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 1vlc-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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/1vlc-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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/1vlc-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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 335 and 0 Target number of residues in the AU: 335 Target solvent content: 0.6146 Checking the provided sequence file Detected sequence length: 366 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 366 Adjusted target solvent content: 0.58 Input MTZ file: 1vlc-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: 150 Cell parameters: 119.541 119.541 57.022 90.000 90.000 120.000 Input sequence file: 1vlc-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2928 target number of atoms Had to go as low as 0.90 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: 103.526 3.601 Wilson plot Bfac: 58.70 5634 reflections ( 99.72 % complete ) and 0 restraints for refining 3262 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3198 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2248 (Rfree = 0.000) for 3262 atoms. Found 15 (20 requested) and removed 39 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 2.94 Search for helices and strands: 0 residues in 0 chains, 3311 seeds are put forward Round 1: 173 peptides, 31 chains. Longest chain 20 peptides. Score 0.361 Round 2: 222 peptides, 31 chains. Longest chain 22 peptides. Score 0.520 Round 3: 236 peptides, 30 chains. Longest chain 19 peptides. Score 0.572 Round 4: 229 peptides, 30 chains. Longest chain 18 peptides. Score 0.553 Round 5: 229 peptides, 32 chains. Longest chain 14 peptides. Score 0.528 Taking the results from Round 3 Chains 32, Residues 206, Estimated correctness of the model 3.3 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5634 reflections ( 99.72 % complete ) and 5572 restraints for refining 2654 atoms. 4684 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2613 (Rfree = 0.000) for 2654 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 2: After refmac, R = 0.2453 (Rfree = 0.000) for 2629 atoms. Found 11 (17 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.2397 (Rfree = 0.000) for 2614 atoms. Found 6 (16 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2342 (Rfree = 0.000) for 2600 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2237 (Rfree = 0.000) for 2590 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 2.97 Search for helices and strands: 0 residues in 0 chains, 2698 seeds are put forward Round 1: 220 peptides, 36 chains. Longest chain 15 peptides. Score 0.447 Round 2: 234 peptides, 30 chains. Longest chain 18 peptides. Score 0.567 Round 3: 236 peptides, 33 chains. Longest chain 21 peptides. Score 0.535 Round 4: 240 peptides, 30 chains. Longest chain 19 peptides. Score 0.583 Round 5: 232 peptides, 31 chains. Longest chain 24 peptides. Score 0.549 Taking the results from Round 4 Chains 32, Residues 210, Estimated correctness of the model 7.8 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5634 reflections ( 99.72 % complete ) and 5709 restraints for refining 2655 atoms. 4846 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2549 (Rfree = 0.000) for 2655 atoms. Found 13 (17 requested) and removed 17 (8 requested) atoms. Cycle 7: After refmac, R = 0.2447 (Rfree = 0.000) for 2628 atoms. Found 10 (16 requested) and removed 15 (8 requested) atoms. Cycle 8: After refmac, R = 0.2333 (Rfree = 0.000) for 2619 atoms. Found 8 (16 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2288 (Rfree = 0.000) for 2612 atoms. Found 12 (16 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2187 (Rfree = 0.000) for 2607 atoms. Found 8 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 2.99 Search for helices and strands: 0 residues in 0 chains, 2736 seeds are put forward Round 1: 205 peptides, 32 chains. Longest chain 17 peptides. Score 0.454 Round 2: 221 peptides, 25 chains. Longest chain 31 peptides. Score 0.593 Round 3: 224 peptides, 28 chains. Longest chain 19 peptides. Score 0.564 Round 4: 226 peptides, 25 chains. Longest chain 25 peptides. Score 0.606 Round 5: 228 peptides, 27 chains. Longest chain 24 peptides. Score 0.587 Taking the results from Round 4 Chains 26, Residues 201, Estimated correctness of the model 16.9 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 5634 reflections ( 99.72 % complete ) and 5559 restraints for refining 2655 atoms. 