Sun 23 Dec 22:22:46 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 1vli-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vli-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vli-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-3.4-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/1vli-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-3.4-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/1vli-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-3.4-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 374 and 0 Target number of residues in the AU: 374 Target solvent content: 0.6578 Checking the provided sequence file Detected sequence length: 385 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 385 Adjusted target solvent content: 0.65 Input MTZ file: 1vli-3.4-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: 154 Cell parameters: 70.614 70.614 205.438 90.000 90.000 120.000 Input sequence file: 1vli-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3080 target number of atoms Had to go as low as 1.10 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: 68.479 3.400 Wilson plot Bfac: 82.80 8675 reflections ( 99.74 % complete ) and 0 restraints for refining 3435 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3640 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3306 (Rfree = 0.000) for 3435 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 2.82 Search for helices and strands: 0 residues in 0 chains, 3500 seeds are put forward Round 1: 198 peptides, 30 chains. Longest chain 14 peptides. Score 0.417 Round 2: 238 peptides, 30 chains. Longest chain 23 peptides. Score 0.519 Round 3: 240 peptides, 24 chains. Longest chain 20 peptides. Score 0.587 Round 4: 253 peptides, 22 chains. Longest chain 31 peptides. Score 0.633 Round 5: 259 peptides, 27 chains. Longest chain 20 peptides. Score 0.597 Taking the results from Round 4 Chains 24, Residues 231, Estimated correctness of the model 39.1 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8675 reflections ( 99.74 % complete ) and 5804 restraints for refining 2796 atoms. 4776 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2821 (Rfree = 0.000) for 2796 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 2: After refmac, R = 0.2538 (Rfree = 0.000) for 2737 atoms. Found 19 (21 requested) and removed 10 (10 requested) atoms. Cycle 3: After refmac, R = 0.2425 (Rfree = 0.000) for 2724 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. Cycle 4: After refmac, R = 0.2347 (Rfree = 0.000) for 2705 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 5: After refmac, R = 0.2304 (Rfree = 0.000) for 2695 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 2.81 Search for helices and strands: 0 residues in 0 chains, 2821 seeds are put forward Round 1: 238 peptides, 27 chains. Longest chain 24 peptides. Score 0.551 Round 2: 265 peptides, 25 chains. Longest chain 21 peptides. Score 0.628 Round 3: 250 peptides, 24 chains. Longest chain 27 peptides. Score 0.608 Round 4: 250 peptides, 20 chains. Longest chain 31 peptides. Score 0.647 Round 5: 267 peptides, 25 chains. Longest chain 37 peptides. Score 0.632 Taking the results from Round 4 Chains 21, Residues 230, Estimated correctness of the model 43.3 % 3 chains (50 residues) have been docked in sequence ------------------------------------------------------ 8675 reflections ( 99.74 % complete ) and 5683 restraints for refining 2800 atoms. 4592 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2505 (Rfree = 0.000) for 2800 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 7: After refmac, R = 0.2344 (Rfree = 0.000) for 2778 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. Cycle 8: After refmac, R = 0.2250 (Rfree = 0.000) for 2763 atoms. Found 12 (20 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.2177 (Rfree = 0.000) for 2753 atoms. Found 10 (20 requested) and removed 13 (10 requested) atoms. Cycle 10: After refmac, R = 0.2116 (Rfree = 0.000) for 2736 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.79 Search for helices and strands: 0 residues in 0 chains, 2846 seeds are put forward Round 1: 247 peptides, 27 chains. Longest chain 34 peptides. Score 0.571 Round 2: 271 peptides, 25 chains. Longest chain 30 peptides. Score 0.640 Round 3: 267 peptides, 24 chains. Longest chain 25 peptides. Score 0.642 Round 4: 271 peptides, 26 chains. Longest chain 26 peptides. Score 0.631 Round 5: 275 peptides, 25 chains. Longest chain 25 peptides. Score 0.648 Taking the results from Round 5 Chains 27, Residues 250, Estimated correctness of the model 43.6 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 8675 reflections ( 99.74 % complete ) and 5407 restraints for refining 2800 atoms. 