null Sun 23 Dec 22:22:42 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 2hag-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hag-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hag-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-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/2hag-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-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 22:22:56 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/2hag-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-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 314 and 0 Target number of residues in the AU: 314 Target solvent content: 0.6679 Checking the provided sequence file Detected sequence length: 312 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 312 Adjusted target solvent content: 0.67 Input MTZ file: 2hag-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: 96 Cell parameters: 94.680 94.680 114.160 90.000 90.000 90.000 Input sequence file: 2hag-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2496 target number of atoms Had to go as low as 1.00 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: 29.659 4.000 Wilson plot Bfac: 90.34 4712 reflections ( 99.51 % complete ) and 0 restraints for refining 2779 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3493 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3464 (Rfree = 0.000) for 2779 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.03 Search for helices and strands: 0 residues in 0 chains, 2820 seeds are put forward Round 1: 145 peptides, 24 chains. Longest chain 15 peptides. Score 0.358 Round 2: 173 peptides, 24 chains. Longest chain 17 peptides. Score 0.449 Round 3: 182 peptides, 23 chains. Longest chain 20 peptides. Score 0.490 Round 4: 191 peptides, 22 chains. Longest chain 17 peptides. Score 0.528 Round 5: 190 peptides, 23 chains. Longest chain 18 peptides. Score 0.513 Taking the results from Round 4 Chains 22, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4712 reflections ( 99.51 % complete ) and 5002 restraints for refining 2254 atoms. 4348 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2842 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 2: After refmac, R = 0.2760 (Rfree = 0.000) for 2216 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.2547 (Rfree = 0.000) for 2198 atoms. Found 5 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2547 (Rfree = 0.000) for 2185 atoms. Found 6 (10 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.2455 (Rfree = 0.000) for 2176 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.02 Search for helices and strands: 0 residues in 0 chains, 2271 seeds are put forward Round 1: 171 peptides, 23 chains. Longest chain 15 peptides. Score 0.457 Round 2: 200 peptides, 25 chains. Longest chain 22 peptides. Score 0.515 Round 3: 197 peptides, 23 chains. Longest chain 21 peptides. Score 0.532 Round 4: 193 peptides, 24 chains. Longest chain 21 peptides. Score 0.508 Round 5: 183 peptides, 21 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 3 Chains 24, Residues 174, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4712 reflections ( 99.51 % complete ) and 4773 restraints for refining 2254 atoms. 3972 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2789 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 7: After refmac, R = 0.2596 (Rfree = 0.000) for 2223 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 8: After refmac, R = 0.2512 (Rfree = 0.000) for 2206 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.2475 (Rfree = 0.000) for 2198 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2447 (Rfree = 0.000) for 2192 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.03 Search for helices and strands: 0 residues in 0 chains, 2296 seeds are put forward Round 1: 179 peptides, 25 chains. Longest chain 14 peptides. Score 0.454 Round 2: 191 peptides, 19 chains. Longest chain 27 peptides. Score 0.566 Round 3: 186 peptides, 19 chains. Longest chain 28 peptides. Score 0.553 Round 4: 193 peptides, 21 chains. Longest chain 29 peptides. Score 0.546 Round 5: 178 peptides, 20 chains. Longest chain 18 peptides. Score 0.518 Taking the results from Round 2 Chains 19, Residues 172, Estimated correctness of the model 0.0 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4712 reflections ( 99.51 % complete ) and 4732 restraints for refining 2253 atoms. 3953 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2690 (Rfree = 0.000) for 2253 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 12: After refmac, R = 0.2572 (Rfree = 0.000) for 2225 atoms. Found 7 (10 requested) and removed 15 (5 requested) atoms. Cycle 13: After refmac, R = 0.2493 (Rfree = 0.000) for 2214 atoms. Found 5 (10 requested) and removed 19 (5 requested) atoms. Cycle 14: After refmac, R = 0.2378 (Rfree = 0.000) for 2197 atoms. Found 7 (10 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.2318 (Rfree = 0.000) for 2191 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.03 Search for helices and strands: 0 residues in 0 chains, 2279 seeds are put forward Round 1: 162 peptides, 23 chains. Longest chain 15 peptides. Score 0.429 Round 2: 175 peptides, 21 chains. Longest chain 23 peptides. Score 0.496 Round 3: 183 peptides, 23 chains. Longest chain 16 peptides. Score 0.493 Round 4: 186 peptides, 18 chains. Longest chain 20 peptides. Score 0.566 Round 5: 181 peptides, 20 chains. Longest chain 19 peptides. Score 0.527 Taking the results from Round 4 Chains 18, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4712 reflections ( 99.51 % complete ) and 5101 restraints for refining 2254 atoms. 4447 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2773 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.2600 (Rfree = 0.000) for 2238 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.2392 (Rfree = 0.000) for 2227 atoms. Found 0 (10 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2372 (Rfree = 0.000) for 2213 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2425 (Rfree = 0.000) for 2210 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.01 Search for helices and strands: 0 residues in 0 chains, 2271 seeds are put forward Round 1: 170 peptides, 25 chains. Longest chain 16 peptides. Score 0.426 Round 2: 172 peptides, 21 chains. Longest chain 18 peptides. Score 0.488 Round 3: 188 peptides, 21 chains. Longest chain 19 peptides. Score 0.533 Round 4: 173 peptides, 20 chains. Longest chain 22 peptides. Score 0.504 Round 5: 180 peptides, 19 chains. Longest chain 19 peptides. Score 0.537 Taking the results from Round 5 Chains 20, Residues 161, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4712 reflections ( 99.51 % complete ) and 4826 restraints for refining 2254 atoms. 