and 4845 restraints for refining 2343 atoms. 4090 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2745 (Rfree = 0.000) for 2343 atoms. Found 11 (11 requested) and removed 30 (5 requested) atoms. Cycle 22: After refmac, R = 0.2370 (Rfree = 0.000) for 2285 atoms. Found 7 (11 requested) and removed 21 (5 requested) atoms. Cycle 23: After refmac, R = 0.2289 (Rfree = 0.000) for 2248 atoms. Found 8 (10 requested) and removed 34 (5 requested) atoms. Cycle 24: After refmac, R = 0.2135 (Rfree = 0.000) for 2212 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2097 (Rfree = 0.000) for 2197 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.44 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward Round 1: 164 peptides, 24 chains. Longest chain 14 peptides. Score 0.444 Round 2: 186 peptides, 22 chains. Longest chain 17 peptides. Score 0.545 Round 3: 194 peptides, 24 chains. Longest chain 21 peptides. Score 0.541 Round 4: 193 peptides, 23 chains. Longest chain 23 peptides. Score 0.552 Round 5: 196 peptides, 21 chains. Longest chain 28 peptides. Score 0.587 Taking the results from Round 5 Chains 26, Residues 175, Estimated correctness of the model 0.0 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 4287 reflections ( 99.51 % complete ) and 4953 restraints for refining 2418 atoms. 4151 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2802 (Rfree = 0.000) for 2418 atoms. Found 9 (11 requested) and removed 44 (5 requested) atoms. Cycle 27: After refmac, R = 0.2421 (Rfree = 0.000) for 2363 atoms. Found 5 (11 requested) and removed 15 (5 requested) atoms. Cycle 28: After refmac, R = 0.2346 (Rfree = 0.000) for 2332 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 29: After refmac, R = 0.2260 (Rfree = 0.000) for 2312 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 30: After refmac, R = 0.2337 (Rfree = 0.000) for 2297 atoms. Found 10 (10 requested) and removed 26 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 2390 seeds are put forward Round 1: 155 peptides, 28 chains. Longest chain 10 peptides. Score 0.347 Round 2: 177 peptides, 22 chains. Longest chain 19 peptides. Score 0.517 Round 3: 178 peptides, 24 chains. Longest chain 25 peptides. Score 0.491 Round 4: 168 peptides, 22 chains. Longest chain 19 peptides. Score 0.488 Round 5: 185 peptides, 25 chains. Longest chain 15 peptides. Score 0.499 Taking the results from Round 2 Chains 23, Residues 155, Estimated correctness of the model 0.0 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 4287 reflections ( 99.51 % complete ) and 4853 restraints for refining 2333 atoms. 4144 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2807 (Rfree = 0.000) for 2333 atoms. Found 11 (11 requested) and removed 61 (5 requested) atoms. Cycle 32: After refmac, R = 0.2761 (Rfree = 0.000) for 2271 atoms. Found 10 (10 requested) and removed 41 (5 requested) atoms. Cycle 33: After refmac, R = 0.2639 (Rfree = 0.000) for 2234 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 34: After refmac, R = 0.2312 (Rfree = 0.000) for 2212 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 35: After refmac, R = 0.2227 (Rfree = 0.000) for 2200 atoms. Found 7 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.89 3.54 Search for helices and strands: 0 residues in 0 chains, 2290 seeds are put forward Round 1: 154 peptides, 27 chains. Longest chain 15 peptides. Score 0.360 Round 2: 171 peptides, 25 chains. Longest chain 15 peptides. Score 0.453 Round 3: 181 peptides, 23 chains. Longest chain 18 peptides. Score 0.515 Round 4: 178 peptides, 21 chains. Longest chain 17 peptides. Score 0.535 Round 5: 181 peptides, 24 chains. Longest chain 18 peptides. Score 0.501 Taking the results from Round 4 Chains 22, Residues 157, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4287 reflections ( 99.51 % complete ) and 4722 restraints for refining 2336 atoms. 4036 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2572 (Rfree = 0.000) for 2336 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 37: After refmac, R = 0.2502 (Rfree = 0.000) for 2319 atoms. Found 7 (11 requested) and removed 21 (5 requested) atoms. Cycle 38: After refmac, R = 0.2537 (Rfree = 0.000) for 2297 atoms. Found 10 (10 requested) and removed 25 (5 requested) atoms. Cycle 39: After refmac, R = 0.2397 (Rfree = 0.000) for 2272 atoms. Found 8 (10 requested) and removed 21 (5 requested) atoms. Cycle 40: After refmac, R = 0.2086 (Rfree = 0.000) for 2251 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.88 3.53 Search for helices and strands: 0 residues in 0 chains, 2354 seeds are put forward Round 1: 134 peptides, 24 chains. Longest chain 10 peptides. Score 0.333 Round 2: 151 peptides, 22 chains. Longest chain 12 peptides. Score 0.430 Round 3: 154 peptides, 20 chains. Longest chain 12 peptides. Score 0.472 Round 4: 156 peptides, 22 chains. Longest chain 12 peptides. Score 0.448 Round 5: 150 peptides, 21 chains. Longest chain 18 peptides. Score 0.443 Taking the results from Round 3 Chains 20, Residues 134, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4287 reflections ( 99.51 % complete ) and 5170 restraints for refining 2295 atoms. 4628 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2634 (Rfree = 0.000) for 2295 atoms. Found 10 (10 requested) and removed 34 (5 requested) atoms. Cycle 42: After refmac, R = 0.2471 (Rfree = 0.000) for 2258 atoms. Found 9 (10 requested) and removed 23 (5 requested) atoms. Cycle 43: After refmac, R = 0.2636 (Rfree = 0.000) for 2239 atoms. Found 10 (10 requested) and removed 25 (5 requested) atoms. Cycle 44: After refmac, R = 0.2392 (Rfree = 0.000) for 2214 atoms. Found 10 (10 requested) and removed 33 (5 requested) atoms. Cycle 45: After refmac, R = 0.2588 (Rfree = 0.000) for 2180 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 2280 seeds are put forward Round 1: 128 peptides, 25 chains. Longest chain 8 peptides. Score 0.291 Round 2: 124 peptides, 21 chains. Longest chain 11 peptides. Score 0.346 Round 3: 141 peptides, 23 chains. Longest chain 10 peptides. Score 0.377 Round 4: 142 peptides, 19 chains. Longest chain 17 peptides. Score 0.447 Round 5: 151 peptides, 19 chains. Longest chain 25 peptides. Score 0.478 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 132, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 1vmi-4_warpNtrace.pdb as input Building loops using Loopy2018 20 chains (132 residues) following loop building 2 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4287 reflections ( 99.51 % complete ) and 4869 restraints for refining 2297 atoms. 4270 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2592 (Rfree = 0.000) for 2297 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2386 (Rfree = 0.000) for 2269 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2404 (Rfree = 0.000) for 2251 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2463 (Rfree = 0.000) for 2230 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:16:12 GMT 2018 Job finished. TimeTaking 53.39 Used memory is bytes: 3813472