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 1vqz-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-3.2-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/1vqz-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-3.2-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 19:28:07 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/1vqz-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-3.2-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 272 and 0 Target number of residues in the AU: 272 Target solvent content: 0.5949 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.49 Input MTZ file: 1vqz-3.2-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: 19 Cell parameters: 45.503 70.280 113.629 90.000 90.000 90.000 Input sequence file: 1vqz-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 target number of atoms Had to go as low as 0.70 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: 59.771 3.200 Wilson plot Bfac: 50.34 6399 reflections ( 99.80 % complete ) and 0 restraints for refining 3016 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2600 (Rfree = 0.000) for 3016 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.95 2.99 Search for helices and strands: 0 residues in 0 chains, 3093 seeds are put forward Round 1: 200 peptides, 33 chains. Longest chain 27 peptides. Score 0.478 Round 2: 195 peptides, 26 chains. Longest chain 16 peptides. Score 0.572 Round 3: 216 peptides, 27 chains. Longest chain 22 peptides. Score 0.626 Round 4: 229 peptides, 26 chains. Longest chain 32 peptides. Score 0.677 Round 5: 223 peptides, 23 chains. Longest chain 22 peptides. Score 0.698 Taking the results from Round 5 Chains 23, Residues 200, Estimated correctness of the model 64.8 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6399 reflections ( 99.80 % complete ) and 5168 restraints for refining 2489 atoms. 4307 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2403 (Rfree = 0.000) for 2489 atoms. Found 17 (22 requested) and removed 22 (11 requested) atoms. Cycle 2: After refmac, R = 0.2265 (Rfree = 0.000) for 2462 atoms. Found 12 (22 requested) and removed 12 (11 requested) atoms. Cycle 3: After refmac, R = 0.2173 (Rfree = 0.000) for 2454 atoms. Found 8 (22 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.2080 (Rfree = 0.000) for 2442 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 5: After refmac, R = 0.2000 (Rfree = 0.000) for 2424 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.97 3.01 Search for helices and strands: 0 residues in 0 chains, 2489 seeds are put forward Round 1: 194 peptides, 23 chains. Longest chain 35 peptides. Score 0.614 Round 2: 215 peptides, 26 chains. Longest chain 29 peptides. Score 0.637 Round 3: 236 peptides, 28 chains. Longest chain 28 peptides. Score 0.671 Round 4: 231 peptides, 23 chains. Longest chain 31 peptides. Score 0.718 Round 5: 223 peptides, 22 chains. Longest chain 29 peptides. Score 0.710 Taking the results from Round 4 Chains 23, Residues 208, Estimated correctness of the model 68.9 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6399 reflections ( 99.80 % complete ) and 5013 restraints for refining 2491 atoms. 4069 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2348 (Rfree = 0.000) for 2491 atoms. Found 14 (22 requested) and removed 16 (11 requested) atoms. Cycle 7: After refmac, R = 0.2178 (Rfree = 0.000) for 2476 atoms. Found 15 (22 requested) and removed 12 (11 requested) atoms. Cycle 8: After refmac, R = 0.2032 (Rfree = 0.000) for 2477 atoms. Found 5 (21 requested) and removed 11 (11 requested) atoms. Cycle 9: After refmac, R = 0.1961 (Rfree = 0.000) for 2471 atoms. Found 3 (21 requested) and removed 11 (11 requested) atoms. Cycle 10: After refmac, R = 0.1922 (Rfree = 0.000) for 2463 atoms. Found 3 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.99 3.03 Search for helices and strands: 0 residues in 0 chains, 2541 seeds are put forward Round 1: 189 peptides, 25 chains. Longest chain 20 peptides. Score 0.567 Round 2: 218 peptides, 22 chains. Longest chain 22 peptides. Score 0.697 Round 3: 206 peptides, 23 chains. Longest chain 24 peptides. Score 0.651 Round 4: 225 peptides, 22 chains. Longest chain 21 peptides. Score 0.715 Round 5: 235 peptides, 22 chains. Longest chain 33 peptides. Score 0.738 Taking the results from Round 5 Chains 23, Residues 213, Estimated correctness of the model 72.8 % 1 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6399 reflections ( 99.80 % complete ) and 5051 restraints for refining 2491 atoms. 