Mon 24 Dec 07:33:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ogi-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:33:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-noncs/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 262 and 0 Target number of residues in the AU: 262 Target solvent content: 0.6790 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.52 Input MTZ file: 2ogi-4.0-parrot-noncs.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: 4 Cell parameters: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3136 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 63.833 4.001 Wilson plot Bfac: 100.06 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3807 reflections ( 99.76 % complete ) and 0 restraints for refining 3491 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3674 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3256 (Rfree = 0.000) for 3491 atoms. Found 16 (16 requested) and removed 60 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.94 3.84 Search for helices and strands: 0 residues in 0 chains, 3509 seeds are put forward NCS extension: 0 residues added, 3509 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 9 peptides. Score 0.244 Round 2: 165 peptides, 31 chains. Longest chain 14 peptides. Score 0.339 Round 3: 168 peptides, 29 chains. Longest chain 12 peptides. Score 0.383 Round 4: 173 peptides, 29 chains. Longest chain 15 peptides. Score 0.402 Round 5: 171 peptides, 27 chains. Longest chain 15 peptides. Score 0.426 Taking the results from Round 5 Chains 27, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6812 restraints for refining 2828 atoms. 6263 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2622 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 33 (6 requested) atoms. Cycle 2: After refmac, R = 0.2519 (Rfree = 0.000) for 2771 atoms. Found 7 (13 requested) and removed 29 (6 requested) atoms. Cycle 3: After refmac, R = 0.2544 (Rfree = 0.000) for 2722 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 4: After refmac, R = 0.2376 (Rfree = 0.000) for 2683 atoms. Found 9 (12 requested) and removed 15 (6 requested) atoms. Cycle 5: After refmac, R = 0.2444 (Rfree = 0.000) for 2666 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.93 3.83 Search for helices and strands: 0 residues in 0 chains, 2801 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2818 seeds are put forward Round 1: 167 peptides, 32 chains. Longest chain 11 peptides. Score 0.331 Round 2: 163 peptides, 27 chains. Longest chain 15 peptides. Score 0.397 Round 3: 170 peptides, 30 chains. Longest chain 14 peptides. Score 0.375 Round 4: 176 peptides, 29 chains. Longest chain 12 peptides. Score 0.413 Round 5: 178 peptides, 26 chains. Longest chain 15 peptides. Score 0.466 Taking the results from Round 5 Chains 26, Residues 152, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6304 restraints for refining 2804 atoms. 5673 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2375 (Rfree = 0.000) for 2804 atoms. Found 7 (13 requested) and removed 33 (6 requested) atoms. Cycle 7: After refmac, R = 0.2278 (Rfree = 0.000) for 2759 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 8: After refmac, R = 0.2220 (Rfree = 0.000) for 2736 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 9: After refmac, R = 0.2183 (Rfree = 0.000) for 2706 atoms. Found 11 (12 requested) and removed 18 (6 requested) atoms. Cycle 10: After refmac, R = 0.2240 (Rfree = 0.000) for 2688 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.92 3.82 Search for helices and strands: 0 residues in 0 chains, 2792 seeds are put forward NCS extension: 0 residues added, 2792 seeds are put forward Round 1: 151 peptides, 31 chains. Longest chain 10 peptides. Score 0.284 Round 2: 175 peptides, 25 chains. Longest chain 14 peptides. Score 0.471 Round 3: 169 peptides, 28 chains. Longest chain 15 peptides. Score 0.403 Round 4: 177 peptides, 25 chains. Longest chain 19 peptides. Score 0.478 Round 5: 160 peptides, 22 chains. Longest chain 19 peptides. Score 0.466 Taking the results from Round 4 Chains 25, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6206 restraints for refining 2729 atoms. 5623 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2237 (Rfree = 0.000) for 2729 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 12: After refmac, R = 0.2221 (Rfree = 0.000) for 2700 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 13: After refmac, R = 0.2323 (Rfree = 0.000) for 2677 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 14: After refmac, R = 0.2164 (Rfree = 0.000) for 2663 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.2398 (Rfree = 0.000) for 2656 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.93 3.83 Search for helices and strands: 0 residues in 0 chains, 2772 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 2809 seeds are put forward Round 1: 152 peptides, 28 chains. Longest chain 12 peptides. Score 0.339 Round 2: 179 peptides, 25 chains. Longest chain 21 peptides. Score 0.485 Round 3: 183 peptides, 23 chains. Longest chain 22 peptides. Score 0.527 Round 4: 178 peptides, 26 chains. Longest chain 20 peptides. Score 0.466 Round 5: 196 peptides, 24 chains. Longest chain 20 peptides. Score 0.553 Taking the results from Round 5 Chains 24, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6431 restraints for refining 2832 atoms. 5767 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2001 (Rfree = 0.000) for 2832 atoms. Found 10 (13 requested) and removed 24 (6 requested) atoms. Cycle 17: After refmac, R = 0.1918 (Rfree = 0.000) for 2798 atoms. Found 10 (13 requested) and removed 13 (6 requested) atoms. Cycle 18: After refmac, R = 0.2085 (Rfree = 0.000) for 2784 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 19: After refmac, R = 0.2279 (Rfree = 0.000) for 2779 atoms. Found 12 (13 requested) and removed 19 (6 requested) atoms. Cycle 20: After refmac, R = 0.2060 (Rfree = 0.000) for 2764 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 2860 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2883 seeds are put forward Round 1: 142 peptides, 30 chains. Longest chain 7 peptides. Score 0.264 Round 2: 168 peptides, 29 chains. Longest chain 12 peptides. Score 0.383 Round 3: 170 peptides, 28 chains. Longest chain 11 peptides. Score 0.407 Round 4: 176 peptides, 28 chains. Longest chain 13 peptides. Score 0.428 Round 5: 165 peptides, 27 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 4 Chains 28, Residues 148, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6538 restraints for refining 2832 atoms. 