Mon 24 Dec 00:12:09 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ogi-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-mrncs ############### 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 00:12:13 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-parrot-mrncs/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-mrncs.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-mrncs.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 3457 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3671 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3264 (Rfree = 0.000) for 3457 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.93 3.83 Search for helices and strands: 0 residues in 0 chains, 3531 seeds are put forward NCS extension: 0 residues added, 3531 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 9 peptides. Score 0.269 Round 2: 153 peptides, 27 chains. Longest chain 13 peptides. Score 0.359 Round 3: 167 peptides, 28 chains. Longest chain 13 peptides. Score 0.396 Round 4: 166 peptides, 25 chains. Longest chain 20 peptides. Score 0.440 Round 5: 182 peptides, 30 chains. Longest chain 15 peptides. Score 0.419 Taking the results from Round 4 Chains 25, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6965 restraints for refining 2832 atoms. 6426 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2589 (Rfree = 0.000) for 2832 atoms. Found 7 (13 requested) and removed 19 (6 requested) atoms. Cycle 2: After refmac, R = 0.2528 (Rfree = 0.000) for 2774 atoms. Found 7 (13 requested) and removed 25 (6 requested) atoms. Cycle 3: After refmac, R = 0.2615 (Rfree = 0.000) for 2731 atoms. Found 11 (13 requested) and removed 24 (6 requested) atoms. Cycle 4: After refmac, R = 0.2422 (Rfree = 0.000) for 2700 atoms. Found 7 (12 requested) and removed 17 (6 requested) atoms. Cycle 5: After refmac, R = 0.2522 (Rfree = 0.000) for 2670 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.89 3.79 Search for helices and strands: 0 residues in 0 chains, 2766 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2781 seeds are put forward Round 1: 137 peptides, 26 chains. Longest chain 14 peptides. Score 0.313 Round 2: 153 peptides, 26 chains. Longest chain 13 peptides. Score 0.376 Round 3: 147 peptides, 24 chains. Longest chain 11 peptides. Score 0.387 Round 4: 156 peptides, 25 chains. Longest chain 16 peptides. Score 0.404 Round 5: 146 peptides, 24 chains. Longest chain 18 peptides. Score 0.383 Taking the results from Round 4 Chains 25, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6256 restraints for refining 2653 atoms. 5757 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2487 (Rfree = 0.000) for 2653 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. Cycle 7: After refmac, R = 0.2277 (Rfree = 0.000) for 2606 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 8: After refmac, R = 0.2330 (Rfree = 0.000) for 2579 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 9: After refmac, R = 0.2225 (Rfree = 0.000) for 2568 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 10: After refmac, R = 0.2173 (Rfree = 0.000) for 2558 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.94 3.84 Search for helices and strands: 0 residues in 0 chains, 2713 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2736 seeds are put forward Round 1: 147 peptides, 29 chains. Longest chain 12 peptides. Score 0.302 Round 2: 169 peptides, 25 chains. Longest chain 17 peptides. Score 0.450 Round 3: 180 peptides, 26 chains. Longest chain 26 peptides. Score 0.473 Round 4: 176 peptides, 29 chains. Longest chain 15 peptides. Score 0.413 Round 5: 184 peptides, 30 chains. Longest chain 21 peptides. Score 0.426 Taking the results from Round 3 Chains 28, Residues 154, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 5471 restraints for refining 2568 atoms. 4852 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2258 (Rfree = 0.000) for 2568 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.2098 (Rfree = 0.000) for 2541 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 13: After refmac, R = 0.1981 (Rfree = 0.000) for 2524 atoms. Found 8 (12 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.1991 (Rfree = 0.000) for 2512 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.1766 (Rfree = 0.000) for 2507 atoms. Found 4 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.93 3.83 Search for helices and strands: 0 residues in 0 chains, 2644 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2665 seeds are put forward Round 1: 143 peptides, 28 chains. Longest chain 8 peptides. Score 0.303 Round 2: 169 peptides, 30 chains. Longest chain 12 peptides. Score 0.371 Round 3: 181 peptides, 28 chains. Longest chain 13 peptides. Score 0.446 Round 4: 173 peptides, 26 chains. Longest chain 12 peptides. Score 0.449 Round 5: 176 peptides, 28 chains. Longest chain 11 peptides. Score 0.428 Taking the results from Round 4 Chains 27, Residues 147, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6094 restraints for refining 2730 atoms. 5488 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2304 (Rfree = 0.000) for 2730 atoms. Found 11 (12 requested) and removed 29 (6 requested) atoms. Cycle 17: After refmac, R = 0.2204 (Rfree = 0.000) for 2691 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 18: After refmac, R = 0.2282 (Rfree = 0.000) for 2666 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 19: After refmac, R = 0.2135 (Rfree = 0.000) for 2652 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 20: After refmac, R = 0.2110 (Rfree = 0.000) for 2640 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.91 3.81 Search for helices and strands: 0 residues in 0 chains, 2759 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2773 seeds are put forward Round 1: 148 peptides, 32 chains. Longest chain 8 peptides. Score 0.254 Round 2: 164 peptides, 29 chains. Longest chain 14 peptides. Score 0.368 Round 3: 157 peptides, 26 chains. Longest chain 14 peptides. Score 0.391 Round 4: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.426 Round 5: 170 peptides, 28 chains. Longest chain 16 peptides. Score 0.407 Taking the results from Round 4 Chains 27, Residues 144, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6001 restraints for refining 2724 atoms. 