Starting phenix.real_space_refine on Mon Sep 14 18:05:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ua2_20704/09_2026/6ua2_20704.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ua2_20704/09_2026/6ua2_20704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ua2_20704/09_2026/6ua2_20704.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ua2_20704/09_2026/6ua2_20704.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ua2_20704/09_2026/6ua2_20704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ua2_20704/09_2026/6ua2_20704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ua2_20704/09_2026/6ua2_20704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ua2_20704/09_2026/6ua2_20704.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.091 sd= 2.383 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 84 5.49 5 S 176 5.16 5 C 19696 2.51 5 N 5420 2.21 5 O 6284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31660 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "D" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "E" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "F" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "G" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "H" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'ATP': 3, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ATP': 1, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'ATP': 3, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ATP': 1, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 7.50, per 1000 atoms: 0.24 Number of scatterers: 31660 At special positions: 0 Unit cell: (143.85, 148.05, 142.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 P 84 15.00 O 6284 8.00 N 5420 7.00 C 19696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 48 sheets defined 37.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.562A pdb=" N GLN A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.704A pdb=" N ILE A 163 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.924A pdb=" N GLU A 177 " --> pdb=" O PHE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.726A pdb=" N ASP A 184 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 185 " --> pdb=" O ARG A 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 185' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.692A pdb=" N LYS A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.208A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.507A pdb=" N ILE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.824A pdb=" N LYS A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.722A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 455 Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.885A pdb=" N GLY A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 removed outlier: 3.592A pdb=" N ASN B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.581A pdb=" N PHE B 35 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 108 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.894A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.558A pdb=" N ALA B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.571A pdb=" N LYS B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 267 removed outlier: 4.519A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.633A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.518A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.723A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 455 removed outlier: 3.663A pdb=" N LYS B 455 " --> pdb=" O SER B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 455' Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.565A pdb=" N THR C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.633A pdb=" N GLN C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.542A pdb=" N VAL C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 removed outlier: 3.589A pdb=" N ALA C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.805A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 removed outlier: 4.067A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 343 through 348 Processing helix chain 'C' and resid 348 through 355 Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.964A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 375 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 452 through 454 No H-bonds generated for 'chain 'C' and resid 452 through 454' Processing helix chain 'C' and resid 455 through 470 removed outlier: 3.662A pdb=" N TYR C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.506A pdb=" N LEU D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 110 removed outlier: 4.334A pdb=" N LYS D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 removed outlier: 4.193A pdb=" N PHE D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 removed outlier: 4.077A pdb=" N ILE D 163 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.805A pdb=" N ILE D 178 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 266 removed outlier: 3.826A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.990A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 removed outlier: 4.998A pdb=" N GLU D 500 " --> pdb=" O SER D 496 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 removed outlier: 3.565A pdb=" N SER N 7 " --> pdb=" O ASP N 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 109 removed outlier: 3.563A pdb=" N GLN E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 136 removed outlier: 3.531A pdb=" N VAL E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.655A pdb=" N ILE E 163 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.969A pdb=" N GLU E 177 " --> pdb=" O PHE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 185 removed outlier: 3.697A pdb=" N ASP E 184 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 185 " --> pdb=" O ARG E 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 181 through 185' Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 233 removed outlier: 3.697A pdb=" N LYS E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 267 removed outlier: 4.252A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.862A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.946A pdb=" N LYS E 349 " --> pdb=" O THR E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.707A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 494 through 502 removed outlier: 3.809A pdb=" N GLY E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.533A pdb=" N ASN F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 108 Processing helix chain 'F' and resid 126 through 138 removed outlier: 3.958A pdb=" N VAL F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 193 through 205 removed outlier: 3.562A pdb=" N ALA F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 267 removed outlier: 4.513A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 removed outlier: 3.659A pdb=" N ILE F 284 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.502A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.641A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 455 removed outlier: 3.715A pdb=" N LYS F 455 " --> pdb=" O SER F 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 452 through 455' Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.633A pdb=" N THR G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 108 removed outlier: 3.624A pdb=" N GLN G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 138 removed outlier: 3.511A pdb=" N VAL G 130 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 203 removed outlier: 3.675A pdb=" N ALA G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 229 Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 267 removed outlier: 3.798A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 292 removed outlier: 4.079A pdb=" N ILE G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 343 through 348 Processing helix chain 'G' and resid 348 through 355 Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.972A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS G 375 " --> pdb=" O GLY G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 416 through 420 Processing helix chain 'G' and resid 452 through 454 No H-bonds generated for 'chain 'G' and resid 452 through 454' Processing helix