Sun 23 Dec 22:22:43 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vli-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vli-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-3.8-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 22:22:53 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-3.8-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 354 and 0 Target number of residues in the AU: 354 Target solvent content: 0.6761 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 97.26 6286 reflections ( 99.64 % complete ) and 0 restraints for refining 3436 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3743 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3539 (Rfree = 0.000) for 3436 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3511 seeds are put forward Round 1: 194 peptides, 31 chains. Longest chain 14 peptides. Score 0.393 Round 2: 198 peptides, 23 chains. Longest chain 21 peptides. Score 0.501 Round 3: 214 peptides, 22 chains. Longest chain 31 peptides. Score 0.551 Round 4: 225 peptides, 25 chains. Longest chain 21 peptides. Score 0.543 Round 5: 237 peptides, 25 chains. Longest chain 21 peptides. Score 0.570 Taking the results from Round 5 Chains 31, Residues 212, Estimated correctness of the model 0.0 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6286 reflections ( 99.64 % complete ) and 6024 restraints for refining 2785 atoms. 5071 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2786 (Rfree = 0.000) for 2785 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 2: After refmac, R = 0.2889 (Rfree = 0.000) for 2722 atoms. Found 13 (15 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.2686 (Rfree = 0.000) for 2702 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 4: After refmac, R = 0.2662 (Rfree = 0.000) for 2690 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 5: After refmac, R = 0.2451 (Rfree = 0.000) for 2684 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 3.08 Search for helices and strands: 0 residues in 0 chains, 2808 seeds are put forward Round 1: 212 peptides, 28 chains. Longest chain 19 peptides. Score 0.478 Round 2: 222 peptides, 22 chains. Longest chain 35 peptides. Score 0.569 Round 3: 227 peptides, 22 chains. Longest chain 34 peptides. Score 0.580 Round 4: 221 peptides, 23 chains. Longest chain 21 peptides. Score 0.556 Round 5: 205 peptides, 22 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 3 Chains 26, Residues 205, Estimated correctness of the model 0.0 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 6286 reflections ( 99.64 % complete ) and 5632 restraints for refining 2786 atoms. 4629 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2685 (Rfree = 0.000) for 2786 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 7: After refmac, R = 0.2518 (Rfree = 0.000) for 2768 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 8: After refmac, R = 0.2390 (Rfree = 0.000) for 2750 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 9: After refmac, R = 0.2346 (Rfree = 0.000) for 2735 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 10: After refmac, R = 0.2198 (Rfree = 0.000) for 2732 atoms. Found 7 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.05 Search for helices and strands: 0 residues in 0 chains, 2822 seeds are put forward Round 1: 205 peptides, 27 chains. Longest chain 25 peptides. Score 0.471 Round 2: 221 peptides, 27 chains. Longest chain 28 peptides. Score 0.511 Round 3: 219 peptides, 25 chains. Longest chain 25 peptides. Score 0.529 Round 4: 234 peptides, 26 chains. Longest chain 39 peptides. Score 0.553 Round 5: 235 peptides, 22 chains. Longest chain 51 peptides. Score 0.597 Taking the results from Round 5 Chains 24, Residues 213, Estimated correctness of the model 0.0 % 2 chains (60 residues) have been docked in sequence ------------------------------------------------------ 6286 reflections ( 99.64 % complete ) and 5567 restraints for refining 2784 atoms. 