5421 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2319 (Rfree = 0.000) for 2724 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 22: After refmac, R = 0.2205 (Rfree = 0.000) for 2692 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 23: After refmac, R = 0.2087 (Rfree = 0.000) for 2675 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 24: After refmac, R = 0.1914 (Rfree = 0.000) for 2666 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 25: After refmac, R = 0.1840 (Rfree = 0.000) for 2657 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.95 3.85 Search for helices and strands: 0 residues in 0 chains, 2798 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2816 seeds are put forward Round 1: 137 peptides, 29 chains. Longest chain 12 peptides. Score 0.260 Round 2: 151 peptides, 29 chains. Longest chain 10 peptides. Score 0.318 Round 3: 155 peptides, 26 chains. Longest chain 14 peptides. Score 0.384 Round 4: 167 peptides, 30 chains. Longest chain 10 peptides. Score 0.363 Round 5: 176 peptides, 30 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 5 Chains 30, Residues 146, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6256 restraints for refining 2767 atoms. 5659 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2228 (Rfree = 0.000) for 2767 atoms. Found 12 (13 requested) and removed 27 (6 requested) atoms. Cycle 27: After refmac, R = 0.2129 (Rfree = 0.000) for 2728 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 28: After refmac, R = 0.2070 (Rfree = 0.000) for 2701 atoms. Found 3 (12 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.2111 (Rfree = 0.000) for 2675 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 30: After refmac, R = 0.1908 (Rfree = 0.000) for 2668 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.86 3.76 Search for helices and strands: 0 residues in 0 chains, 2776 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2793 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 7 peptides. Score 0.249 Round 2: 145 peptides, 26 chains. Longest chain 10 peptides. Score 0.345 Round 3: 150 peptides, 27 chains. Longest chain 9 peptides. Score 0.348 Round 4: 158 peptides, 27 chains. Longest chain 9 peptides. Score 0.378 Round 5: 162 peptides, 25 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 5 Chains 26, Residues 137, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6242 restraints for refining 2816 atoms. 5654 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1988 (Rfree = 0.000) for 2816 atoms. Found 11 (13 requested) and removed 19 (6 requested) atoms. Cycle 32: After refmac, R = 0.1984 (Rfree = 0.000) for 2781 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 33: After refmac, R = 0.1888 (Rfree = 0.000) for 2771 atoms. Found 12 (13 requested) and removed 15 (6 requested) atoms. Cycle 34: After refmac, R = 0.2134 (Rfree = 0.000) for 2762 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 35: After refmac, R = 0.2027 (Rfree = 0.000) for 2740 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.86 3.76 Search for helices and strands: 0 residues in 0 chains, 2850 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2866 seeds are put forward Round 1: 145 peptides, 30 chains. Longest chain 8 peptides. Score 0.276 Round 2: 162 peptides, 28 chains. Longest chain 14 peptides. Score 0.377 Round 3: 168 peptides, 27 chains. Longest chain 14 peptides. Score 0.415 Round 4: 159 peptides, 26 chains. Longest chain 14 peptides. Score 0.399 Round 5: 167 peptides, 28 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 3 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6394 restraints for refining 2832 atoms. 5857 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2162 (Rfree = 0.000) for 2832 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 37: After refmac, R = 0.2090 (Rfree = 0.000) for 2791 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 38: After refmac, R = 0.2036 (Rfree = 0.000) for 2766 atoms. Found 12 (13 requested) and removed 17 (6 requested) atoms. Cycle 39: After refmac, R = 0.2001 (Rfree = 0.000) for 2744 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 40: After refmac, R = 0.2025 (Rfree = 0.000) for 2736 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 2860 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2878 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 8 peptides. Score 0.263 Round 2: 119 peptides, 20 chains. Longest chain 14 peptides. Score 0.346 Round 3: 119 peptides, 19 chains. Longest chain 12 peptides. Score 0.364 Round 4: 131 peptides, 21 chains. Longest chain 13 peptides. Score 0.376 Round 5: 131 peptides, 22 chains. Longest chain 14 peptides. Score 0.359 Taking the results from Round 4 Chains 21, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6063 restraints for refining 2721 atoms. 5644 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2048 (Rfree = 0.000) for 2721 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 42: After refmac, R = 0.2112 (Rfree = 0.000) for 2706 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 43: After refmac, R = 0.1946 (Rfree = 0.000) for 2697 atoms. Found 10 (12 requested) and removed 19 (6 requested) atoms. Cycle 44: After refmac, R = 0.2063 (Rfree = 0.000) for 2675 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 45: After refmac, R = 0.1887 (Rfree = 0.000) for 2666 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.90 3.80 Search for helices and strands: 0 residues in 0 chains, 2765 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2780 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 10 peptides. Score 0.256 Round 2: 121 peptides, 23 chains. Longest chain 9 peptides. Score 0.300 Round 3: 109 peptides, 20 chains. Longest chain 11 peptides. Score 0.304 Round 4: 106 peptides, 20 chains. Longest chain 11 peptides. Score 0.291 Round 5: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.309 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 90, 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 5934 restraints for refining 2626 atoms. 5594 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2076 (Rfree = 0.000) for 2626 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1983 (Rfree = 0.000) for 2613 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1888 (Rfree = 0.000) for 2600 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1529 (Rfree = 0.000) for 2587 atoms. TimeTaking 29.27