chain 'G' and resid 455 through 470 removed outlier: 3.663A pdb=" N TYR G 459 " --> pdb=" O LYS G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 495 through 500 Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 75 through 84 Processing helix chain 'H' and resid 96 through 110 removed outlier: 4.217A pdb=" N LYS H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 134 Processing helix chain 'H' and resid 159 through 163 removed outlier: 4.025A pdb=" N ILE H 163 " --> pdb=" O SER H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 225 through 229 Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 266 removed outlier: 3.845A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.983A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 369 through 378 Processing helix chain 'H' and resid 452 through 455 removed outlier: 3.500A pdb=" N LYS H 455 " --> pdb=" O SER H 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 452 through 455' Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 removed outlier: 4.951A pdb=" N GLU H 500 " --> pdb=" O SER H 496 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 6 removed outlier: 3.591A pdb=" N TYR I 4 " --> pdb=" O MET I 1 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE I 6 " --> pdb=" O ASP I 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 removed outlier: 3.595A pdb=" N SER J 7 " --> pdb=" O ASP J 3 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.902A pdb=" N GLU A 491 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.569A pdb=" N ILE A 144 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 189 removed outlier: 5.557A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.087A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.535A pdb=" N SER A 403 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU D 510 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 4.066A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 66 removed outlier: 5.991A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 145 Processing sheet with id=AB2, first strand: chain 'B' and resid 188 through 189 removed outlier: 5.815A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 493 removed outlier: 7.824A pdb=" N LYS B 492 " --> pdb=" O GLY C 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 508 through 510 removed outlier: 4.389A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.611A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 7.370A pdb=" N ILE C 142 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE C 157 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 144 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 211 through 212 removed outlier: 7.527A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.575A pdb=" N VAL D 447 " --> pdb=" O LYS D 409 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 409 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 142 through 145 removed outlier: 6.752A pdb=" N ILE D 142 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE D 157 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE D 144 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.110A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.055A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLY D 302 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.898A pdb=" N GLU E 491 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.610A pdb=" N ILE E 144 " --> pdb=" O GLY E 156 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 188 through 189 removed outlier: 5.575A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.063A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N GLY E 302 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.531A pdb=" N SER E 403 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU H 510 " --> pdb=" O SER E 444 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.912A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 removed outlier: 8.823A pdb=" N GLY G 29 " --> pdb=" O PHE F 490 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LYS F 492 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 66 removed outlier: 6.183A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 5.807A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 508 through 509 Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 66 removed outlier: 6.599A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 removed outlier: 7.631A pdb=" N ILE G 142 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE G 157 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE G 144 " --> pdb=" O VAL G 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 211 through 212 removed outlier: 7.517A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.533A pdb=" N VAL H 447 " --> pdb=" O LYS H 409 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS H 409 " --> pdb=" O VAL H 447 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'H' and resid 88 through 89 removed outlier: 4.212A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY H 302 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 6.684A pdb=" N ILE H 142 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE H 157 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE H 144 " --> pdb=" O VAL H 155 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 188 through 189 removed outlier: 6.410A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5296 1.29 - 1.42: 7667 1.42 - 1.55: 18727 1.55 - 1.68: 222 1.68 - 1.81: 300 Bond restraints: 32212 Sorted by residual: bond pdb=" C2' ATP F 603 " pdb=" C3' ATP F 603 " ideal model delta sigma weight residual 1.531 1.239 0.292 1.20e-02 6.94e+03 5.91e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.240 0.291 1.20e-02 6.94e+03 5.86e+02 bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.245 0.286 1.20e-02 6.94e+03 5.68e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.246 0.285 1.20e-02 6.94e+03 5.66e+02 bond pdb=" C2' ATP C 601 " pdb=" C3' ATP C 601 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.61e+02 ... (remaining 32207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 42568 4.49 - 8.97: 929 8.97 - 13.46: 127 13.46 - 17.94: 50 17.94 - 22.43: 38 Bond angle restraints: 43712 Sorted by residual: angle pdb=" PB ATP F 603 " pdb=" O3B ATP F 603 " pdb=" PG ATP F 603 " ideal model delta sigma weight residual 139.87 117.44 22.43 1.00e+00 1.00e+00 5.03e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 117.74 22.13 1.00e+00 1.00e+00 4.90e+02 angle pdb=" PB ATP H 601 " pdb=" O3B ATP H 601 " pdb=" PG ATP H 601 " ideal model delta sigma weight residual 139.87 118.03 21.84 1.00e+00 1.00e+00 4.77e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 118.79 21.08 1.00e+00 1.00e+00 4.44e+02 angle pdb=" PA ATP C 605 " pdb=" O3A ATP C 605 " pdb=" PB ATP C 605 " ideal model delta sigma weight residual 136.83 117.23 19.60 1.00e+00 1.00e+00 3.84e+02 ... (remaining 43707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 18491 34.69 - 69.39: 509 69.39 - 104.08: 30 104.08 - 138.78: 17 138.78 - 173.47: 13 Dihedral angle restraints: 19060 sinusoidal: 7652 harmonic: 11408 Sorted by residual: dihedral pdb=" CA SER N 11 " pdb=" C SER N 11 " pdb=" N TYR N 12 " pdb=" CA TYR N 12 " ideal model delta harmonic sigma weight residual 180.00 139.54 40.46 0 5.00e+00 4.00e-02 6.55e+01 dihedral pdb=" CA GLY O 9 " pdb=" C GLY O 9 " pdb=" N THR O 10 " pdb=" CA THR O 10 " ideal model delta harmonic sigma weight residual -180.00 -141.00 -39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA GLY K 9 " pdb=" C GLY K 9 " pdb=" N THR K 10 " pdb=" CA THR K 10 " ideal model delta harmonic sigma weight residual 180.00 -141.48 -38.52 0 5.00e+00 4.00e-02 5.94e+01 ... (remaining 19057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3845 0.091 - 0.181: 950 0.181 - 0.272: 154 0.272 - 0.362: 27 0.362 - 0.453: 8 Chirality restraints: 4984 Sorted by residual: chirality pdb=" CB ILE F 300 " pdb=" CA ILE F 300 " pdb=" CG1 ILE F 300 " pdb=" CG2 ILE F 300 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CB ILE B 300 " pdb=" CA ILE B 300 " pdb=" CG1 ILE B 300 " pdb=" CG2 ILE B 300 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CB VAL E 479 " pdb=" CA VAL E 479 " pdb=" CG1 VAL E 479 " pdb=" CG2 VAL E 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 