4511 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2585 (Rfree = 0.000) for 2784 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 12: After refmac, R = 0.2372 (Rfree = 0.000) for 2730 atoms. Found 11 (15 requested) and removed 14 (7 requested) atoms. Cycle 13: After refmac, R = 0.2299 (Rfree = 0.000) for 2716 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 14: After refmac, R = 0.2260 (Rfree = 0.000) for 2711 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2219 (Rfree = 0.000) for 2703 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 3.08 Search for helices and strands: 0 residues in 0 chains, 2790 seeds are put forward Round 1: 212 peptides, 24 chains. Longest chain 35 peptides. Score 0.524 Round 2: 224 peptides, 24 chains. Longest chain 32 peptides. Score 0.552 Round 3: 225 peptides, 23 chains. Longest chain 39 peptides. Score 0.565 Round 4: 223 peptides, 22 chains. Longest chain 24 peptides. Score 0.571 Round 5: 225 peptides, 23 chains. Longest chain 31 peptides. Score 0.565 Taking the results from Round 4 Chains 26, Residues 201, Estimated correctness of the model 0.0 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 6286 reflections ( 99.64 % complete ) and 5877 restraints for refining 2785 atoms. 4948 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2757 (Rfree = 0.000) for 2785 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 17: After refmac, R = 0.2529 (Rfree = 0.000) for 2745 atoms. Found 10 (15 requested) and removed 14 (7 requested) atoms. Cycle 18: After refmac, R = 0.2306 (Rfree = 0.000) for 2714 atoms. Found 9 (15 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.2276 (Rfree = 0.000) for 2700 atoms. Found 9 (14 requested) and removed 12 (7 requested) atoms. Cycle 20: After refmac, R = 0.2210 (Rfree = 0.000) for 2686 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.07 Search for helices and strands: 0 residues in 0 chains, 2801 seeds are put forward Round 1: 203 peptides, 32 chains. Longest chain 13 peptides. Score 0.406 Round 2: 209 peptides, 26 chains. Longest chain 17 peptides. Score 0.493 Round 3: 219 peptides, 25 chains. Longest chain 18 peptides. Score 0.529 Round 4: 219 peptides, 26 chains. Longest chain 21 peptides. Score 0.518 Round 5: 222 peptides, 24 chains. Longest chain 16 peptides. Score 0.547 Taking the results from Round 5 Chains 24, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6286 reflections ( 99.64 % complete ) and 6392 restraints for refining 2786 atoms. 5624 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2585 (Rfree = 0.000) for 2786 atoms. Found 15 (15 requested) and removed 82 (7 requested) atoms. Cycle 22: After refmac, R = 0.2374 (Rfree = 0.000) for 2672 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 23: After refmac, R = 0.2237 (Rfree = 0.000) for 2658 atoms. Found 13 (14 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.2070 (Rfree = 0.000) for 2657 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2001 (Rfree = 0.000) for 2645 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.04 Search for helices and strands: 0 residues in 0 chains, 2779 seeds are put forward Round 1: 216 peptides, 32 chains. Longest chain 16 peptides. Score 0.441 Round 2: 233 peptides, 29 chains. Longest chain 25 peptides. Score 0.518 Round 3: 236 peptides, 27 chains. Longest chain 27 peptides. Score 0.547 Round 4: 249 peptides, 31 chains. Longest chain 21 peptides. Score 0.534 Round 5: 243 peptides, 29 chains. Longest chain 27 peptides. Score 0.541 Taking the results from Round 3 Chains 27, Residues 209, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6286 reflections ( 99.64 % complete ) and 6012 restraints for refining 2786 atoms. 5156 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2361 (Rfree = 0.000) for 2786 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 27: After refmac, R = 0.2168 (Rfree = 0.000) for 2767 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.2083 (Rfree = 0.000) for 2756 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.2052 (Rfree = 0.000) for 2749 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.2037 (Rfree = 0.000) for 2744 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.06 Search for helices and strands: 0 residues in 0 chains, 2840 seeds are put forward Round 1: 200 peptides, 34 chains. Longest chain 15 peptides. Score 0.372 Round 2: 231 peptides, 31 chains. Longest chain 15 peptides. Score 0.491 Round 3: 238 peptides, 30 chains. Longest chain 22 peptides. Score 0.519 Round 4: 234 peptides, 26 chains. Longest chain 27 peptides. Score 0.553 Round 5: 234 peptides, 27 chains. Longest chain 28 peptides. Score 0.542 Taking the results from Round 4 Chains 26, Residues 208, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6286 reflections ( 99.64 % complete ) and 5980 restraints for refining 2786 atoms. 