4111 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2460 (Rfree = 0.000) for 2491 atoms. Found 20 (20 requested) and removed 16 (11 requested) atoms. Cycle 12: After refmac, R = 0.2197 (Rfree = 0.000) for 2483 atoms. Found 5 (19 requested) and removed 12 (11 requested) atoms. Cycle 13: After refmac, R = 0.2087 (Rfree = 0.000) for 2473 atoms. Found 5 (19 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.2007 (Rfree = 0.000) for 2465 atoms. Found 5 (18 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.1921 (Rfree = 0.000) for 2457 atoms. Found 9 (18 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 3.03 Search for helices and strands: 0 residues in 0 chains, 2536 seeds are put forward Round 1: 193 peptides, 26 chains. Longest chain 20 peptides. Score 0.565 Round 2: 215 peptides, 23 chains. Longest chain 29 peptides. Score 0.676 Round 3: 221 peptides, 23 chains. Longest chain 24 peptides. Score 0.693 Round 4: 217 peptides, 24 chains. Longest chain 22 peptides. Score 0.669 Round 5: 219 peptides, 24 chains. Longest chain 24 peptides. Score 0.675 Taking the results from Round 3 Chains 25, Residues 198, Estimated correctness of the model 63.7 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6399 reflections ( 99.80 % complete ) and 5289 restraints for refining 2491 atoms. 4464 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2174 (Rfree = 0.000) for 2491 atoms. Found 13 (18 requested) and removed 14 (11 requested) atoms. Cycle 17: After refmac, R = 0.2030 (Rfree = 0.000) for 2488 atoms. Found 9 (18 requested) and removed 12 (11 requested) atoms. Cycle 18: After refmac, R = 0.1970 (Rfree = 0.000) for 2484 atoms. Found 4 (18 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.1948 (Rfree = 0.000) for 2475 atoms. Found 6 (18 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.1929 (Rfree = 0.000) for 2468 atoms. Found 4 (18 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.12 Search for helices and strands: 0 residues in 0 chains, 2541 seeds are put forward Round 1: 184 peptides, 27 chains. Longest chain 16 peptides. Score 0.517 Round 2: 204 peptides, 25 chains. Longest chain 19 peptides. Score 0.617 Round 3: 212 peptides, 24 chains. Longest chain 26 peptides. Score 0.655 Round 4: 216 peptides, 24 chains. Longest chain 26 peptides. Score 0.666 Round 5: 211 peptides, 24 chains. Longest chain 27 peptides. Score 0.652 Taking the results from Round 4 Chains 24, Residues 192, Estimated correctness of the model 57.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6399 reflections ( 99.80 % complete ) and 5444 restraints for refining 2491 atoms. 4700 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2158 (Rfree = 0.000) for 2491 atoms. Found 12 (18 requested) and removed 14 (11 requested) atoms. Cycle 22: After refmac, R = 0.2050 (Rfree = 0.000) for 2485 atoms. Found 8 (18 requested) and removed 12 (11 requested) atoms. Cycle 23: After refmac, R = 0.1957 (Rfree = 0.000) for 2480 atoms. Found 3 (18 requested) and removed 11 (11 requested) atoms. Cycle 24: After refmac, R = 0.1943 (Rfree = 0.000) for 2471 atoms. Found 5 (18 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.1922 (Rfree = 0.000) for 2464 atoms. Found 5 (18 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 3.06 Search for helices and strands: 0 residues in 0 chains, 2538 seeds are put forward Round 1: 190 peptides, 26 chains. Longest chain 17 peptides. Score 0.555 Round 2: 210 peptides, 21 chains. Longest chain 21 peptides. Score 0.688 Round 3: 211 peptides, 22 chains. Longest chain 26 peptides. Score 0.678 Round 4: 213 peptides, 23 chains. Longest chain 22 peptides. Score 0.671 Round 5: 212 peptides, 20 chains. Longest chain 21 peptides. Score 0.706 Taking the results from Round 5 Chains 20, Residues 192, Estimated correctness of the model 66.4 % 2 chains (38 residues) have been docked in sequence Building loops using Loopy2018 20 chains (192 residues) following loop building 2 chains (38 residues) in sequence following loop building ------------------------------------------------------ 6399 reflections ( 99.80 % complete ) and 5041 restraints for refining 2491 atoms. 4151 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2373 (Rfree = 0.000) for 2491 atoms. Found 18 (18 requested) and removed 19 (11 requested) atoms. Cycle 27: After refmac, R = 0.2191 (Rfree = 0.000) for 2485 atoms. Found 12 (17 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.2112 (Rfree = 0.000) for 2477 atoms. Found 5 (17 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.2059 (Rfree = 0.000) for 2470 atoms. Found 4 (16 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2079 (Rfree = 0.000) for 2457 atoms. Found 8 (16 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.01 3.05 Search for helices and strands: 0 residues in 0 chains, 2516 seeds are put forward Round 1: 174 peptides, 22 chains. Longest chain 20 peptides. Score 0.562 Round 2: 199 peptides, 20 chains. Longest chain 20 peptides. Score 0.671 Round 3: 194 peptides, 21 chains. Longest chain 26 peptides. Score 0.643 Round 4: 201 peptides, 20 chains. Longest chain 22 peptides. Score 0.677 Round 5: 199 peptides, 22 chains. Longest chain 27 peptides. Score 0.644 Taking the results from Round 4 Chains 21, Residues 181, Estimated correctness of the model 60.1 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6399 reflections ( 99.80 % complete ) and 5432 restraints for refining 2491 atoms. 