4981 not shown) Planarity restraints: 5452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 359 " 0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 360 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 104 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C VAL F 104 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL F 104 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG F 105 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 104 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C VAL B 104 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL B 104 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG B 105 " -0.018 2.00e-02 2.50e+03 ... (remaining 5449 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4356 2.73 - 3.27: 33394 3.27 - 3.82: 59903 3.82 - 4.36: 68016 4.36 - 4.90: 105544 Nonbonded interactions: 271213 Sorted by model distance: nonbonded pdb=" O HIS A 504 " pdb=" OG SER B 329 " model vdw 2.191 3.040 nonbonded pdb=" OG SER G 475 " pdb=" OE1 GLN G 478 " model vdw 2.218 3.040 nonbonded pdb=" OG SER C 475 " pdb=" OE1 GLN C 478 " model vdw 2.219 3.040 nonbonded pdb=" OG SER E 475 " pdb=" OE1 GLN E 478 " model vdw 2.229 3.040 nonbonded pdb=" O THR D 393 " pdb=" OH TYR D 400 " model vdw 2.235 3.040 ... (remaining 271208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 514) selection = (chain 'B' and resid 11 through 514) selection = (chain 'C' and resid 11 through 514) selection = (chain 'D' and resid 11 through 514) selection = (chain 'E' and resid 11 through 514) selection = (chain 'F' and resid 11 through 514) selection = (chain 'G' and resid 11 through 514) selection = (chain 'H' and resid 11 through 514) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.000 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.296 32220 Z= 1.022 Angle : 1.758 22.429 43712 Z= 1.033 Chirality : 0.082 0.453 4984 Planarity : 0.008 0.081 5452 Dihedral : 16.735 173.474 11780 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.27 % Favored : 88.68 % Rotamer: Outliers : 4.10 % Allowed : 15.62 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 1.47 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.10), residues: 3968 helix: -3.55 (0.10), residues: 1174 sheet: -3.44 (0.21), residues: 404 loop : -3.01 (0.11), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG D 128 TYR 0.041 0.004 TYR F 233 PHE 0.038 0.004 PHE E 401 HIS 0.015 0.004 HIS F 504 Details of bonding type rmsd/Z covalent geometry : bond 0.01748 / 1.02 (32212) covalent geometry : angle 1.75843 / 1.03 (43712) hydrogen bonds : bond 0.21040 / 14.04 ( 966) hydrogen bonds : angle 9.28298 / 6.40 ( 2655) Misc. bond : bond 0.00086 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1429 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.9042 (t70) cc_final: 0.8465 (t70) REVERT: A 32 TYR cc_start: 0.9141 (m-80) cc_final: 0.8535 (m-80) REVERT: A 36 LEU cc_start: 0.9426 (tp) cc_final: 0.8756 (tp) REVERT: A 38 LEU cc_start: 0.9668 (mm) cc_final: 0.9104 (mm) REVERT: A 48 GLN cc_start: 0.9392 (mm-40) cc_final: 0.9108 (mt0) REVERT: A 108 LYS cc_start: 0.9502 (tptp) cc_final: 0.9112 (mmtt) REVERT: A 150 MET cc_start: 0.8262 (tmt) cc_final: 0.8038 (tpt) REVERT: A 158 ILE cc_start: 0.8480 (mm) cc_final: 0.7979 (tp) REVERT: A 194 LEU cc_start: 0.9628 (mm) cc_final: 0.9193 (pp) REVERT: A 224 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7369 (mmt-90) REVERT: A 246 CYS cc_start: 0.9478 (t) cc_final: 0.9277 (t) REVERT: A 256 ASP cc_start: 0.9292 (p0) cc_final: 0.8950 (p0) REVERT: A 262 LEU cc_start: 0.9578 (pt) cc_final: 0.9056 (mt) REVERT: A 269 ASP cc_start: 0.8358 (m-30) cc_final: 0.8047 (m-30) REVERT: A 283 GLN cc_start: 0.9148 (mp-120) cc_final: 0.8816 (mm-40) REVERT: A 284 ILE cc_start: 0.9082 (pp) cc_final: 0.8750 (pp) REVERT: A 288 LYS cc_start: 0.9597 (mtmm) cc_final: 0.9361 (ptpt) REVERT: A 294 TYR cc_start: 0.9471 (m-80) cc_final: 0.8950 (m-80) REVERT: A 297 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8645 (tm) REVERT: A 303 ASN cc_start: 0.7092 (m-40) cc_final: 0.6860 (m-40) REVERT: A 332 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8758 (pp) REVERT: A 334 GLN cc_start: 0.9460 (mp10) cc_final: 0.8637 (mp10) REVERT: A 335 GLU cc_start: 0.8501 (mp0) cc_final: 0.7780 (mp0) REVERT: A 337 LEU cc_start: 0.9161 (tp) cc_final: 0.8718 (tp) REVERT: A 343 GLN cc_start: 0.8888 (pp30) cc_final: 0.7974 (pp30) REVERT: A 352 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8730 (tm-30) REVERT: A 355 ARG cc_start: 0.8860 (ptt90) cc_final: 0.8506 (ptm-80) REVERT: A 364 ASP cc_start: 0.8004 (m-30) cc_final: 0.6500 (m-30) REVERT: A 369 ASN cc_start: 0.9037 (p0) cc_final: 0.8340 (p0) REVERT: A 372 HIS cc_start: 0.9313 (m170) cc_final: 0.8500 (m-70) REVERT: A 375 LYS cc_start: 0.9581 (pttm) cc_final: 0.9315 (pttm) REVERT: A 385 MET cc_start: 0.8543 (ttp) cc_final: 0.7980 (ttp) REVERT: A 386 MET cc_start: 0.8706 (ppp) cc_final: 0.8344 (ppp) REVERT: A 389 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9380 (pp) REVERT: A 420 MET cc_start: 0.8395 (mtm) cc_final: 0.7997 (mtp) REVERT: A 448 GLN cc_start: 0.8774 (mp10) cc_final: 0.8437 (mp10) REVERT: A 482 MET cc_start: 0.8752 (tmt) cc_final: 0.8475 (tmt) REVERT: A 507 HIS cc_start: 0.8837 (t-90) cc_final: 0.8614 (t70) REVERT: A 509 TYR cc_start: 0.9115 (p90) cc_final: 0.8624 (p90) REVERT: B 18 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9050 (tm) REVERT: B 48 GLN cc_start: 0.8848 (tt0) cc_final: 0.8607 (mt0) REVERT: B 62 LYS cc_start: 0.8856 (pttt) cc_final: 0.8524 (pttt) REVERT: B 70 MET cc_start: 0.8424 (tpp) cc_final: 0.7641 (tpp) REVERT: B 71 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: B 82 MET cc_start: 0.9367 (ttm) cc_final: 0.9166 (ttm) REVERT: B 98 GLU cc_start: 0.9717 (mp0) cc_final: 0.9427 (mp0) REVERT: B 108 LYS cc_start: 0.9475 (pmtt) cc_final: 0.8460 (tptt) REVERT: B 131 PHE cc_start: 0.9214 (m-10) cc_final: 0.8780 (m-80) REVERT: B 132 GLU cc_start: 0.9503 (pt0) cc_final: 0.9095 (pp20) REVERT: B 166 LEU cc_start: 0.9323 (mm) cc_final: 0.8886 (tp) REVERT: B 176 GLU cc_start: 0.8262 (mp0) cc_final: 0.7903 (mp0) REVERT: B 177 GLU cc_start: 0.8753 (pm20) cc_final: 0.8251 (pm20) REVERT: B 183 GLU cc_start: 0.9106 (pm20) cc_final: 0.8610 (pm20) REVERT: B 216 ASP cc_start: 0.9502 (t70) cc_final: 0.9255 (t0) REVERT: B 224 ARG cc_start: 0.8975 (ttt-90) cc_final: 0.8755 (ttt180) REVERT: B 243 GLN cc_start: 0.9450 (mm110) cc_final: 0.9091 (mm110) REVERT: B 244 LEU cc_start: 0.9215 (tp) cc_final: 0.8984 (tp) REVERT: B 311 LYS cc_start: 0.9244 (ptmm) cc_final: 0.8895 (tmmt) REVERT: B 322 ARG cc_start: 0.9333 (tmt90) cc_final: 0.9036 (ttt90) REVERT: B 334 GLN cc_start: 0.9146 (mt0) cc_final: 0.8861 (mm-40) REVERT: B 337 LEU cc_start: 0.9491 (mm) cc_final: 0.9254 (mm) REVERT: B 343 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 355 ARG cc_start: 0.8222 (ppt170) cc_final: 0.7980 (ttp-170) REVERT: B 364 ASP cc_start: 0.8149 (m-30) cc_final: 0.7877 (m-30) REVERT: B 417 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9391 (pp) REVERT: B 466 HIS cc_start: 0.8665 (t-170) cc_final: 0.8357 (t-90) REVERT: B 478 GLN cc_start: 0.9256 (tt0) cc_final: 0.8622 (tt0) REVERT: B 491 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 493 ARG cc_start: 0.8424 (pmt-80) cc_final: 0.8042 (pmt-80) REVERT: C 32 TYR cc_start: 0.9090 (m-10) cc_final: 0.8638 (m-10) REVERT: C 43 ASP cc_start: 0.8524 (m-30) cc_final: 0.8293 (m-30) REVERT: C 47 ASP cc_start: 0.9598 (m-30) cc_final: 0.9078 (p0) REVERT: C 55 LEU cc_start: 0.8024 (mm) cc_final: 0.7725 (mm) REVERT: C 78 MET cc_start: 0.9314 (mmm) cc_final: 0.9096 (mmm) REVERT: C 82 MET cc_start: 0.9630 (tpp) cc_final: 0.9310 (tpp) REVERT: C 111 GLU cc_start: 0.9215 (tp30) cc_final: 0.8851 (mp0) REVERT: C 112 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8996 (tm-30) REVERT: C 199 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8674 (tp30) REVERT: C 200 ILE cc_start: 0.9147 (mm) cc_final: 0.8906 (mm) REVERT: C 216 ASP cc_start: 0.9473 (m-30) cc_final: 0.9087 (t0) REVERT: C 229 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8770 (mmmt) REVERT: C 244 LEU cc_start: 0.9282 (tm) cc_final: 0.9074 (tm) REVERT: C 274 ASP cc_start: 0.9258 (t0) cc_final: 0.8891 (t0) REVERT: C 289 