Sun 23 Dec 22:22:53 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 1vjv-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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/1vjv-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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 22:23:03 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/1vjv-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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 293 and 0 Target number of residues in the AU: 293 Target solvent content: 0.6345 Checking the provided sequence file Detected sequence length: 415 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 415 Adjusted target solvent content: 0.48 Input MTZ file: 1vjv-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: 19 Cell parameters: 49.299 81.862 107.491 90.000 90.000 90.000 Input sequence file: 1vjv-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3320 target number of atoms Had to go as low as 0.60 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: 65.126 4.001 Wilson plot Bfac: 68.41 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3818 reflections ( 96.00 % complete ) and 0 restraints for refining 3653 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3106 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3137 (Rfree = 0.000) for 3653 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 3704 seeds are put forward Round 1: 142 peptides, 27 chains. Longest chain 9 peptides. Score 0.318 Round 2: 190 peptides, 30 chains. Longest chain 13 peptides. Score 0.451 Round 3: 206 peptides, 28 chains. Longest chain 14 peptides. Score 0.533 Round 4: 206 peptides, 27 chains. Longest chain 14 peptides. Score 0.547 Round 5: 209 peptides, 26 chains. Longest chain 16 peptides. Score 0.569 Taking the results from Round 5 Chains 26, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3818 reflections ( 96.00 % complete ) and 6983 restraints for refining 2932 atoms. 6277 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2726 (Rfree = 0.000) for 2932 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 2: After refmac, R = 0.2466 (Rfree = 0.000) for 2836 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 3: After refmac, R = 0.2228 (Rfree = 0.000) for 2791 atoms. Found 3 (13 requested) and removed 19 (6 requested) atoms. Cycle 4: After refmac, R = 0.2183 (Rfree = 0.000) for 2746 atoms. Found 7 (13 requested) and removed 18 (6 requested) atoms. Cycle 5: After refmac, R = 0.2128 (Rfree = 0.000) for 2715 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 2830 seeds are put forward Round 1: 172 peptides, 31 chains. Longest chain 14 peptides. Score 0.369 Round 2: 189 peptides, 23 chains. Longest chain 17 peptides. Score 0.550 Round 3: 214 peptides, 29 chains. Longest chain 20 peptides. Score 0.544 Round 4: 208 peptides, 24 chains. Longest chain 19 peptides. Score 0.593 Round 5: 209 peptides, 27 chains. Longest chain 18 peptides. Score 0.556 Taking the results from Round 4 Chains 24, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3818 reflections ( 96.00 % complete ) and 6295 restraints for refining 2752 atoms. 5583 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2151 (Rfree = 0.000) for 2752 atoms. Found 6 (13 requested) and removed 22 (6 requested) atoms. Cycle 7: After refmac, R = 0.1904 (Rfree = 0.000) for 2711 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.1806 (Rfree = 0.000) for 2690 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.1761 (Rfree = 0.000) for 2683 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.1748 (Rfree = 0.000) for 2672 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 2777 seeds are put forward Round 1: 180 peptides, 31 chains. Longest chain 10 peptides. Score 0.399 Round 2: 180 peptides, 25 chains. Longest chain 15 peptides. Score 0.492 Round 3: 188 peptides, 25 chains. Longest chain 26 peptides. Score 0.519 Round 4: 204 peptides, 27 chains. Longest chain 20 peptides. Score 0.541 Round 5: 198 peptides, 29 chains. Longest chain 15 peptides. Score 0.493 Taking the results from Round 4 Chains 27, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3818 reflections ( 96.00 % complete ) and 6437 restraints for refining 2794 atoms. 5756 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2047 (Rfree = 0.000) for 2794 atoms. Found 11 (13 requested) and removed 14 (6 requested) atoms. Cycle 12: After refmac, R = 0.1859 (Rfree = 0.000) for 2770 atoms. Found 7 (13 requested) and removed 11 (6 requested) atoms. Cycle 13: After refmac, R = 0.1759 (Rfree = 0.000) for 2754 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.1742 (Rfree = 0.000) for 2746 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.1732 (Rfree = 0.000) for 2742 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 2816 seeds are put forward Round 1: 168 peptides, 28 chains. Longest chain 20 peptides. Score 0.403 Round 2: 197 peptides, 28 chains. Longest chain 13 peptides. Score 0.504 Round 3: 198 peptides, 27 chains. Longest chain 15 peptides. Score 0.522 Round 4: 190 peptides, 24 chains. Longest chain 24 peptides. Score 0.539 Round 5: 191 peptides, 25 chains. Longest chain 15 peptides. Score 0.528 Taking the results from Round 4 Chains 24, Residues 166, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3818 reflections ( 96.00 % complete ) and 6458 restraints for refining 2835 atoms. 5767 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2138 (Rfree = 0.000) for 2835 atoms. Found 9 (13 requested) and removed 29 (6 requested) atoms. Cycle 17: After refmac, R = 0.1857 (Rfree = 0.000) for 2797 atoms. Found 5 (13 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.1742 (Rfree = 0.000) for 2780 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1826 (Rfree = 0.000) for 2773 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.1731 (Rfree = 0.000) for 2760 atoms. Found 7 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 2844 seeds are put forward Round 1: 169 peptides, 29 chains. Longest chain 13 peptides. Score 0.390 Round 2: 188 peptides, 28 chains. Longest chain 15 peptides. Score 0.474 Round 3: 188 peptides, 29 chains. Longest chain 13 peptides. Score 0.459 Round 4: 190 peptides, 28 chains. Longest chain 21 peptides. Score 0.481 Round 5: 189 peptides, 30 chains. Longest chain 13 peptides. Score 0.447 Taking the results from Round 4 Chains 28, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3818 reflections ( 96.00 % complete ) and 6571 restraints for refining 2812 atoms. 