5081 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2543 (Rfree = 0.000) for 2786 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 32: After refmac, R = 0.2329 (Rfree = 0.000) for 2772 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.2256 (Rfree = 0.000) for 2768 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.2227 (Rfree = 0.000) for 2757 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 35: After refmac, R = 0.2195 (Rfree = 0.000) for 2749 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.04 Search for helices and strands provided no result - WARNING Search for helices and strands: 0 residues in 0 chains, 2763 seeds are put forward Round 1: 189 peptides, 32 chains. Longest chain 13 peptides. Score 0.366 Round 2: 215 peptides, 27 chains. Longest chain 18 peptides. Score 0.497 Round 3: 223 peptides, 27 chains. Longest chain 19 peptides. Score 0.516 Round 4: 232 peptides, 23 chains. Longest chain 28 peptides. Score 0.580 Round 5: 243 peptides, 24 chains. Longest chain 30 peptides. Score 0.593 Taking the results from Round 5 Chains 31, Residues 219, Estimated correctness of the model 0.0 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ 6286 reflections ( 99.64 % complete ) and 5490 restraints for refining 2786 atoms. 4386 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2367 (Rfree = 0.000) for 2786 atoms. Found 12 (15 requested) and removed 13 (7 requested) atoms. Cycle 37: After refmac, R = 0.2149 (Rfree = 0.000) for 2768 atoms. Found 10 (15 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.2080 (Rfree = 0.000) for 2761 atoms. Found 9 (15 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.2014 (Rfree = 0.000) for 2754 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.1960 (Rfree = 0.000) for 2744 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.05 Search for helices and strands: 0 residues in 0 chains, 2860 seeds are put forward Round 1: 200 peptides, 31 chains. Longest chain 14 peptides. Score 0.410 Round 2: 217 peptides, 26 chains. Longest chain 26 peptides. Score 0.513 Round 3: 209 peptides, 23 chains. Longest chain 37 peptides. Score 0.528 Round 4: 214 peptides, 24 chains. Longest chain 26 peptides. Score 0.528 Round 5: 213 peptides, 21 chains. Longest chain 38 peptides. Score 0.559 Taking the results from Round 5 Chains 23, Residues 192, Estimated correctness of the model 0.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6286 reflections ( 99.64 % complete ) and 5916 restraints for refining 2786 atoms. 5041 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2376 (Rfree = 0.000) for 2786 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.2178 (Rfree = 0.000) for 2770 atoms. Found 6 (15 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.2114 (Rfree = 0.000) for 2762 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.2091 (Rfree = 0.000) for 2755 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.2057 (Rfree = 0.000) for 2747 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.08 Search for helices and strands: 0 residues in 0 chains, 2833 seeds are put forward Round 1: 209 peptides, 33 chains. Longest chain 19 peptides. Score 0.410 Round 2: 219 peptides, 28 chains. Longest chain 29 peptides. Score 0.495 Round 3: 218 peptides, 27 chains. Longest chain 27 peptides. Score 0.504 Round 4: 229 peptides, 26 chains. Longest chain 27 peptides. Score 0.541 Round 5: 223 peptides, 26 chains. Longest chain 28 peptides. Score 0.527 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 203, Estimated correctness of the model 0.0 % 3 chains (38 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 1vli-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (203 residues) following loop building 3 chains (38 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6286 reflections ( 99.64 % complete ) and 5880 restraints for refining 2786 atoms. 4923 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2429 (Rfree = 0.000) for 2786 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2270 (Rfree = 0.000) for 2766 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2220 (Rfree = 0.000) for 2755 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2194 (Rfree = 0.000) for 2746 atoms. TimeTaking 54.47