TYR cc_start: 0.9421 (t80) cc_final: 0.9019 (t80) REVERT: C 331 CYS cc_start: 0.8929 (t) cc_final: 0.8721 (t) REVERT: C 333 THR cc_start: 0.9751 (p) cc_final: 0.9273 (p) REVERT: C 334 GLN cc_start: 0.9277 (mp10) cc_final: 0.8804 (mp10) REVERT: C 335 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8112 (tm-30) REVERT: C 336 VAL cc_start: 0.9555 (m) cc_final: 0.8891 (m) REVERT: C 492 LYS cc_start: 0.8581 (pptt) cc_final: 0.8369 (pptt) REVERT: C 500 GLU cc_start: 0.9309 (pp20) cc_final: 0.8706 (pp20) REVERT: C 504 HIS cc_start: 0.8354 (p90) cc_final: 0.7904 (p-80) REVERT: D 21 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8669 (tm-30) REVERT: D 32 TYR cc_start: 0.9128 (m-80) cc_final: 0.8705 (m-80) REVERT: D 33 ASN cc_start: 0.9173 (t0) cc_final: 0.8668 (t0) REVERT: D 51 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9215 (pp) REVERT: D 91 ILE cc_start: 0.9258 (tp) cc_final: 0.9039 (tp) REVERT: D 140 CYS cc_start: 0.8415 (m) cc_final: 0.7888 (m) REVERT: D 157 ILE cc_start: 0.8764 (mm) cc_final: 0.8544 (pt) REVERT: D 215 ASP cc_start: 0.9490 (m-30) cc_final: 0.9040 (p0) REVERT: D 286 MET cc_start: 0.9700 (tpt) cc_final: 0.9412 (tpt) REVERT: D 289 TYR cc_start: 0.9501 (t80) cc_final: 0.9250 (t80) REVERT: D 311 LYS cc_start: 0.9247 (ttpp) cc_final: 0.8889 (ttpp) REVERT: D 341 ARG cc_start: 0.8321 (ptp-110) cc_final: 0.7969 (ptp-170) REVERT: D 345 THR cc_start: 0.9453 (p) cc_final: 0.9218 (p) REVERT: D 349 LYS cc_start: 0.9565 (mptm) cc_final: 0.9315 (mmmm) REVERT: D 352 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8932 (tm-30) REVERT: D 379 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9235 (tm) REVERT: D 385 MET cc_start: 0.8457 (tpt) cc_final: 0.7390 (tpt) REVERT: D 386 MET cc_start: 0.8682 (ptm) cc_final: 0.8124 (ptm) REVERT: D 399 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7713 (tm-30) REVERT: D 410 LYS cc_start: 0.9444 (mptp) cc_final: 0.9022 (mmtm) REVERT: D 418 ASP cc_start: 0.9426 (t70) cc_final: 0.9116 (t70) REVERT: D 465 GLN cc_start: 0.8959 (pp30) cc_final: 0.8360 (pp30) REVERT: D 469 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8502 (mm-40) REVERT: D 482 MET cc_start: 0.9177 (tpt) cc_final: 0.8832 (tpp) REVERT: E 16 ASP cc_start: 0.8473 (t70) cc_final: 0.8269 (t70) REVERT: E 28 ASP cc_start: 0.9108 (t70) cc_final: 0.8497 (t70) REVERT: E 32 TYR cc_start: 0.9304 (m-80) cc_final: 0.8885 (m-80) REVERT: E 36 LEU cc_start: 0.9428 (tp) cc_final: 0.8757 (tp) REVERT: E 38 LEU cc_start: 0.9659 (mm) cc_final: 0.9055 (mm) REVERT: E 48 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9128 (mt0) REVERT: E 82 MET cc_start: 0.9259 (ttp) cc_final: 0.9039 (tmm) REVERT: E 137 HIS cc_start: 0.9431 (m90) cc_final: 0.8971 (m90) REVERT: E 142 ILE cc_start: 0.8518 (tp) cc_final: 0.8203 (tp) REVERT: E 150 MET cc_start: 0.8092 (tmt) cc_final: 0.7748 (tpt) REVERT: E 158 ILE cc_start: 0.8556 (mm) cc_final: 0.8059 (tp) REVERT: E 165 PHE cc_start: 0.8681 (p90) cc_final: 0.8327 (p90) REVERT: E 228 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9295 (ptmt) REVERT: E 231 ARG cc_start: 0.9192 (ptp-170) cc_final: 0.8950 (mtm-85) REVERT: E 288 LYS cc_start: 0.9602 (mtmm) cc_final: 0.9292 (ptpt) REVERT: E 294 TYR cc_start: 0.9427 (m-80) cc_final: 0.8914 (m-80) REVERT: E 297 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8785 (tm) REVERT: E 332 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8458 (pp) REVERT: E 334 GLN cc_start: 0.9405 (mp10) cc_final: 0.8547 (mp10) REVERT: E 335 GLU cc_start: 0.8513 (mp0) cc_final: 0.7694 (mp0) REVERT: E 337 LEU cc_start: 0.9193 (tp) cc_final: 0.8767 (tp) REVERT: E 352 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8712 (tm-30) REVERT: E 364 ASP cc_start: 0.8115 (m-30) cc_final: 0.6430 (m-30) REVERT: E 372 HIS cc_start: 0.9324 (m170) cc_final: 0.8368 (m170) REVERT: E 385 MET cc_start: 0.8241 (ttp) cc_final: 0.7768 (ttp) REVERT: E 386 MET cc_start: 0.8682 (ppp) cc_final: 0.8419 (ppp) REVERT: E 389 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9375 (pp) REVERT: E 420 MET cc_start: 0.8371 (mtm) cc_final: 0.7963 (mtp) REVERT: E 448 GLN cc_start: 0.8803 (mp10) cc_final: 0.8446 (mp10) REVERT: E 482 MET cc_start: 0.8715 (tmt) cc_final: 0.8429 (tmt) REVERT: E 507 HIS cc_start: 0.8992 (t-90) cc_final: 0.8786 (t70) REVERT: E 509 TYR cc_start: 0.9177 (p90) cc_final: 0.8668 (p90) REVERT: E 513 LEU cc_start: 0.9271 (mp) cc_final: 0.8989 (mp) REVERT: F 18 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9154 (tm) REVERT: F 62 LYS cc_start: 0.8988 (pttt) cc_final: 0.8707 (pttt) REVERT: F 70 MET cc_start: 0.8098 (tpp) cc_final: 0.5232 (tpp) REVERT: F 102 ASN cc_start: 0.9522 (t0) cc_final: 0.9279 (t0) REVERT: F 103 GLU cc_start: 0.9658 (tp30) cc_final: 0.9339 (tp30) REVERT: F 108 LYS cc_start: 0.9472 (pmtt) cc_final: 0.8649 (tppt) REVERT: F 131 PHE cc_start: 0.9199 (m-10) cc_final: 0.8839 (m-80) REVERT: F 132 GLU cc_start: 0.9440 (pt0) cc_final: 0.9086 (pp20) REVERT: F 136 ARG cc_start: 0.9364 (mmp-170) cc_final: 0.9073 (mmm160) REVERT: F 166 LEU cc_start: 0.9396 (mm) cc_final: 0.8310 (tp) REVERT: F 176 GLU cc_start: 0.8278 (mp0) cc_final: 0.7987 (mp0) REVERT: F 183 GLU cc_start: 0.9136 (pm20) cc_final: 0.8668 (pm20) REVERT: F 216 ASP cc_start: 0.9441 (t70) cc_final: 0.9212 (t0) REVERT: F 243 GLN cc_start: 0.9421 (mm110) cc_final: 0.9156 (mm110) REVERT: F 244 LEU cc_start: 0.9246 (tp) cc_final: 0.8972 (tp) REVERT: F 262 LEU cc_start: 0.9460 (pt) cc_final: 0.9224 (pt) REVERT: F 265 GLN cc_start: 0.9391 (pm20) cc_final: 0.9184 (pm20) REVERT: F 311 LYS cc_start: 0.9244 (ptmm) cc_final: 0.8901 (tmmt) REVERT: F 322 ARG cc_start: 0.8981 (tmt90) cc_final: 0.8739 (ttt90) REVERT: F 334 GLN cc_start: 0.9181 (mt0) cc_final: 0.8866 (mm-40) REVERT: F 335 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8160 (tm-30) REVERT: F 336 VAL cc_start: 0.9663 (p) cc_final: 0.9113 (p) REVERT: F 337 LEU cc_start: 0.9493 (mm) cc_final: 0.9271 (mm) REVERT: F 343 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8067 (tm-30) REVERT: F 348 TYR cc_start: 0.9293 (t80) cc_final: 0.9080 (t80) REVERT: F 355 ARG cc_start: 0.8371 (ppt170) cc_final: 0.8108 (ttp-170) REVERT: F 399 GLU cc_start: 0.8584 (pm20) cc_final: 0.8286 (pm20) REVERT: F 455 LYS cc_start: 0.9350 (pttp) cc_final: 0.9007 (ptmm) REVERT: F 466 HIS cc_start: 0.8650 (t-170) cc_final: 0.8346 (t-90) REVERT: F 478 GLN cc_start: 0.9296 (tt0) cc_final: 0.8556 (tt0) REVERT: F 491 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8153 (tm-30) REVERT: F 493 ARG cc_start: 0.8374 (pmt-80) cc_final: 0.7781 (pmt-80) REVERT: F 507 HIS cc_start: 0.8766 (t-90) cc_final: 0.8488 (t-90) REVERT: G 32 TYR cc_start: 0.9111 (m-10) cc_final: 0.8594 (m-10) REVERT: G 43 ASP cc_start: 0.8507 (m-30) cc_final: 0.8243 (m-30) REVERT: G 55 LEU cc_start: 0.8039 (mm) cc_final: 0.7778 (mm) REVERT: G 67 SER cc_start: 0.9569 (p) cc_final: 0.9245 (p) REVERT: G 78 MET cc_start: 0.9562 (tpp) cc_final: 0.9212 (tpp) REVERT: G 82 MET cc_start: 0.9644 (tpp) cc_final: 0.9377 (tpp) REVERT: G 106 LYS cc_start: 0.7962 (mttp) cc_final: 0.7535 (mttm) REVERT: G 112 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8917 (tm-30) REVERT: G 199 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8681 (tp30) REVERT: G 200 ILE cc_start: 0.9179 (mm) cc_final: 0.8964 (mm) REVERT: G 216 ASP cc_start: 0.9474 (m-30) cc_final: 0.9087 (t0) REVERT: G 229 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8778 (mmmt) REVERT: G 274 ASP cc_start: 0.9308 (t0) cc_final: 0.8954 (t0) REVERT: G 289 TYR cc_start: 0.9419 (t80) cc_final: 0.8906 (t80) REVERT: G 331 CYS cc_start: 0.9090 (t) cc_final: 0.8817 (t) REVERT: G 333 THR cc_start: 0.9759 (p) cc_final: 0.9268 (p) REVERT: G 334 GLN cc_start: 0.9328 (mp10) cc_final: 0.8848 (mp10) REVERT: G 335 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8051 (tm-30) REVERT: G 336 VAL cc_start: 0.9558 (m) cc_final: 0.8665 (m) REVERT: G 339 CYS cc_start: 0.8908 (t) cc_final: 0.8472 (t) REVERT: G 410 LYS cc_start: 0.9175 (tmmm) cc_final: 0.8689 (tppt) REVERT: G 411 TYR cc_start: 0.9533 (t80) cc_final: 0.9268 (t80) REVERT: G 418 ASP cc_start: 0.9420 (t70) cc_final: 0.9063 (t70) REVERT: G 444 SER cc_start: 0.8733 (t) cc_final: 0.8294 (t) REVERT: G 482 MET cc_start: 0.9265 (tpp) cc_final: 0.8734 (mmm) REVERT: G 492 LYS