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 1vlc-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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/1vlc-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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 22:22:58 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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 309 and 0 Target number of residues in the AU: 309 Target solvent content: 0.6445 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-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: 150 Cell parameters: 119.541 119.541 57.022 90.000 90.000 120.000 Input sequence file: 1vlc-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2928 target number of atoms Had to go as low as 0.95 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 4.000 Wilson plot Bfac: 74.50 4126 reflections ( 99.61 % complete ) and 0 restraints for refining 3266 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3338 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3189 (Rfree = 0.000) for 3266 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.32 Search for helices and strands: 0 residues in 0 chains, 3338 seeds are put forward Round 1: 152 peptides, 26 chains. Longest chain 14 peptides. Score 0.363 Round 2: 172 peptides, 26 chains. Longest chain 17 peptides. Score 0.433 Round 3: 193 peptides, 24 chains. Longest chain 15 peptides. Score 0.528 Round 4: 181 peptides, 27 chains. Longest chain 15 peptides. Score 0.448 Round 5: 205 peptides, 29 chains. Longest chain 16 peptides. Score 0.496 Taking the results from Round 3 Chains 24, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4126 reflections ( 99.61 % complete ) and 6188 restraints for refining 2645 atoms. 5536 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2817 (Rfree = 0.000) for 2645 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 2: After refmac, R = 0.2203 (Rfree = 0.000) for 2600 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2352 (Rfree = 0.000) for 2572 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2239 (Rfree = 0.000) for 2560 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 5: After refmac, R = 0.2288 (Rfree = 0.000) for 2544 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.17 Search for helices and strands: 0 residues in 0 chains, 2623 seeds are put forward Round 1: 200 peptides, 34 chains. Longest chain 15 peptides. Score 0.409 Round 2: 207 peptides, 32 chains. Longest chain 15 peptides. Score 0.461 Round 3: 212 peptides, 29 chains. Longest chain 15 peptides. Score 0.517 Round 4: 229 peptides, 29 chains. Longest chain 19 peptides. Score 0.565 Round 5: 233 peptides, 29 chains. Longest chain 26 peptides. Score 0.576 Taking the results from Round 5 Chains 31, Residues 204, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4126 reflections ( 99.61 % complete ) and 5785 restraints for refining 2644 atoms. 4966 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2618 (Rfree = 0.000) for 2644 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 7: After refmac, R = 0.2133 (Rfree = 0.000) for 2595 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 8: After refmac, R = 0.2055 (Rfree = 0.000) for 2566 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 9: After refmac, R = 0.2019 (Rfree = 0.000) for 2535 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.1978 (Rfree = 0.000) for 2521 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.16 Search for helices and strands: 0 residues in 0 chains, 2594 seeds are put forward Round 1: 188 peptides, 31 chains. Longest chain 19 peptides. Score 0.413 Round 2: 214 peptides, 33 chains. Longest chain 20 peptides. Score 0.469 Round 3: 204 peptides, 31 chains. Longest chain 27 peptides. Score 0.465 Round 4: 216 peptides, 33 chains. Longest chain 14 peptides. Score 0.475 Round 5: 219 peptides, 30 chains. Longest chain 19 peptides. Score 0.524 Taking the results from Round 5 Chains 31, Residues 189, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4126 reflections ( 99.61 % complete ) and 5870 restraints for refining 2644 atoms. 5111 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2706 (Rfree = 0.000) for 2644 atoms. Found 12 (12 requested) and removed 68 (6 requested) atoms. Cycle 12: After refmac, R = 0.2146 (Rfree = 0.000) for 2559 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2143 (Rfree = 0.000) for 2541 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2037 (Rfree = 0.000) for 2526 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.2127 (Rfree = 0.000) for 2519 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.20 Search for helices and strands: 0 residues in 0 chains, 2612 seeds are put forward Round 1: 201 peptides, 37 chains. Longest chain 13 peptides. Score 0.369 Round 2: 220 peptides, 30 chains. Longest chain 24 peptides. Score 0.527 Round 3: 222 peptides, 31 chains. Longest chain 26 peptides. Score 0.520 Round 4: 214 peptides, 27 chains. Longest chain 25 peptides. Score 0.549 Round 5: 213 peptides, 27 chains. Longest chain 29 peptides. Score 0.546 Taking the results from Round 4 Chains 29, Residues 187, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 4126 reflections ( 99.61 % complete ) and 5528 restraints for refining 2643 atoms. 4687 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2115 (Rfree = 0.000) for 2643 atoms. Found 9 (12 requested) and removed 14 (6 requested) atoms. Cycle 17: After refmac, R = 0.2115 (Rfree = 0.000) for 2610 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 18: After refmac, R = 0.1937 (Rfree = 0.000) for 2587 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.1937 (Rfree = 0.000) for 2577 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.1900 (Rfree = 0.000) for 2561 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.25 Search for helices and strands: 0 residues in 0 chains, 2642 seeds are put forward Round 1: 170 peptides, 34 chains. Longest chain 8 peptides. Score 0.303 Round 2: 195 peptides, 28 chains. Longest chain 17 peptides. Score 0.479 Round 3: 202 peptides, 29 chains. Longest chain 14 peptides. Score 0.487 Round 4: 199 peptides, 28 chains. Longest chain 21 peptides. Score 0.491 Round 5: 205 peptides, 25 chains. Longest chain 22 peptides. Score 0.549 Taking the results from Round 5 Chains 25, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4126 reflections ( 99.61 % complete ) and 6126 restraints for refining 2643 atoms. 