4216 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2700 (Rfree = 0.000) for 2800 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 12: After refmac, R = 0.2445 (Rfree = 0.000) for 2790 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. Cycle 13: After refmac, R = 0.2362 (Rfree = 0.000) for 2782 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.2538 (Rfree = 0.000) for 2777 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 15: After refmac, R = 0.2207 (Rfree = 0.000) for 2759 atoms. Found 7 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 2.77 Search for helices and strands: 0 residues in 0 chains, 2866 seeds are put forward Round 1: 261 peptides, 28 chains. Longest chain 27 peptides. Score 0.591 Round 2: 280 peptides, 23 chains. Longest chain 42 peptides. Score 0.674 Round 3: 274 peptides, 20 chains. Longest chain 43 peptides. Score 0.690 Round 4: 285 peptides, 22 chains. Longest chain 37 peptides. Score 0.692 Round 5: 268 peptides, 24 chains. Longest chain 28 peptides. Score 0.644 Taking the results from Round 4 Chains 24, Residues 263, Estimated correctness of the model 55.8 % 3 chains (76 residues) have been docked in sequence ------------------------------------------------------ 8675 reflections ( 99.74 % complete ) and 5166 restraints for refining 2800 atoms. 3833 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2619 (Rfree = 0.000) for 2800 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 17: After refmac, R = 0.2412 (Rfree = 0.000) for 2783 atoms. Found 15 (21 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.2326 (Rfree = 0.000) for 2768 atoms. Found 9 (21 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.2253 (Rfree = 0.000) for 2755 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.2227 (Rfree = 0.000) for 2747 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 2.80 Search for helices and strands: 0 residues in 0 chains, 2840 seeds are put forward Round 1: 255 peptides, 27 chains. Longest chain 32 peptides. Score 0.589 Round 2: 263 peptides, 30 chains. Longest chain 23 peptides. Score 0.576 Round 3: 279 peptides, 29 chains. Longest chain 26 peptides. Score 0.619 Round 4: 270 peptides, 24 chains. Longest chain 34 peptides. Score 0.647 Round 5: 249 peptides, 27 chains. Longest chain 24 peptides. Score 0.576 Taking the results from Round 4 Chains 26, Residues 246, Estimated correctness of the model 43.3 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 8675 reflections ( 99.74 % complete ) and 5532 restraints for refining 2800 atoms. 4384 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2583 (Rfree = 0.000) for 2800 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 22: After refmac, R = 0.2380 (Rfree = 0.000) for 2796 atoms. Found 11 (21 requested) and removed 13 (10 requested) atoms. Cycle 23: After refmac, R = 0.2145 (Rfree = 0.000) for 2781 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. Cycle 24: After refmac, R = 0.2117 (Rfree = 0.000) for 2765 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.2025 (Rfree = 0.000) for 2758 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 2.79 Search for helices and strands: 0 residues in 0 chains, 2849 seeds are put forward Round 1: 240 peptides, 26 chains. Longest chain 19 peptides. Score 0.566 Round 2: 263 peptides, 27 chains. Longest chain 19 peptides. Score 0.605 Round 3: 267 peptides, 29 chains. Longest chain 24 peptides. Score 0.594 Round 4: 278 peptides, 28 chains. Longest chain 27 peptides. Score 0.626 Round 5: 269 peptides, 27 chains. Longest chain 23 peptides. Score 0.618 Taking the results from Round 4 Chains 29, Residues 250, Estimated correctness of the model 36.9 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8675 reflections ( 99.74 % complete ) and 5839 restraints for refining 2799 atoms. 4801 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2411 (Rfree = 0.000) for 2799 atoms. Found 18 (21 requested) and removed 14 (10 requested) atoms. Cycle 27: After refmac, R = 0.2226 (Rfree = 0.000) for 2789 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. Cycle 28: After refmac, R = 0.2107 (Rfree = 0.000) for 2774 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2130 (Rfree = 0.000) for 2767 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. Cycle 30: After refmac, R = 0.2093 (Rfree = 0.000) for 2760 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 2.79 Search for helices and strands: 0 residues in 0 chains, 2858 seeds are put forward Round 1: 242 peptides, 34 chains. Longest chain 19 peptides. Score 0.485 Round 2: 241 peptides, 29 chains. Longest chain 19 peptides. Score 0.537 Round 3: 251 peptides, 28 chains. Longest chain 19 peptides. Score 0.570 Round 4: 244 peptides, 23 chains. Longest chain 30 peptides. Score 0.606 Round 5: 251 peptides, 23 chains. Longest chain 40 peptides. Score 0.620 Taking the results from Round 5 Chains 25, Residues 228, Estimated correctness of the model 35.1 % 6 chains (83 residues) have been docked in sequence ------------------------------------------------------ 8675 reflections ( 99.74 % complete ) and 5293 restraints for refining 2800 atoms. 