cc_start: 0.8547 (pptt) cc_final: 0.8300 (pptt) REVERT: G 500 GLU cc_start: 0.9292 (pp20) cc_final: 0.8700 (pp20) REVERT: H 21 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8676 (tm-30) REVERT: H 32 TYR cc_start: 0.9136 (m-80) cc_final: 0.8687 (m-80) REVERT: H 33 ASN cc_start: 0.9179 (t0) cc_final: 0.8647 (t0) REVERT: H 91 ILE cc_start: 0.9200 (tp) cc_final: 0.8969 (tp) REVERT: H 93 HIS cc_start: 0.9263 (p-80) cc_final: 0.8760 (p-80) REVERT: H 108 LYS cc_start: 0.8909 (tptm) cc_final: 0.8303 (tptt) REVERT: H 112 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8871 (tm-30) REVERT: H 150 MET cc_start: 0.6933 (ttt) cc_final: 0.6725 (tmm) REVERT: H 157 ILE cc_start: 0.8605 (mm) cc_final: 0.8304 (pt) REVERT: H 203 ARG cc_start: 0.9149 (tpp-160) cc_final: 0.8877 (ttm110) REVERT: H 208 LYS cc_start: 0.8013 (tppp) cc_final: 0.7615 (tmtt) REVERT: H 215 ASP cc_start: 0.9506 (m-30) cc_final: 0.8951 (p0) REVERT: H 258 TYR cc_start: 0.9529 (t80) cc_final: 0.9308 (t80) REVERT: H 286 MET cc_start: 0.9701 (tpt) cc_final: 0.9362 (tpt) REVERT: H 289 TYR cc_start: 0.9519 (t80) cc_final: 0.9291 (t80) REVERT: H 341 ARG cc_start: 0.8393 (ptp-110) cc_final: 0.8076 (ptp-170) REVERT: H 345 THR cc_start: 0.9448 (p) cc_final: 0.9205 (p) REVERT: H 349 LYS cc_start: 0.9552 (mptm) cc_final: 0.9303 (mmmm) REVERT: H 352 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8948 (tm-30) REVERT: H 362 ILE cc_start: 0.9477 (tp) cc_final: 0.9190 (tp) REVERT: H 379 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9235 (tm) REVERT: H 385 MET cc_start: 0.8394 (tpt) cc_final: 0.7367 (tpt) REVERT: H 386 MET cc_start: 0.8577 (ptm) cc_final: 0.8008 (ptm) REVERT: H 418 ASP cc_start: 0.9402 (t70) cc_final: 0.9031 (t70) REVERT: H 465 GLN cc_start: 0.8968 (pp30) cc_final: 0.8381 (pp30) REVERT: H 469 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8504 (mm-40) REVERT: H 482 MET cc_start: 0.9069 (tpt) cc_final: 0.8801 (tpp) outliers start: 134 outliers final: 38 residues processed: 1481 average time/residue: 0.1955 time to fit residues: 467.1764 Evaluate side-chains 1183 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 1129 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 93 HIS A 94 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 466 HIS B 25 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 466 HIS B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 465 GLN D 25 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS E 94 ASN E 112 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS E 466 HIS F 21 GLN F 25 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN G 303 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS G 465 GLN G 507 HIS H 25 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.124114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.088565 restraints weight = 71591.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092506 restraints weight = 39217.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095234 restraints weight = 25356.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097112 restraints weight = 18317.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098586 restraints weight = 14324.616| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32220 Z= 0.165 Angle : 0.888 10.933 43712 Z= 0.442 Chirality : 0.052 0.330 4984 Planarity : 0.008 0.417 5452 Dihedral : 15.228 178.362 4572 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.74 % Favored : 92.21 % Rotamer: Outliers : 0.49 % Allowed : 7.64 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.11), residues: 3968 helix: -2.49 (0.12), residues: 1250 sheet: -3.02 (0.21), residues: 424 loop : -2.53 (0.12), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 322 TYR 0.029 0.002 TYR F 233 PHE 0.021 0.002 PHE C 131 HIS 0.009 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (32212) covalent geometry : angle 0.88839 / 0.44 (43712) hydrogen bonds : bond 0.04947 / 3.20 ( 966) hydrogen bonds : angle 7.05260 / 4.85 ( 2655) Misc. bond : bond 0.00255 / 0.18 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1547 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 1531 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.9242 (pm20) cc_final: 0.8745 (pm20) REVERT: A 28 ASP cc_start: 0.8882 (t70) cc_final: 0.8462 (t70) REVERT: A 32 TYR cc_start: 0.8998 (m-80) cc_final: 0.8481 (m-80) REVERT: A 36 LEU cc_start: 0.8947 (tp) cc_final: 0.8053 (tp) REVERT: A 38 LEU cc_start: 0.9611 (mm) cc_final: 0.8816 (mm) REVERT: A 69 PRO cc_start: 0.9466 (Cg_endo) cc_final: 0.9122 (Cg_exo) REVERT: A 105 ARG cc_start: 0.9016 (mmm160) cc_final: 0.8564 (tpm170) REVERT: A 108 LYS cc_start: 0.9479 (tptp) cc_final: 0.8998 (mmtt) REVERT: A 158 ILE cc_start: 0.8819 (mm) cc_final: 0.8263 (tp) REVERT: A 179 MET cc_start: 0.7338 (pmm) cc_final: 0.7086 (pmm) REVERT: A 203 ARG cc_start: 0.9397 (ttp-110) cc_final: 0.9061 (mtm110) REVERT: A 269 ASP cc_start: 0.7987 (m-30) cc_final: 0.7752 (m-30) REVERT: A 294 TYR cc_start: 0.9301 (m-80) cc_final: 0.9073 (m-80) REVERT: A 332 ILE cc_start: 0.9276 (pt) cc_final: 0.8727 (pt) REVERT: A 334 GLN cc_start: 0.9504 (mp10) cc_final: 0.8535 (mp10) REVERT: A 335 GLU cc_start: 0.8585 (mp0) cc_final: 0.7672 (mp0) REVERT: A 343 GLN cc_start: 0.8539 (pp30) cc_final: 0.7694 (pp30) REVERT: A 352 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8807 (tm-30) REVERT: A 364 ASP cc_start: 0.8120 (m-30) cc_final: 0.7555 (m-30) REVERT: A 372 HIS cc_start: 0.9306 (m170) cc_final: 0.8140 (m90) REVERT: A 386 MET cc_start: 0.8855 (ppp) cc_final: 0.8410 (ppp) REVERT: A 414 MET cc_start: 0.8034 (ptt) cc_final: 0.7713 (ptt) REVERT: A 420 MET cc_start: 0.8391 (mtm) cc_final: 0.7844 (mtp) REVERT: A 448 GLN cc_start: 0.8667 (mp10) cc_final: 0.8438 (mp10) REVERT: A 450 LYS cc_start: 0.9417 (mttp) cc_final: 0.9178 (mttp) REVERT: A 480 ARG cc_start: 0.9029 (mtm110) cc_final: 0.8652 (mtm110) REVERT: A 507 HIS cc_start: 0.8792 (t-90) cc_final: 0.8355 (t70) REVERT: A 509 TYR cc_start: 0.9078 (p90) cc_final: 0.8874 (p90) REVERT: B 16 ASP cc_start: 0.7637 (t0) cc_final: 0.6529 (t0) REVERT: B 18 LEU cc_start: 0.9556 (tp) cc_final: 0.9275 (tp) REVERT: B 37 ILE cc_start: 0.9007 (mm) cc_final: 0.8607 (mm) REVERT: B 41 TYR cc_start: 0.9217 (t80) cc_final: 0.8959 (t80) REVERT: B 82 MET cc_start: 0.9481 (ttm) cc_final: 0.9271 (ttm) REVERT: B 93 HIS cc_start: 0.8999 (p-80) cc_final: 0.8661 (p-80) REVERT: B 103 GLU cc_start: 0.9545 (tp30) cc_final: 0.9201 (tp30) REVERT: B 108 LYS cc_start: 0.9393 (pttm) cc_final: 0.8439 (tppt) REVERT: B 131 PHE cc_start: 0.9167 (m-10) cc_final: 0.8185 (m-80) REVERT: B 132 GLU cc_start: 0.9530 (pt0) cc_final: 0.9108 (pt0) REVERT: B 172 ASP cc_start: 0.8509 (t0) cc_final: 0.8167 (t0) REVERT: B 216 ASP cc_start: 0.9407 (t70) cc_final: 0.9193 (t0) REVERT: B 224 ARG cc_start: 0.8846 (ttt-90) cc_final: 0.8608 (ttt180) REVERT: B 238 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8661 (tppt) REVERT: B 259 ARG cc_start: 0.9086 (mtp85) cc_final: 0.8855 (ttt90) REVERT: B 289 TYR cc_start: 0.9436 (t80) cc_final: 0.9114 (t80) REVERT: B 291 LYS cc_start: 0.9619 (mmmt) cc_final: 0.9054 (tppt) REVERT: B 334 GLN cc_start: 0.9231 (mt0) cc_final: 0.8889 (mm-40) REVERT: B 335 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8310 (tm-30) REVERT: B 348 TYR cc_start: 0.9221 (t80) cc_final: 0.8784 (t80) REVERT: B 349 LYS cc_start: 0.9307 (mtpt) cc_final: 0.9084 (mmmm) REVERT: B 355 ARG cc_start: 0.8167 (ppt170) cc_final: 0.7885 (ttp-170) REVERT: B 364 ASP cc_start: 0.7371 (m-30) cc_final: 0.7069 (m-30) REVERT: B 372 HIS cc_start: 0.8925 (m170) cc_final: 0.8315 (m170) REVERT: B 400 TYR cc_start: 0.7636 (m-80) cc_final: 0.7039 (m-80) REVERT: B 403 SER cc_start: 0.9224 (t) cc_final: 0.9024 (t) REVERT: B 404 ASP cc_start: 0.8457 (t0) cc_final: 0.8168 (t0) REVERT: B 491 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 493 ARG cc_start: 0.8066 (pmt-80) cc_final: 0.7756 (pmt-80) REVERT: C 16 ASP cc_start: 0.7490 (t0) cc_final: 0.6994 (t0) REVERT: C 32 TYR cc_start: 0.8947 (m-10) cc_final: 0.8622 (m-10) REVERT: C 43 ASP cc_start: 0.8196 (m-30) cc_final: 0.7928 (m-30) REVERT: C 74 THR cc_start: 0.6569 (t) cc_final: 0.6324 (t) REVERT: C 78 MET cc_start: 0.9050 (mmm) cc_final: 0.8821 (mmm) REVERT: C 82 MET cc_start: 0.9590 (tpp) cc_final: 