4701 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2568 (Rfree = 0.000) for 2655 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2407 (Rfree = 0.000) for 2651 atoms. Found 12 (17 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.2239 (Rfree = 0.000) for 2647 atoms. Found 3 (16 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.2243 (Rfree = 0.000) for 2634 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.2205 (Rfree = 0.000) for 2633 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.04 Search for helices and strands: 0 residues in 0 chains, 2748 seeds are put forward Round 1: 201 peptides, 30 chains. Longest chain 20 peptides. Score 0.470 Round 2: 221 peptides, 25 chains. Longest chain 17 peptides. Score 0.593 Round 3: 224 peptides, 25 chains. Longest chain 24 peptides. Score 0.601 Round 4: 238 peptides, 27 chains. Longest chain 33 peptides. Score 0.613 Round 5: 224 peptides, 27 chains. Longest chain 20 peptides. Score 0.576 Taking the results from Round 4 Chains 29, Residues 211, Estimated correctness of the model 19.6 % 3 chains (55 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5634 reflections ( 99.72 % complete ) and 5295 restraints for refining 2655 atoms. 4280 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2576 (Rfree = 0.000) for 2655 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2276 (Rfree = 0.000) for 2638 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 18: After refmac, R = 0.2216 (Rfree = 0.000) for 2624 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2223 (Rfree = 0.000) for 2616 atoms. Found 6 (16 requested) and removed 16 (8 requested) atoms. Cycle 20: After refmac, R = 0.2206 (Rfree = 0.000) for 2601 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 2.99 Search for helices and strands: 0 residues in 0 chains, 2713 seeds are put forward Round 1: 204 peptides, 31 chains. Longest chain 16 peptides. Score 0.465 Round 2: 211 peptides, 28 chains. Longest chain 24 peptides. Score 0.527 Round 3: 222 peptides, 29 chains. Longest chain 17 peptides. Score 0.546 Round 4: 228 peptides, 27 chains. Longest chain 21 peptides. Score 0.587 Round 5: 214 peptides, 22 chains. Longest chain 26 peptides. Score 0.611 Taking the results from Round 5 Chains 24, Residues 192, Estimated correctness of the model 18.8 % 5 chains (53 residues) have been docked in sequence ------------------------------------------------------ 5634 reflections ( 99.72 % complete ) and 5412 restraints for refining 2653 atoms. 4479 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2583 (Rfree = 0.000) for 2653 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 22: After refmac, R = 0.2283 (Rfree = 0.000) for 2637 atoms. Found 9 (17 requested) and removed 14 (8 requested) atoms. Cycle 23: After refmac, R = 0.2273 (Rfree = 0.000) for 2620 atoms. Found 6 (16 requested) and removed 18 (8 requested) atoms. Cycle 24: After refmac, R = 0.2224 (Rfree = 0.000) for 2605 atoms. Found 9 (16 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.2136 (Rfree = 0.000) for 2596 atoms. Found 8 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.04 Search for helices and strands: 0 residues in 0 chains, 2680 seeds are put forward Round 1: 198 peptides, 30 chains. Longest chain 13 peptides. Score 0.460 Round 2: 210 peptides, 29 chains. Longest chain 12 peptides. Score 0.511 Round 3: 212 peptides, 27 chains. Longest chain 16 peptides. Score 0.543 Round 4: 196 peptides, 27 chains. Longest chain 16 peptides. Score 0.496 Round 5: 207 peptides, 26 chains. Longest chain 18 peptides. Score 0.542 Taking the results from Round 3 Chains 27, Residues 185, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5634 reflections ( 99.72 % complete ) and 5960 restraints for refining 2655 atoms. 5233 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2505 (Rfree = 0.000) for 2655 atoms. Found 13 (17 requested) and removed 12 (8 requested) atoms. Cycle 27: After refmac, R = 0.2327 (Rfree = 0.000) for 2647 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2276 (Rfree = 0.000) for 2636 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.2166 (Rfree = 0.000) for 2629 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2494 (Rfree = 0.000) for 2620 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.02 Search for helices and strands: 0 residues in 0 chains, 2717 seeds are put forward Round 1: 183 peptides, 32 chains. Longest chain 15 peptides. Score 0.381 Round 2: 188 peptides, 28 chains. Longest chain 16 peptides. Score 0.456 Round 3: 202 peptides, 29 chains. Longest chain 27 peptides. Score 0.487 Round 4: 205 peptides, 28 chains. Longest chain 28 peptides. Score 0.509 Round 5: 201 peptides, 27 chains. Longest chain 29 peptides. Score 0.511 Taking the results from Round 5 Chains 27, Residues 174, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5634 reflections ( 99.72 % complete ) and 6039 restraints for refining 2654 atoms. 