4100 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2784 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 22: After refmac, R = 0.2720 (Rfree = 0.000) for 2231 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.2562 (Rfree = 0.000) for 2223 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 24: After refmac, R = 0.2532 (Rfree = 0.000) for 2212 atoms. Found 6 (10 requested) and removed 14 (5 requested) atoms. Cycle 25: After refmac, R = 0.2382 (Rfree = 0.000) for 2203 atoms. Found 8 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.03 Search for helices and strands: 0 residues in 0 chains, 2307 seeds are put forward Round 1: 162 peptides, 25 chains. Longest chain 15 peptides. Score 0.400 Round 2: 162 peptides, 22 chains. Longest chain 17 peptides. Score 0.444 Round 3: 184 peptides, 23 chains. Longest chain 20 peptides. Score 0.496 Round 4: 188 peptides, 22 chains. Longest chain 19 peptides. Score 0.520 Round 5: 183 peptides, 20 chains. Longest chain 30 peptides. Score 0.532 Taking the results from Round 5 Chains 21, Residues 163, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4712 reflections ( 99.51 % complete ) and 4715 restraints for refining 2254 atoms. 3958 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2704 (Rfree = 0.000) for 2254 atoms. Found 7 (10 requested) and removed 12 (5 requested) atoms. Cycle 27: After refmac, R = 0.2542 (Rfree = 0.000) for 2235 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. Cycle 28: After refmac, R = 0.2475 (Rfree = 0.000) for 2227 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2432 (Rfree = 0.000) for 2222 atoms. Found 1 (10 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2406 (Rfree = 0.000) for 2211 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.01 Search for helices and strands: 0 residues in 0 chains, 2271 seeds are put forward Round 1: 151 peptides, 27 chains. Longest chain 10 peptides. Score 0.333 Round 2: 164 peptides, 23 chains. Longest chain 16 peptides. Score 0.436 Round 3: 159 peptides, 21 chains. Longest chain 18 peptides. Score 0.449 Round 4: 158 peptides, 22 chains. Longest chain 13 peptides. Score 0.431 Round 5: 164 peptides, 24 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 3 Chains 21, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4712 reflections ( 99.51 % complete ) and 5340 restraints for refining 2254 atoms. 4809 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2799 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 32: After refmac, R = 0.2601 (Rfree = 0.000) for 2244 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 33: After refmac, R = 0.2328 (Rfree = 0.000) for 2231 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.2353 (Rfree = 0.000) for 2224 atoms. Found 3 (10 requested) and removed 12 (5 requested) atoms. Cycle 35: After refmac, R = 0.2597 (Rfree = 0.000) for 2210 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 3.03 Search for helices and strands: 0 residues in 0 chains, 2267 seeds are put forward Round 1: 148 peptides, 24 chains. Longest chain 12 peptides. Score 0.369 Round 2: 164 peptides, 23 chains. Longest chain 15 peptides. Score 0.436 Round 3: 165 peptides, 19 chains. Longest chain 21 peptides. Score 0.495 Round 4: 181 peptides, 19 chains. Longest chain 26 peptides. Score 0.540 Round 5: 171 peptides, 21 chains. Longest chain 26 peptides. Score 0.485 Taking the results from Round 4 Chains 20, Residues 162, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4712 reflections ( 99.51 % complete ) and 4829 restraints for refining 2254 atoms. 4143 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2598 (Rfree = 0.000) for 2254 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.2478 (Rfree = 0.000) for 2241 atoms. Found 7 (10 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2438 (Rfree = 0.000) for 2233 atoms. Found 4 (10 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.2416 (Rfree = 0.000) for 2223 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.2202 (Rfree = 0.000) for 2216 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.03 Search for helices and strands: 0 residues in 0 chains, 2275 seeds are put forward Round 1: 151 peptides, 29 chains. Longest chain 11 peptides. Score 0.303 Round 2: 168 peptides, 26 chains. Longest chain 12 peptides. Score 0.405 Round 3: 169 peptides, 23 chains. Longest chain 14 peptides. Score 0.451 Round 4: 178 peptides, 26 chains. Longest chain 15 peptides. Score 0.437 Round 5: 174 peptides, 24 chains. Longest chain 17 peptides. Score 0.452 Taking the results from Round 5 Chains 24, Residues 150, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4712 reflections ( 99.51 % complete ) and 5019 restraints for refining 2254 atoms. 4407 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2692 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2481 (Rfree = 0.000) for 2242 atoms. Found 8 (10 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.2492 (Rfree = 0.000) for 2237 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2455 (Rfree = 0.000) for 2232 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.2378 (Rfree = 0.000) for 2227 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.01 Search for helices and strands: 0 residues in 0 chains, 2304 seeds are put forward Round 1: 139 peptides, 25 chains. Longest chain 12 peptides. Score 0.322 Round 2: 157 peptides, 24 chains. Longest chain 13 peptides. Score 0.399 Round 3: 160 peptides, 22 chains. Longest chain 20 peptides. Score 0.437 Round 4: 157 peptides, 23 chains. Longest chain 17 peptides. Score 0.413 Round 5: 157 peptides, 22 chains. Longest chain 15 peptides. Score 0.428 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 138, 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 2hag-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4712 reflections ( 99.51 % complete ) and 5254 restraints for refining 2254 atoms. 4724 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2999 (Rfree = 0.000) for 2254 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2678 (Rfree = 0.000) for 2239 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2668 (Rfree = 0.000) for 2229 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2615 (Rfree = 0.000) for 2222 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:43:45 GMT 2018 Job finished. TimeTaking 81.06 Used memory is bytes: 21261192