4667 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2289 (Rfree = 0.000) for 2491 atoms. Found 15 (15 requested) and removed 15 (11 requested) atoms. Cycle 32: After refmac, R = 0.2102 (Rfree = 0.000) for 2489 atoms. Found 14 (15 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.1953 (Rfree = 0.000) for 2488 atoms. Found 7 (15 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.1894 (Rfree = 0.000) for 2482 atoms. Found 9 (15 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1891 (Rfree = 0.000) for 2479 atoms. Found 7 (15 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 3.04 Search for helices and strands: 0 residues in 0 chains, 2548 seeds are put forward Round 1: 183 peptides, 25 chains. Longest chain 17 peptides. Score 0.546 Round 2: 198 peptides, 21 chains. Longest chain 21 peptides. Score 0.655 Round 3: 203 peptides, 19 chains. Longest chain 27 peptides. Score 0.695 Round 4: 198 peptides, 23 chains. Longest chain 21 peptides. Score 0.627 Round 5: 192 peptides, 20 chains. Longest chain 29 peptides. Score 0.651 Taking the results from Round 3 Chains 20, Residues 184, Estimated correctness of the model 64.1 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 6399 reflections ( 99.80 % complete ) and 5038 restraints for refining 2490 atoms. 4171 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2260 (Rfree = 0.000) for 2490 atoms. Found 15 (15 requested) and removed 15 (11 requested) atoms. Cycle 37: After refmac, R = 0.2085 (Rfree = 0.000) for 2488 atoms. Found 14 (15 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.2026 (Rfree = 0.000) for 2489 atoms. Found 7 (15 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1933 (Rfree = 0.000) for 2484 atoms. Found 9 (15 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1855 (Rfree = 0.000) for 2482 atoms. Found 8 (15 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.96 3.00 Search for helices and strands: 0 residues in 0 chains, 2543 seeds are put forward Round 1: 181 peptides, 21 chains. Longest chain 27 peptides. Score 0.602 Round 2: 187 peptides, 24 chains. Longest chain 19 peptides. Score 0.576 Round 3: 187 peptides, 22 chains. Longest chain 21 peptides. Score 0.606 Round 4: 191 peptides, 21 chains. Longest chain 28 peptides. Score 0.634 Round 5: 190 peptides, 20 chains. Longest chain 21 peptides. Score 0.645 Taking the results from Round 5 Chains 21, Residues 170, Estimated correctness of the model 52.6 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6399 reflections ( 99.80 % complete ) and 5284 restraints for refining 2491 atoms. 4531 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2144 (Rfree = 0.000) for 2491 atoms. Found 15 (15 requested) and removed 12 (11 requested) atoms. Cycle 42: After refmac, R = 0.2023 (Rfree = 0.000) for 2490 atoms. Found 15 (15 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.1895 (Rfree = 0.000) for 2491 atoms. Found 3 (15 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.1879 (Rfree = 0.000) for 2482 atoms. Found 8 (15 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1869 (Rfree = 0.000) for 2478 atoms. Found 5 (15 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 3.03 Search for helices and strands: 0 residues in 0 chains, 2538 seeds are put forward Round 1: 165 peptides, 20 chains. Longest chain 24 peptides. Score 0.562 Round 2: 176 peptides, 21 chains. Longest chain 28 peptides. Score 0.585 Round 3: 178 peptides, 20 chains. Longest chain 24 peptides. Score 0.607 Round 4: 185 peptides, 20 chains. Longest chain 28 peptides. Score 0.629 Round 5: 179 peptides, 22 chains. Longest chain 28 peptides. Score 0.579 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 165, Estimated correctness of the model 48.6 % 2 chains (34 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 1vqz-3_warpNtrace.pdb as input Building loops using Loopy2018 23 chains (165 residues) following loop building 2 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6399 reflections ( 99.80 % complete ) and 5118 restraints for refining 2491 atoms. 4344 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2136 (Rfree = 0.000) for 2491 atoms. Found 0 (15 requested) and removed 6 (11 requested) atoms. Cycle 47: After refmac, R = 0.2001 (Rfree = 0.000) for 2484 atoms. Found 0 (15 requested) and removed 3 (11 requested) atoms. Cycle 48: After refmac, R = 0.1943 (Rfree = 0.000) for 2479 atoms. Found 0 (15 requested) and removed 2 (11 requested) atoms. Cycle 49: After refmac, R = 0.1869 (Rfree = 0.000) for 2477 atoms. Found 0 (15 requested) and removed 7 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:16:59 GMT 2018 Job finished. TimeTaking 49.03 Used memory is bytes: 19365536