5959 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2068 (Rfree = 0.000) for 2832 atoms. Found 12 (13 requested) and removed 20 (6 requested) atoms. Cycle 22: After refmac, R = 0.2126 (Rfree = 0.000) for 2807 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 23: After refmac, R = 0.2381 (Rfree = 0.000) for 2794 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 24: After refmac, R = 0.2064 (Rfree = 0.000) for 2770 atoms. Found 9 (13 requested) and removed 20 (6 requested) atoms. Cycle 25: After refmac, R = 0.2439 (Rfree = 0.000) for 2751 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.96 3.86 Search for helices and strands: 0 residues in 0 chains, 2852 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2868 seeds are put forward Round 1: 115 peptides, 25 chains. Longest chain 9 peptides. Score 0.237 Round 2: 125 peptides, 23 chains. Longest chain 10 peptides. Score 0.317 Round 3: 135 peptides, 25 chains. Longest chain 9 peptides. Score 0.322 Round 4: 137 peptides, 23 chains. Longest chain 17 peptides. Score 0.365 Round 5: 134 peptides, 22 chains. Longest chain 15 peptides. Score 0.371 Taking the results from Round 5 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6547 restraints for refining 2766 atoms. 6121 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2409 (Rfree = 0.000) for 2766 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 27: After refmac, R = 0.2442 (Rfree = 0.000) for 2745 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 28: After refmac, R = 0.2210 (Rfree = 0.000) for 2723 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 29: After refmac, R = 0.2096 (Rfree = 0.000) for 2702 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.2428 (Rfree = 0.000) for 2697 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.94 3.84 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward NCS extension: 0 residues added, 2793 seeds are put forward Round 1: 106 peptides, 24 chains. Longest chain 7 peptides. Score 0.215 Round 2: 126 peptides, 25 chains. Longest chain 8 peptides. Score 0.285 Round 3: 134 peptides, 25 chains. Longest chain 10 peptides. Score 0.318 Round 4: 131 peptides, 25 chains. Longest chain 7 peptides. Score 0.306 Round 5: 126 peptides, 25 chains. Longest chain 9 peptides. Score 0.285 Taking the results from Round 3 Chains 25, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6301 restraints for refining 2704 atoms. 5890 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2240 (Rfree = 0.000) for 2704 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 32: After refmac, R = 0.2310 (Rfree = 0.000) for 2683 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 33: After refmac, R = 0.2189 (Rfree = 0.000) for 2670 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 34: After refmac, R = 0.2259 (Rfree = 0.000) for 2661 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 35: After refmac, R = 0.2084 (Rfree = 0.000) for 2647 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.93 3.83 Search for helices and strands: 0 residues in 0 chains, 2749 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2755 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 8 peptides. Score 0.227 Round 2: 123 peptides, 26 chains. Longest chain 10 peptides. Score 0.254 Round 3: 120 peptides, 24 chains. Longest chain 9 peptides. Score 0.278 Round 4: 128 peptides, 25 chains. Longest chain 10 peptides. Score 0.293 Round 5: 129 peptides, 25 chains. Longest chain 10 peptides. Score 0.298 Taking the results from Round 5 Chains 25, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6035 restraints for refining 2651 atoms. 5644 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2286 (Rfree = 0.000) for 2651 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 37: After refmac, R = 0.2399 (Rfree = 0.000) for 2625 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 38: After refmac, R = 0.2417 (Rfree = 0.000) for 2607 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.2340 (Rfree = 0.000) for 2600 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 40: After refmac, R = 0.2404 (Rfree = 0.000) for 2594 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.94 3.84 Search for helices and strands: 0 residues in 0 chains, 2714 seeds are put forward NCS extension: 0 residues added, 2714 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.222 Round 2: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.280 Round 3: 90 peptides, 17 chains. Longest chain 7 peptides. Score 0.278 Round 4: 100 peptides, 17 chains. Longest chain 11 peptides. Score 0.323 Round 5: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.281 Taking the results from Round 4 Chains 17, Residues 83, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6115 restraints for refining 2639 atoms. 5788 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2602 (Rfree = 0.000) for 2639 atoms. Found 12 (12 requested) and removed 49 (6 requested) atoms. Cycle 42: After refmac, R = 0.2648 (Rfree = 0.000) for 2589 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 43: After refmac, R = 0.2389 (Rfree = 0.000) for 2575 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 44: After refmac, R = 0.1879 (Rfree = 0.000) for 2567 atoms. Found 12 (12 requested) and removed 251 (6 requested) atoms. Cycle 45: After refmac, R = 0.2524 (Rfree = 0.000) for 2325 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.94 3.84 Search for helices and strands: 0 residues in 0 chains, 2424 seeds are put forward NCS extension: 0 residues added, 2424 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.241 Round 2: 118 peptides, 24 chains. Longest chain 7 peptides. Score 0.269 Round 3: 117 peptides, 22 chains. Longest chain 13 peptides. Score 0.301 Round 4: 115 peptides, 22 chains. Longest chain 9 peptides. Score 0.293 Round 5: 117 peptides, 21 chains. Longest chain 10 peptides. Score 0.320 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 96, 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 2ogi-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3807 reflections ( 99.76 % complete ) and 5386 restraints for refining 2454 atoms. 5023 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2253 (Rfree = 0.000) for 2454 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2645 (Rfree = 0.000) for 2443 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2282 (Rfree = 0.000) for 2432 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2400 (Rfree = 0.000) for 2423 atoms. TimeTaking 30.25