5951 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2195 (Rfree = 0.000) for 2812 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 22: After refmac, R = 0.2455 (Rfree = 0.000) for 2784 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 23: After refmac, R = 0.2212 (Rfree = 0.000) for 2748 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 24: After refmac, R = 0.2339 (Rfree = 0.000) for 2709 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 25: After refmac, R = 0.2428 (Rfree = 0.000) for 2693 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 2801 seeds are put forward Round 1: 135 peptides, 27 chains. Longest chain 11 peptides. Score 0.289 Round 2: 156 peptides, 27 chains. Longest chain 12 peptides. Score 0.374 Round 3: 172 peptides, 30 chains. Longest chain 13 peptides. Score 0.385 Round 4: 174 peptides, 32 chains. Longest chain 11 peptides. Score 0.360 Round 5: 173 peptides, 31 chains. Longest chain 11 peptides. Score 0.373 Taking the results from Round 3 Chains 30, Residues 142, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3818 reflections ( 96.00 % complete ) and 6012 restraints for refining 2655 atoms. 5464 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2375 (Rfree = 0.000) for 2655 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 27: After refmac, R = 0.2113 (Rfree = 0.000) for 2635 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 28: After refmac, R = 0.2197 (Rfree = 0.000) for 2607 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 29: After refmac, R = 0.2231 (Rfree = 0.000) for 2593 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.2170 (Rfree = 0.000) for 2577 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 2701 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 9 peptides. Score 0.251 Round 2: 126 peptides, 23 chains. Longest chain 11 peptides. Score 0.323 Round 3: 130 peptides, 22 chains. Longest chain 11 peptides. Score 0.357 Round 4: 143 peptides, 23 chains. Longest chain 15 peptides. Score 0.391 Round 5: 148 peptides, 25 chains. Longest chain 17 peptides. Score 0.377 Taking the results from Round 4 Chains 23, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3818 reflections ( 96.00 % complete ) and 5811 restraints for refining 2532 atoms. 5354 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2255 (Rfree = 0.000) for 2532 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2317 (Rfree = 0.000) for 2514 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 33: After refmac, R = 0.2213 (Rfree = 0.000) for 2499 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.2230 (Rfree = 0.000) for 2486 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.2323 (Rfree = 0.000) for 2482 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 2597 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 7 peptides. Score 0.225 Round 2: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.331 Round 3: 140 peptides, 26 chains. Longest chain 10 peptides. Score 0.327 Round 4: 149 peptides, 26 chains. Longest chain 14 peptides. Score 0.363 Round 5: 152 peptides, 27 chains. Longest chain 15 peptides. Score 0.358 Taking the results from Round 4 Chains 26, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3818 reflections ( 96.00 % complete ) and 5991 restraints for refining 2627 atoms. 5525 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2166 (Rfree = 0.000) for 2627 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.2235 (Rfree = 0.000) for 2604 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 38: After refmac, R = 0.2254 (Rfree = 0.000) for 2590 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.2210 (Rfree = 0.000) for 2576 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.2145 (Rfree = 0.000) for 2560 atoms. Found 9 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 2640 seeds are put forward Round 1: 103 peptides, 23 chains. Longest chain 6 peptides. Score 0.221 Round 2: 131 peptides, 24 chains. Longest chain 10 peptides. Score 0.326 Round 3: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.320 Round 4: 121 peptides, 20 chains. Longest chain 11 peptides. Score 0.357 Round 5: 128 peptides, 22 chains. Longest chain 10 peptides. Score 0.349 Taking the results from Round 4 Chains 20, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3818 reflections ( 96.00 % complete ) and 5737 restraints for refining 2522 atoms. 5353 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2203 (Rfree = 0.000) for 2522 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.2170 (Rfree = 0.000) for 2508 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 43: After refmac, R = 0.2090 (Rfree = 0.000) for 2496 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2227 (Rfree = 0.000) for 2493 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 45: After refmac, R = 0.2251 (Rfree = 0.000) for 2480 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.59 Search for helices and strands: 0 residues in 0 chains, 2574 seeds are put forward Round 1: 101 peptides, 24 chains. Longest chain 7 peptides. Score 0.191 Round 2: 108 peptides, 23 chains. Longest chain 9 peptides. Score 0.244 Round 3: 120 peptides, 24 chains. Longest chain 8 peptides. Score 0.279 Round 4: 129 peptides, 24 chains. Longest chain 9 peptides. Score 0.318 Round 5: 126 peptides, 24 chains. Longest chain 10 peptides. Score 0.305 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vjv-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3818 reflections ( 96.00 % complete ) and 5413 restraints for refining 2457 atoms. 5017 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2180 (Rfree = 0.000) for 2457 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2134 (Rfree = 0.000) for 2441 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1926 (Rfree = 0.000) for 2421 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2127 (Rfree = 0.000) for 2407 atoms. TimeTaking 47.8