4077 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2715 (Rfree = 0.000) for 2800 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 32: After refmac, R = 0.2383 (Rfree = 0.000) for 2778 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 33: After refmac, R = 0.2178 (Rfree = 0.000) for 2771 atoms. Found 11 (21 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.2182 (Rfree = 0.000) for 2761 atoms. Found 4 (20 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.2115 (Rfree = 0.000) for 2749 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 2.82 Search for helices and strands: 0 residues in 0 chains, 2844 seeds are put forward Round 1: 238 peptides, 28 chains. Longest chain 34 peptides. Score 0.541 Round 2: 253 peptides, 25 chains. Longest chain 24 peptides. Score 0.604 Round 3: 256 peptides, 28 chains. Longest chain 20 peptides. Score 0.581 Round 4: 253 peptides, 26 chains. Longest chain 24 peptides. Score 0.594 Round 5: 262 peptides, 25 chains. Longest chain 33 peptides. Score 0.623 Taking the results from Round 5 Chains 29, Residues 237, Estimated correctness of the model 36.0 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 8675 reflections ( 99.74 % complete ) and 5658 restraints for refining 2800 atoms. 4560 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2431 (Rfree = 0.000) for 2800 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 37: After refmac, R = 0.2219 (Rfree = 0.000) for 2802 atoms. Found 8 (21 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.2126 (Rfree = 0.000) for 2791 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. Cycle 39: After refmac, R = 0.2188 (Rfree = 0.000) for 2774 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.2078 (Rfree = 0.000) for 2762 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 2.79 Search for helices and strands: 0 residues in 0 chains, 2859 seeds are put forward Round 1: 231 peptides, 31 chains. Longest chain 16 peptides. Score 0.491 Round 2: 255 peptides, 30 chains. Longest chain 21 peptides. Score 0.558 Round 3: 246 peptides, 27 chains. Longest chain 21 peptides. Score 0.569 Round 4: 233 peptides, 26 chains. Longest chain 21 peptides. Score 0.551 Round 5: 241 peptides, 29 chains. Longest chain 21 peptides. Score 0.537 Taking the results from Round 3 Chains 28, Residues 219, Estimated correctness of the model 18.2 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8675 reflections ( 99.74 % complete ) and 6078 restraints for refining 2800 atoms. 5183 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2314 (Rfree = 0.000) for 2800 atoms. Found 14 (21 requested) and removed 12 (10 requested) atoms. Cycle 42: After refmac, R = 0.2187 (Rfree = 0.000) for 2795 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2239 (Rfree = 0.000) for 2788 atoms. Found 12 (21 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.2055 (Rfree = 0.000) for 2787 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.2031 (Rfree = 0.000) for 2778 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 2.81 Search for helices and strands: 0 residues in 0 chains, 2874 seeds are put forward Round 1: 225 peptides, 30 chains. Longest chain 20 peptides. Score 0.487 Round 2: 245 peptides, 30 chains. Longest chain 23 peptides. Score 0.535 Round 3: 245 peptides, 28 chains. Longest chain 21 peptides. Score 0.557 Round 4: 244 peptides, 27 chains. Longest chain 21 peptides. Score 0.565 Round 5: 238 peptides, 27 chains. Longest chain 21 peptides. Score 0.551 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 217, Estimated correctness of the model 16.8 % 3 chains (27 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vli-3_warpNtrace.pdb as input Building loops using Loopy2018 29 chains (217 residues) following loop building 3 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8675 reflections ( 99.74 % complete ) and 6001 restraints for refining 2800 atoms. 5053 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2356 (Rfree = 0.000) for 2800 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2209 (Rfree = 0.000) for 2785 atoms. Found 0 (21 requested) and removed 8 (10 requested) atoms. Cycle 48: After refmac, R = 0.2200 (Rfree = 0.000) for 2772 atoms. Found 0 (20 requested) and removed 1 (10 requested) atoms. Cycle 49: After refmac, R = 0.2250 (Rfree = 0.000) for 2770 atoms. Found 0 (20 requested) and removed 2 (10 requested) atoms. Writing output files ... TimeTaking 57.45