0.9337 (tpp) REVERT: C 90 PHE cc_start: 0.9016 (m-80) cc_final: 0.8691 (m-80) REVERT: C 102 ASN cc_start: 0.9191 (m-40) cc_final: 0.8910 (m-40) REVERT: C 110 TYR cc_start: 0.9022 (t80) cc_final: 0.8706 (t80) REVERT: C 111 GLU cc_start: 0.9183 (tp30) cc_final: 0.8935 (mp0) REVERT: C 199 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8569 (tp30) REVERT: C 200 ILE cc_start: 0.9235 (mm) cc_final: 0.8452 (mm) REVERT: C 203 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.7620 (ptt90) REVERT: C 229 LYS cc_start: 0.9447 (ptpp) cc_final: 0.9174 (mmmt) REVERT: C 274 ASP cc_start: 0.9251 (t0) cc_final: 0.8913 (t70) REVERT: C 289 TYR cc_start: 0.9359 (t80) cc_final: 0.9068 (t80) REVERT: C 290 ILE cc_start: 0.9496 (pt) cc_final: 0.9142 (pt) REVERT: C 331 CYS cc_start: 0.8864 (t) cc_final: 0.8477 (t) REVERT: C 333 THR cc_start: 0.9735 (p) cc_final: 0.9183 (p) REVERT: C 334 GLN cc_start: 0.9082 (mp10) cc_final: 0.8511 (mp10) REVERT: C 335 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8008 (tm-30) REVERT: C 336 VAL cc_start: 0.9500 (m) cc_final: 0.8657 (m) REVERT: C 385 MET cc_start: 0.8158 (tmm) cc_final: 0.6019 (tmm) REVERT: C 482 MET cc_start: 0.9276 (tpp) cc_final: 0.8767 (tpp) REVERT: C 487 GLU cc_start: 0.8702 (pm20) cc_final: 0.8364 (pm20) REVERT: C 494 THR cc_start: 0.8851 (p) cc_final: 0.8592 (p) REVERT: C 500 GLU cc_start: 0.9197 (pp20) cc_final: 0.8593 (pp20) REVERT: D 12 TYR cc_start: 0.8133 (t80) cc_final: 0.6579 (m-80) REVERT: D 21 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8481 (tp40) REVERT: D 25 ASN cc_start: 0.8642 (m110) cc_final: 0.7237 (m110) REVERT: D 33 ASN cc_start: 0.9108 (t0) cc_final: 0.8428 (t0) REVERT: D 71 ASP cc_start: 0.9385 (t0) cc_final: 0.8992 (t70) REVERT: D 91 ILE cc_start: 0.9265 (tp) cc_final: 0.9043 (tp) REVERT: D 112 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8736 (tm-30) REVERT: D 179 MET cc_start: 0.6926 (ppp) cc_final: 0.6085 (pmm) REVERT: D 192 ILE cc_start: 0.8211 (tp) cc_final: 0.7476 (tt) REVERT: D 215 ASP cc_start: 0.9517 (m-30) cc_final: 0.9037 (p0) REVERT: D 257 LYS cc_start: 0.9773 (ptpp) cc_final: 0.9476 (mmtm) REVERT: D 258 TYR cc_start: 0.9502 (t80) cc_final: 0.9257 (t80) REVERT: D 286 MET cc_start: 0.9644 (tpt) cc_final: 0.9291 (tpt) REVERT: D 289 TYR cc_start: 0.9418 (t80) cc_final: 0.9027 (t80) REVERT: D 290 ILE cc_start: 0.9730 (pt) cc_final: 0.9366 (pt) REVERT: D 311 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8559 (ttpp) REVERT: D 349 LYS cc_start: 0.9556 (mmtp) cc_final: 0.9292 (mmmm) REVERT: D 352 GLU cc_start: 0.9346 (tm-30) cc_final: 0.9011 (tm-30) REVERT: D 375 LYS cc_start: 0.9591 (pttt) cc_final: 0.9315 (pttt) REVERT: D 385 MET cc_start: 0.8362 (tpt) cc_final: 0.7348 (tpt) REVERT: D 386 MET cc_start: 0.8457 (ptm) cc_final: 0.8023 (ptm) REVERT: D 418 ASP cc_start: 0.9287 (t70) cc_final: 0.9080 (t70) REVERT: D 465 GLN cc_start: 0.8755 (pp30) cc_final: 0.7981 (pp30) REVERT: D 468 CYS cc_start: 0.9258 (t) cc_final: 0.9004 (t) REVERT: D 469 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8746 (mm-40) REVERT: P 1 MET cc_start: 0.8659 (mpp) cc_final: 0.8200 (pmm) REVERT: E 28 ASP cc_start: 0.8918 (t70) cc_final: 0.8551 (t70) REVERT: E 32 TYR cc_start: 0.9377 (m-80) cc_final: 0.8825 (m-80) REVERT: E 36 LEU cc_start: 0.8956 (tp) cc_final: 0.8155 (tp) REVERT: E 38 LEU cc_start: 0.9604 (mm) cc_final: 0.8831 (mm) REVERT: E 69 PRO cc_start: 0.9578 (Cg_endo) cc_final: 0.9365 (Cg_exo) REVERT: E 102 ASN cc_start: 0.9312 (t0) cc_final: 0.9064 (t0) REVERT: E 105 ARG cc_start: 0.8965 (mmm160) cc_final: 0.8591 (tpm170) REVERT: E 108 LYS cc_start: 0.9406 (tppt) cc_final: 0.8969 (mmtt) REVERT: E 165 PHE cc_start: 0.8560 (p90) cc_final: 0.8339 (p90) REVERT: E 224 ARG cc_start: 0.7483 (mmt180) cc_final: 0.6852 (mmt180) REVERT: E 227 LEU cc_start: 0.9172 (tt) cc_final: 0.8849 (tt) REVERT: E 231 ARG cc_start: 0.9155 (ptp-170) cc_final: 0.8811 (ptp90) REVERT: E 273 LEU cc_start: 0.9169 (tt) cc_final: 0.8887 (tt) REVERT: E 281 ILE cc_start: 0.9645 (pt) cc_final: 0.9332 (pt) REVERT: E 284 ILE cc_start: 0.9344 (pt) cc_final: 0.9078 (pt) REVERT: E 285 ASN cc_start: 0.9422 (m-40) cc_final: 0.9171 (m-40) REVERT: E 287 ILE cc_start: 0.9813 (mt) cc_final: 0.9571 (mt) REVERT: E 288 LYS cc_start: 0.9604 (mtmm) cc_final: 0.9297 (ptpt) REVERT: E 294 TYR cc_start: 0.9308 (m-80) cc_final: 0.9054 (m-80) REVERT: E 332 ILE cc_start: 0.9233 (pt) cc_final: 0.8939 (pt) REVERT: E 334 GLN cc_start: 0.9479 (mp10) cc_final: 0.8538 (mp10) REVERT: E 335 GLU cc_start: 0.8621 (mp0) cc_final: 0.7957 (mp0) REVERT: E 352 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8761 (tm-30) REVERT: E 355 ARG cc_start: 0.8609 (ptm-80) cc_final: 0.8027 (ptm-80) REVERT: E 364 ASP cc_start: 0.8272 (m-30) cc_final: 0.6704 (m-30) REVERT: E 368 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8133 (mm-40) REVERT: E 385 MET cc_start: 0.8445 (ttp) cc_final: 0.8013 (ttp) REVERT: E 386 MET cc_start: 0.8817 (ppp) cc_final: 0.8392 (ppp) REVERT: E 420 MET cc_start: 0.8413 (mtm) cc_final: 0.7848 (mtp) REVERT: E 441 GLN cc_start: 0.6923 (pp30) cc_final: 0.6697 (pp30) REVERT: E 448 GLN cc_start: 0.8706 (mp10) cc_final: 0.8419 (mp10) REVERT: E 469 GLN cc_start: 0.9302 (tp40) cc_final: 0.8692 (tt0) REVERT: E 507 HIS cc_start: 0.8781 (t-90) cc_final: 0.8386 (t70) REVERT: E 513 LEU cc_start: 0.9156 (mp) cc_final: 0.8777 (mt) REVERT: F 18 LEU cc_start: 0.9580 (tp) cc_final: 0.9328 (tp) REVERT: F 32 TYR cc_start: 0.8686 (m-80) cc_final: 0.8335 (m-80) REVERT: F 37 ILE cc_start: 0.9124 (mm) cc_final: 0.8709 (mm) REVERT: F 70 MET cc_start: 0.8134 (tpp) cc_final: 0.7053 (tpt) REVERT: F 103 GLU cc_start: 0.9653 (tp30) cc_final: 0.9288 (tp30) REVERT: F 106 LYS cc_start: 0.9439 (mtpt) cc_final: 0.9028 (mtpt) REVERT: F 108 LYS cc_start: 0.9310 (pttm) cc_final: 0.8213 (tppt) REVERT: F 131 PHE cc_start: 0.9176 (m-10) cc_final: 0.8191 (m-80) REVERT: F 132 GLU cc_start: 0.9461 (pt0) cc_final: 0.9017 (pt0) REVERT: F 136 ARG cc_start: 0.9271 (mmp-170) cc_final: 0.8762 (mmm160) REVERT: F 291 LYS cc_start: 0.9583 (mmmt) cc_final: 0.8968 (tppt) REVERT: F 334 GLN cc_start: 0.9246 (mt0) cc_final: 0.8903 (mm-40) REVERT: F 343 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7716 (tm-30) REVERT: F 355 ARG cc_start: 0.8213 (ppt170) cc_final: 0.7911 (ttp-170) REVERT: F 399 GLU cc_start: 0.8390 (pm20) cc_final: 0.8170 (pm20) REVERT: F 403 SER cc_start: 0.9149 (t) cc_final: 0.8948 (t) REVERT: F 404 ASP cc_start: 0.8401 (t0) cc_final: 0.8123 (t0) REVERT: F 455 LYS cc_start: 0.9348 (pttp) cc_final: 0.9138 (ptmm) REVERT: F 456 PHE cc_start: 0.9562 (t80) cc_final: 0.9359 (t80) REVERT: F 491 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8160 (tm-30) REVERT: F 493 ARG cc_start: 0.8094 (pmt-80) cc_final: 0.7557 (pmt-80) REVERT: F 507 HIS cc_start: 0.8652 (t-90) cc_final: 0.8318 (t-90) REVERT: G 43 ASP cc_start: 0.8551 (m-30) cc_final: 0.8305 (m-30) REVERT: G 47 ASP cc_start: 0.9570 (m-30) cc_final: 0.8962 (p0) REVERT: G 78 MET cc_start: 0.9507 (tpp) cc_final: 0.9260 (tpp) REVERT: G 106 LYS cc_start: 0.7873 (mttp) cc_final: 0.7642 (mttp) REVERT: G 154 LEU cc_start: 0.9056 (tt) cc_final: 0.8146 (mm) REVERT: G 175 LEU cc_start: 0.9220 (mt) cc_final: 0.8995 (mt) REVERT: G 199 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8652 (tp30) REVERT: G 200 ILE cc_start: 0.9203 (mm) cc_final: 0.8738 (mm) REVERT: G 203 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8149 (mtm110) REVERT: G 216 ASP cc_start: 0.9234 (m-30) cc_final: 0.8932 (t0) REVERT: G 229 LYS cc_start: 0.9425 (ptpp) cc_final: 0.9148 (mmmt) REVERT: G 274 ASP cc_start: 0.9257 (t0) cc_final: 0.8949 (t70) REVERT: G 287 ILE cc_start: 0.9693 (OUTLIER) cc_final: 0.9341 (tt) REVERT: G 289 TYR cc_start: 0.9349 (t80) cc_final: 0.8940 (t80) REVERT: G 290 ILE cc_start: 0.9453 (pt) cc_final: 0.9144 (pt) REVERT: G 291 LYS cc_start: 0.9038 (ptpp) cc_final: 0.8709 (pttt) REVERT: G 331 CYS cc_start: 0.8977 (t) cc_final: 0.8503 (t) REVERT: G 332 ILE cc_start: 0.9555 (pt) cc_final: 0.9299 (pt) REVERT: G 333 THR cc_start: 0.9734 (p) cc_final: 0.9197 (p) REVERT: G 334 GLN cc_start: 0.9086 (mp10) cc_final: 0.8417 (mp10) REVERT: G 335 GLU cc_start: 0.8692 (tm-30) cc_final: 0.7960 (tm-30) REVERT: G 336 VAL cc_start: 0.9534 (m) cc_final: 0.8596 (m) REVERT: G 418 