5431 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2616 (Rfree = 0.000) for 2643 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2223 (Rfree = 0.000) for 2627 atoms. Found 11 (12 requested) and removed 12 (6 requested) atoms. Cycle 23: After refmac, R = 0.2170 (Rfree = 0.000) for 2624 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 24: After refmac, R = 0.1990 (Rfree = 0.000) for 2615 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1788 (Rfree = 0.000) for 2609 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.23 Search for helices and strands: 0 residues in 0 chains, 2704 seeds are put forward Round 1: 172 peptides, 34 chains. Longest chain 11 peptides. Score 0.310 Round 2: 191 peptides, 32 chains. Longest chain 15 peptides. Score 0.408 Round 3: 193 peptides, 34 chains. Longest chain 21 peptides. Score 0.386 Round 4: 192 peptides, 33 chains. Longest chain 12 peptides. Score 0.397 Round 5: 215 peptides, 37 chains. Longest chain 17 peptides. Score 0.416 Taking the results from Round 5 Chains 37, Residues 178, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4126 reflections ( 99.61 % complete ) and 6094 restraints for refining 2645 atoms. 5385 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2596 (Rfree = 0.000) for 2645 atoms. Found 12 (12 requested) and removed 41 (6 requested) atoms. Cycle 27: After refmac, R = 0.2152 (Rfree = 0.000) for 2602 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2175 (Rfree = 0.000) for 2584 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.2076 (Rfree = 0.000) for 2572 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.1872 (Rfree = 0.000) for 2565 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.26 Search for helices and strands: 0 residues in 0 chains, 2682 seeds are put forward Round 1: 144 peptides, 31 chains. Longest chain 9 peptides. Score 0.251 Round 2: 191 peptides, 34 chains. Longest chain 12 peptides. Score 0.379 Round 3: 187 peptides, 30 chains. Longest chain 15 peptides. Score 0.424 Round 4: 192 peptides, 32 chains. Longest chain 11 peptides. Score 0.412 Round 5: 193 peptides, 31 chains. Longest chain 14 peptides. Score 0.430 Taking the results from Round 5 Chains 31, Residues 162, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4126 reflections ( 99.61 % complete ) and 6166 restraints for refining 2645 atoms. 5530 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2276 (Rfree = 0.000) for 2645 atoms. Found 12 (12 requested) and removed 35 (6 requested) atoms. Cycle 32: After refmac, R = 0.2264 (Rfree = 0.000) for 2592 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 33: After refmac, R = 0.2214 (Rfree = 0.000) for 2573 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.2226 (Rfree = 0.000) for 2565 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.2223 (Rfree = 0.000) for 2558 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.26 Search for helices and strands: 0 residues in 0 chains, 2641 seeds are put forward Round 1: 180 peptides, 39 chains. Longest chain 8 peptides. Score 0.262 Round 2: 191 peptides, 35 chains. Longest chain 10 peptides. Score 0.364 Round 3: 187 peptides, 34 chains. Longest chain 11 peptides. Score 0.365 Round 4: 164 peptides, 30 chains. Longest chain 11 peptides. Score 0.344 Round 5: 183 peptides, 31 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 5 Chains 31, Residues 152, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4126 reflections ( 99.61 % complete ) and 6255 restraints for refining 2644 atoms. 5649 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2218 (Rfree = 0.000) for 2644 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.2314 (Rfree = 0.000) for 2622 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2158 (Rfree = 0.000) for 2609 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.2174 (Rfree = 0.000) for 2602 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2021 (Rfree = 0.000) for 2602 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.27 Search for helices and strands: 0 residues in 0 chains, 2702 seeds are put forward Round 1: 132 peptides, 27 chains. Longest chain 9 peptides. Score 0.270 Round 2: 156 peptides, 25 chains. Longest chain 16 peptides. Score 0.393 Round 3: 158 peptides, 26 chains. Longest chain 13 peptides. Score 0.385 Round 4: 160 peptides, 26 chains. Longest chain 16 peptides. Score 0.392 Round 5: 172 peptides, 25 chains. Longest chain 16 peptides. Score 0.448 Taking the results from Round 5 Chains 25, Residues 147, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4126 reflections ( 99.61 % complete ) and 6239 restraints for refining 2645 atoms. 5665 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2460 (Rfree = 0.000) for 2645 atoms. Found 12 (12 requested) and removed 100 (6 requested) atoms. Cycle 42: After refmac, R = 0.2423 (Rfree = 0.000) for 2526 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 43: After refmac, R = 0.2183 (Rfree = 0.000) for 2515 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 44: After refmac, R = 0.2110 (Rfree = 0.000) for 2510 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 45: After refmac, R = 0.2066 (Rfree = 0.000) for 2499 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.24 Search for helices and strands: 0 residues in 0 chains, 2597 seeds are put forward Round 1: 118 peptides, 25 chains. Longest chain 8 peptides. Score 0.247 Round 2: 150 peptides, 26 chains. Longest chain 13 peptides. Score 0.356 Round 3: 150 peptides, 27 chains. Longest chain 14 peptides. Score 0.340 Round 4: 153 peptides, 30 chains. Longest chain 9 peptides. Score 0.302 Round 5: 156 peptides, 28 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 124, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vlc-4_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (124 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4126 reflections ( 99.61 % complete ) and 5964 restraints for refining 2573 atoms. 5455 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2254 (Rfree = 0.000) for 2573 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2316 (Rfree = 0.000) for 2547 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2140 (Rfree = 0.000) for 2533 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2186 (Rfree = 0.000) for 2518 atoms. TimeTaking 55.58