5341 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2433 (Rfree = 0.000) for 2654 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. Cycle 32: After refmac, R = 0.2351 (Rfree = 0.000) for 2642 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. Cycle 33: After refmac, R = 0.2189 (Rfree = 0.000) for 2642 atoms. Found 6 (16 requested) and removed 15 (8 requested) atoms. Cycle 34: After refmac, R = 0.2069 (Rfree = 0.000) for 2626 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2065 (Rfree = 0.000) for 2616 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 2.99 Search for helices and strands: 0 residues in 0 chains, 2711 seeds are put forward Round 1: 175 peptides, 29 chains. Longest chain 12 peptides. Score 0.398 Round 2: 184 peptides, 28 chains. Longest chain 13 peptides. Score 0.444 Round 3: 185 peptides, 29 chains. Longest chain 12 peptides. Score 0.432 Round 4: 187 peptides, 27 chains. Longest chain 13 peptides. Score 0.468 Round 5: 186 peptides, 26 chains. Longest chain 16 peptides. Score 0.479 Taking the results from Round 5 Chains 26, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5634 reflections ( 99.72 % complete ) and 6104 restraints for refining 2655 atoms. 5490 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2336 (Rfree = 0.000) for 2655 atoms. Found 8 (17 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2246 (Rfree = 0.000) for 2644 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2161 (Rfree = 0.000) for 2640 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2163 (Rfree = 0.000) for 2637 atoms. Found 12 (16 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2044 (Rfree = 0.000) for 2633 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.03 Search for helices and strands: 0 residues in 0 chains, 2759 seeds are put forward Round 1: 167 peptides, 30 chains. Longest chain 13 peptides. Score 0.355 Round 2: 181 peptides, 28 chains. Longest chain 13 peptides. Score 0.434 Round 3: 183 peptides, 26 chains. Longest chain 15 peptides. Score 0.469 Round 4: 200 peptides, 28 chains. Longest chain 14 peptides. Score 0.494 Round 5: 191 peptides, 27 chains. Longest chain 25 peptides. Score 0.480 Taking the results from Round 4 Chains 28, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5634 reflections ( 99.72 % complete ) and 6005 restraints for refining 2655 atoms. 5345 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2259 (Rfree = 0.000) for 2655 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.2176 (Rfree = 0.000) for 2650 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2083 (Rfree = 0.000) for 2640 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 44: After refmac, R = 0.1986 (Rfree = 0.000) for 2634 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1978 (Rfree = 0.000) for 2621 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 2.98 Search for helices and strands: 0 residues in 0 chains, 2714 seeds are put forward Round 1: 145 peptides, 25 chains. Longest chain 15 peptides. Score 0.353 Round 2: 153 peptides, 23 chains. Longest chain 15 peptides. Score 0.414 Round 3: 165 peptides, 24 chains. Longest chain 18 peptides. Score 0.440 Round 4: 162 peptides, 29 chains. Longest chain 11 peptides. Score 0.352 Round 5: 179 peptides, 27 chains. Longest chain 21 peptides. Score 0.442 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 152, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vlc-3_warpNtrace.pdb as input Building loops using Loopy2018 29 chains (152 residues) following loop building 2 chains (19 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 5634 reflections ( 99.72 % complete ) and 5993 restraints for refining 2655 atoms. 5363 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2274 (Rfree = 0.000) for 2655 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2159 (Rfree = 0.000) for 2642 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2106 (Rfree = 0.000) for 2630 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2161 (Rfree = 0.000) for 2621 atoms. Found 0 (16 requested) and removed 7 (8 requested) atoms. Writing output files ... TimeTaking 59.57