ASP cc_start: 0.9325 (t70) cc_final: 0.9032 (t0) REVERT: G 482 MET cc_start: 0.9242 (tpp) cc_final: 0.8610 (tpp) REVERT: G 487 GLU cc_start: 0.8742 (pm20) cc_final: 0.8534 (pm20) REVERT: G 492 LYS cc_start: 0.8530 (pptt) cc_final: 0.8169 (pptt) REVERT: G 494 THR cc_start: 0.8833 (p) cc_final: 0.8613 (p) REVERT: G 500 GLU cc_start: 0.9210 (pp20) cc_final: 0.8648 (pp20) REVERT: H 16 ASP cc_start: 0.8164 (m-30) cc_final: 0.7913 (m-30) REVERT: H 21 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8571 (tp40) REVERT: H 25 ASN cc_start: 0.8664 (m110) cc_final: 0.7330 (m110) REVERT: H 33 ASN cc_start: 0.9124 (t0) cc_final: 0.8546 (t0) REVERT: H 63 THR cc_start: 0.8133 (t) cc_final: 0.7925 (t) REVERT: H 91 ILE cc_start: 0.9202 (tp) cc_final: 0.8902 (tp) REVERT: H 93 HIS cc_start: 0.9106 (p-80) cc_final: 0.8869 (p-80) REVERT: H 108 LYS cc_start: 0.8906 (tptm) cc_final: 0.8528 (tptp) REVERT: H 112 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8787 (tm-30) REVERT: H 144 ILE cc_start: 0.8635 (mm) cc_final: 0.8420 (mm) REVERT: H 192 ILE cc_start: 0.8108 (tp) cc_final: 0.7672 (tt) REVERT: H 257 LYS cc_start: 0.9773 (ptpp) cc_final: 0.9495 (mmtm) REVERT: H 286 MET cc_start: 0.9658 (tpt) cc_final: 0.9261 (tpt) REVERT: H 289 TYR cc_start: 0.9406 (t80) cc_final: 0.9048 (t80) REVERT: H 290 ILE cc_start: 0.9739 (pt) cc_final: 0.9353 (pt) REVERT: H 315 ASP cc_start: 0.9405 (m-30) cc_final: 0.9192 (m-30) REVERT: H 343 GLN cc_start: 0.8135 (pm20) cc_final: 0.7824 (pt0) REVERT: H 349 LYS cc_start: 0.9562 (mmtp) cc_final: 0.9170 (mmmm) REVERT: H 352 GLU cc_start: 0.9332 (tm-30) cc_final: 0.8990 (tm-30) REVERT: H 368 GLN cc_start: 0.8576 (mt0) cc_final: 0.8044 (mm-40) REVERT: H 375 LYS cc_start: 0.9556 (pttt) cc_final: 0.9298 (pttt) REVERT: H 385 MET cc_start: 0.8189 (tpt) cc_final: 0.7024 (tpt) REVERT: H 386 MET cc_start: 0.8314 (ptm) cc_final: 0.7840 (ptm) REVERT: H 400 TYR cc_start: 0.7783 (m-80) cc_final: 0.7379 (m-80) REVERT: H 418 ASP cc_start: 0.9326 (t70) cc_final: 0.9090 (t0) REVERT: H 465 GLN cc_start: 0.8782 (pp30) cc_final: 0.7981 (pp30) REVERT: H 468 CYS cc_start: 0.9247 (t) cc_final: 0.8988 (t) REVERT: H 469 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8717 (mm-40) REVERT: H 478 GLN cc_start: 0.9432 (mt0) cc_final: 0.8846 (mt0) REVERT: H 482 MET cc_start: 0.8926 (tpt) cc_final: 0.8509 (tpt) REVERT: L 1 MET cc_start: 0.8484 (mpp) cc_final: 0.8014 (pmm) outliers start: 16 outliers final: 3 residues processed: 1534 average time/residue: 0.1970 time to fit residues: 489.9751 Evaluate side-chains 1273 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1269 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 214 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 255 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 361 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN A 465 GLN A 466 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN E 22 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 265 GLN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.118748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083354 restraints weight = 74416.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086967 restraints weight = 41298.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089454 restraints weight = 27071.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.091301 restraints weight = 19799.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092434 restraints weight = 15554.436| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 32220 Z= 0.258 Angle : 0.898 11.616 43712 Z= 0.453 Chirality : 0.053 0.290 4984 Planarity : 0.005 0.064 5452 Dihedral : 14.761 179.715 4572 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.37 % Allowed : 7.64 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.12), residues: 3968 helix: -1.98 (0.13), residues: 1254 sheet: -2.85 (0.23), residues: 390 loop : -2.30 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG H 322 TYR 0.026 0.002 TYR A 353 PHE 0.021 0.002 PHE C 131 HIS 0.010 0.002 HIS G 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.26 (32212) covalent geometry : angle 0.89762 / 0.45 (43712) hydrogen bonds : bond 0.04785 / 3.12 ( 966) hydrogen bonds : angle 6.81130 / 4.66 ( 2655) Misc. bond : bond 0.00186 / 0.14 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1443 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.9355 (pm20) cc_final: 0.8924 (pm20) REVERT: A 28 ASP cc_start: 0.8900 (t70) cc_final: 0.8434 (t70) REVERT: A 32 TYR cc_start: 0.9103 (m-80) cc_final: 0.8896 (m-10) REVERT: A 36 LEU cc_start: 0.9068 (tp) cc_final: 0.8343 (tp) REVERT: A 38 LEU cc_start: 0.9648 (mm) cc_final: 0.8899 (mm) REVERT: A 48 GLN cc_start: 0.9272 (mt0) cc_final: 0.8916 (mt0) REVERT: A 105 ARG cc_start: 0.9068 (mmm160) cc_final: 0.8522 (tpm170) REVERT: A 108 LYS cc_start: 0.9540 (tptp) cc_final: 0.9032 (mmtt) REVERT: A 158 ILE cc_start: 0.8887 (mm) cc_final: 0.8341 (tp) REVERT: A 179 MET cc_start: 0.7380 (pmm) cc_final: 0.7029 (pmm) REVERT: A 246 CYS cc_start: 0.9417 (t) cc_final: 0.9080 (t) REVERT: A 262 LEU cc_start: 0.9545 (pt) cc_final: 0.8920 (mt) REVERT: A 332 ILE cc_start: 0.9367 (pt) cc_final: 0.8876 (pt) REVERT: A 334 GLN cc_start: 0.9457 (mp10) cc_final: 0.9253 (mp10) REVERT: A 335 GLU cc_start: 0.8742 (mp0) cc_final: 0.7999 (mp0) REVERT: A 352 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8816 (tm-30) REVERT: A 355 ARG cc_start: 0.8842 (ptm-80) cc_final: 0.8495 (ptt90) REVERT: A 364 ASP cc_start: 0.8157 (m-30) cc_final: 0.7919 (m-30) REVERT: A 375 LYS cc_start: 0.9690 (pttt) cc_final: 0.9444 (pttt) REVERT: A 386 MET cc_start: 0.8738 (ppp) cc_final: 0.7997 (ppp) REVERT: A 390 LEU cc_start: 0.9162 (pt) cc_final: 0.8950 (pt) REVERT: A 414 MET cc_start: 0.8184 (ptt) cc_final: 0.7936 (ptt) REVERT: A 420 MET cc_start: 0.8395 (mtm) cc_final: 0.7911 (mtp) REVERT: A 448 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8363 (mp10) REVERT: A 456 PHE cc_start: 0.9532 (t80) cc_final: 0.9321 (t80) REVERT: A 460 LEU cc_start: 0.9707 (mp) cc_final: 0.9387 (mp) REVERT: A 480 ARG cc_start: 0.9006 (mtm110) cc_final: 0.8562 (mtm110) REVERT: A 482 MET cc_start: 0.9129 (ttt) cc_final: 0.8904 (ttt) REVERT: A 507 HIS cc_start: 0.8805 (t-90) cc_final: 0.8398 (t70) REVERT: A 509 TYR cc_start: 0.9090 (p90) cc_final: 0.8842 (p90) REVERT: B 16 ASP cc_start: 0.8025 (t0) cc_final: 0.6375 (t0) REVERT: B 18 LEU cc_start: 0.9592 (tp) cc_final: 0.9334 (tp) REVERT: B 34 ASP cc_start: 0.8296 (m-30) cc_final: 0.8000 (m-30) REVERT: B 37 ILE cc_start: 0.9064 (mm) cc_final: 0.8681 (mm) REVERT: B 82 MET cc_start: 0.9482 (ttm) cc_final: 0.9260 (ttm) REVERT: B 91 ILE cc_start: 0.9326 (mm) cc_final: 0.9066 (mm) REVERT: B 100 GLN cc_start: 0.9240 (pt0) cc_final: 0.8943 (mt0) REVERT: B 106 LYS cc_start: 0.9383 (mtpt) cc_final: 0.9176 (mtpt) REVERT: B 132 GLU cc_start: 0.9569 (pt0) cc_final: 0.9259 (pt0) REVERT: B 165 PHE cc_start: 0.9101 (p90) cc_final: 0.8619 (p90) REVERT: B 166 LEU cc_start: 0.9461 (mm) cc_final: 0.9023 (tp) REVERT: B 172 ASP cc_start: 0.8453 (t0) cc_final: 0.8167 (t0) REVERT: B 176 GLU cc_start: 0.8118 (mp0) cc_final: 0.7801 (mp0) REVERT: B 181 LYS cc_start: 0.9278 (tppt) cc_final: 0.8693 (tppt) REVERT: B 185 LEU cc_start: 0.8968 (mt) cc_final: 0.8455 (mt) REVERT: B 238 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8542 (tppt) REVERT: B 250 ILE cc_start: 0.9279 (mp) cc_final: 0.8752 (tp) REVERT: B 289 TYR cc_start: 0.9515 (t80) cc_final: 0.9131 (t80) REVERT: B 291 LYS cc_start: 0.9616 (mmmt) cc_final: 0.9032 (tppt) REVERT: B 322 ARG cc_start: 0.8809 (ttt90) cc_final: 0.8187 (ttt90) REVERT: B 334 GLN cc_start: 0.9317 (mt0) cc_final: 0.8939 (mm-40) REVERT: B 335 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8363 (tm-30) REVERT: B 343 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 355 ARG cc_start: 0.8310 (ppt170) cc_final: 0.8035 (ttp-170) REVERT: B 364 ASP cc_start: 0.7640 (m-30) cc_final: 0.6979 (m-30) REVERT: B 404 ASP cc_start: 0.8628 (t0) cc_final: 0.8341 (t0) REVERT: B 491 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8121 (tm-30) REVERT: C 32 TYR cc_start: 0.8969 (m-10) cc_final: 0.8572 (m-10) REVERT: C 43 ASP cc_start: 0.8526 (m-30) cc_final: 0.8270 (m-30) REVERT: C 78 MET cc_start: 0.9146 (mmm) cc_final: 0.8922 (mmm) REVERT: C 82 MET cc_start: 0.9608 (tpp) cc_final: 0.9273 (tpp) REVERT: C 90 PHE cc_start: 0.8916 (m-80) cc_final: 0.8575 (m-80) REVERT: C 111 GLU cc_start: 0.9249 (tp30) cc_final: 0.9048 (mp0) REVERT: C 136 ARG cc_start: 0.6755 (pmt-80) cc_final: 0.6416 (pmt-80) REVERT: C 199 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8702 (tp30) REVERT: C 200 ILE cc_start: 0.9253 (mm) cc_final: 0.8926 (mm) REVERT: C 203 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.7953 (mtm110) REVERT: C 229 LYS cc_start: 0.9381 (ptpp) cc_final: 0.9074 (mmmt) REVERT: C 274 ASP cc_start: 0.9237 (t0) cc_final: 0.8969 (t0) REVERT: C 289 TYR cc_start: 0.9375 (t80) cc_final: 0.9062 (t80) REVERT: C 290 ILE cc_start: 0.9449 (pt) cc_final: 0.9103 (pt) REVERT: C 331 CYS cc_start: 0.8930 (t) cc_final: 0.8622 (t) REVERT: C 333 THR cc_start: 0.9727 (p) cc_final: 0.9282 (p) REVERT: C 334 GLN cc_start: 0.9130 (mp10) cc_final: 0.8518 (mp10) REVERT: C 335 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 336 VAL cc_start: 0.9589 (m) cc_final: 0.8822 (m) REVERT: C 349 LYS cc_start: 0.9092 (mtpt) cc_final: 0.8783 (mtmt) REVERT: C 390 LEU cc_start: 0.9445 (pt) cc_final: 0.9109 (pt) REVERT: C 482 MET cc_start: 0.9347 (tpp) cc_final: 0.8814 (tpp) REVERT: C 487 GLU cc_start: 0.8650 (pm20) cc_final: 0.8285 (pm20) REVERT: C 500 GLU cc_start: 0.9249 (pp20) cc_final: 0.8638 (pp20) REVERT: D 12 TYR cc_start: 0.8323 (t80) cc_final: 0.6990 (m-80) REVERT: D 16 ASP cc_start: 0.8387 (m-30) cc_final: 0.8177 (m-30) REVERT: D 21 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8315 (tm-30) REVERT: D 25 ASN cc_start: 0.8496 (m110) cc_final: 0.8020 (m110) REVERT: D 32 TYR cc_start: 0.9072 (m-80) cc_final: 0.8490 (m-80) REVERT: D 33 ASN cc_start: 0.9160 (t0) cc_final: 0.8814 (t0) REVERT: D 51 LEU cc_start: 0.9468 (pp) cc_final: 0.9256 (pp) REVERT: D 71 ASP cc_start: 0.9391 (t0) cc_final: 0.8892 (t0) REVERT: D 91 ILE cc_start: 0.9168 (tp) cc_final: 0.8961 (tp) REVERT: D 112 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8758 (tm-30) REVERT: D 179 MET cc_start: 0.6601 (ppp) cc_final: 0.5445 (pmm) REVERT: D 192 ILE cc_start: 0.8413 (tp) cc_final: 0.7717 (tt) REVERT: D 215 ASP cc_start: 0.9516 (m-30) cc_final: 0.9008 (p0) REVERT: D 257 LYS cc_start: 0.9788 (ptpp) cc_final: 0.9477 (mmtm) REVERT: D 258 TYR cc_start: 0.9457 (t80) cc_final: 0.9225 (t80) REVERT: D 286 MET cc_start: 0.9632 (tpt) cc_final: 0.9301 (tpt) REVERT: D 289 TYR cc_start: 0.9398 (t80) cc_final: 0.8986 (t80) REVERT: D 290 ILE cc_start: 0.9753 (pt) cc_final: 0.9385 (pt) REVERT: D 311 LYS cc_start: 0.9191 (ttpp) cc_final: 0.8796 (ttpp) REVERT: D 343 GLN cc_start: 0.8629 (pm20) cc_final: 0.8201 (pm20) REVERT: D 352 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9007 (tm-30) REVERT: D 385 MET cc_start: 0.8684 (tpt) cc_final: 0.7803 (tpt) REVERT: D 386 MET cc_start: 0.8657 (ptm) cc_final: 0.8382 (ptm) REVERT: D 410 LYS cc_start: 0.9262 (mptt) cc_final: 0.8758 (mmtm) REVERT: D 418 ASP cc_start: 0.9331 (t70) cc_final: 0.9102 (t70) REVERT: D 465 GLN cc_start: 0.8774 (pp30) cc_final: 0.8009 (pp30) REVERT: D 468 CYS cc_start: 0.9283 (t) cc_final: 0.9019 (t) REVERT: D 469 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8853 (mm-40) REVERT: D 482 MET cc_start: 0.9240 (tpt) cc_final: 0.8858 (tpp) REVERT: P 1 MET cc_start: 0.8776 (mpp) cc_final: 0.8289 (pmm) REVERT: E 21 GLN cc_start: 0.9343 (pm20) cc_final: 0.8946 (pm20) REVERT: E 28 ASP cc_start: 0.8905 (t70) cc_final: 0.8549 (t70) REVERT: E 32 TYR cc_start: 0.9429 (m-80) cc_final: 0.8767 (m-80) REVERT: E 36 LEU cc_start: 0.9084 (tp) cc_final: 0.8509 (tp) REVERT: E 38 LEU cc_start: 0.9625 (mm) cc_final: 0.8839 (mm) REVERT: E 42 ILE cc_start: 0.9405 (mt) cc_final: 0.9171 (mm) REVERT: E 48 GLN cc_start: 0.9212 (mt0) cc_final: 0.8843 (mt0) REVERT: E 70 MET cc_start: 0.8440 (tpp) cc_final: 0.6727 (mmm) REVERT: E 100 GLN cc_start: 0.9352 (mp10) cc_final: 0.8685 (mp10) REVERT: E 105 ARG cc_start: 0.8997 (mmm160) cc_final: 0.8436 (tpp-160) REVERT: E 108 LYS cc_start: 0.9386 (tppt) cc_final: 0.8693 (mmtt) REVERT: E 224 ARG cc_start: 0.7694 (mmt180) cc_final: 0.7367 (mmt180) REVERT: E 244 LEU cc_start: 0.9444 (pt) cc_final: 0.9238 (pt) REVERT: E 246 CYS cc_start: 0.9428 (t) cc_final: 0.9070 (t) REVERT: E 262 LEU cc_start: 0.9614 (pt) cc_final: 0.9368 (pt) REVERT: E 288 LYS cc_start: 0.9576 (mtmm) cc_final: 0.9260 (mttt) REVERT: E 294 TYR cc_start: 0.9377 (m-80) cc_final: 0.9164 (m-80) REVERT: E 319 ASP cc_start: 0.7613 (t70) cc_final: 0.7038 (t70) REVERT: E 325 MET cc_start: 0.9043 (ptm) cc_final: 0.8126 (ptm) REVERT: E 332 ILE cc_start: 0.9388 (pt) cc_final: 0.8906 (pt) REVERT: E 334 GLN cc_start: 0.9407 (mp10) cc_final: 0.9200 (mp10) REVERT: E 335 GLU cc_start: 0.8667 (mp0) cc_final: 0.7952 (mp0) REVERT: E 352 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8735 (tm-30) REVERT: E 355 ARG cc_start: 0.8738 (ptm-80) cc_final: 0.8437 (ptt90) REVERT: E 368 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8199 (mm-40) REVERT: E 375 LYS cc_start: 0.9735 (pttt) cc_final: 0.9489 (pttt) REVERT: E 385 MET cc_start: 0.8674 (ttp) cc_final: 0.8443 (ttp) REVERT: E 386 MET cc_start: 0.8706 (ppp) cc_final: 0.8255 (tmm) REVERT: E 420 MET cc_start: 0.8437 (mtm) cc_final: 0.7906 (mtp) REVERT: E 448 GLN cc_start: 0.8853 (mp10) cc_final: 0.8469 (mp10) REVERT: E 460 LEU cc_start: 0.9679 (mp) cc_final: 0.9422 (mp) REVERT: E 507 HIS cc_start: 0.8866 (t-90) cc_final: 0.8534 (t70) REVERT: F 16 ASP cc_start: 0.7879 (t0) cc_final: 0.6370 (t0) REVERT: F 34 ASP cc_start: 0.8346 (m-30) cc_final: 0.8066 (m-30) REVERT: F 37 ILE cc_start: 0.9019 (mm) cc_final: 0.8606 (mm) REVERT: F 70 MET cc_start: 0.8077 (tpp) cc_final: 0.6838 (tpt) REVERT: F 103 GLU cc_start: 0.9644 (tp30) cc_final: 0.9288 (tp30) REVERT: F 106 LYS cc_start: 0.9432 (mtpt) cc_final: 0.9211 (mtpt) REVERT: F 132 GLU cc_start: 0.9493 (pt0) cc_final: 0.9171 (pt0) REVERT: F 136 ARG cc_start: 0.9299 (mmp-170) cc_final: 0.8807 (mmm160) REVERT: F 185 LEU cc_start: 0.9005 (mt) cc_final: 0.8501 (mt) REVERT: F 238 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8609 (tppt) REVERT: F 250 ILE cc_start: 0.9354 (mp) cc_final: 0.8721 (tp) REVERT: F 289 TYR cc_start: 0.9488 (t80) cc_final: 0.9125 (t80) REVERT: F 294 TYR cc_start: 0.9394 (m-80) cc_final: 0.9141 (m-80) REVERT: F 311 LYS cc_start: 0.9162 (tmmt) cc_final: 0.8955 (tmmt) REVERT: F 322 ARG cc_start: 0.8668 (ttt90) cc_final: 0.8308 (ttt90) REVERT: F 334 GLN cc_start: 0.9307 (mt0) cc_final: 0.8908 (mm-40) REVERT: F 335 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8294 (tm-30) REVERT: F 343 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7811 (tm-30) REVERT: F 355 ARG cc_start: 0.8403 (ppt170) cc_final: 0.7290 (ptm-80) REVERT: F 372 HIS cc_start: 0.9212 (m170) cc_final: 0.8597 (m90) REVERT: F 404 ASP cc_start: 0.8614 (t0) cc_final: 0.8365 (t0) REVERT: F 455 LYS cc_start: 0.9455 (pttp) cc_final: 0.9177 (ptmm) REVERT: F 468 CYS cc_start: 0.9312 (t) cc_final: 0.9080 (t) REVERT: F 491 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8141 (tm-30) REVERT: F 506 LEU cc_start: 0.8947 (pt) cc_final: 0.8705 (pt) REVERT: G 41 TYR cc_start: 0.8930 (t80) cc_final: 0.8711 (t80) REVERT: G 43 ASP cc_start: 0.8367 (m-30) cc_final: 0.8020 (m-30) REVERT: G 78 MET cc_start: 0.9521 (tpp) cc_final: 0.9240 (tpp) REVERT: G 175 LEU cc_start: 0.9211 (mt) cc_final: 0.8903 (mt) REVERT: G 179 MET cc_start: 0.7927 (ppp) cc_final: 0.7544 (ppp) REVERT: G 199 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8541 (tp30) REVERT: G 200 ILE cc_start: 0.9300 (mm) cc_final: 0.8860 (mm) REVERT: G 203 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8045 (mtm110) REVERT: G 229 LYS cc_start: 0.9385 (ptpp) cc_final: 0.9070 (mmmt) REVERT: G 274 ASP cc_start: 0.9292 (t0) cc_final: 0.8815 (t0) REVERT: G 287 ILE cc_start: 0.9677 (OUTLIER) cc_final: 0.9214 (tt) REVERT: G 289 TYR cc_start: 0.9353 (t80) cc_final: 0.8984 (t80) REVERT: G 290 ILE cc_start: 0.9421 (pt) cc_final: 0.9135 (pt) REVERT: G 291 LYS cc_start: 0.9098 (ptpp) cc_final: 0.8744 (pttm) REVERT: G 331 CYS cc_start: 0.9110 (t) cc_final: 0.8720 (t) REVERT: G 332 ILE cc_start: 0.9623 (pt) cc_final: 0.9379 (pt) REVERT: G 333 THR cc_start: 0.9717 (p) cc_final: 0.9192 (p) REVERT: G 334 GLN cc_start: 0.9131 (mp10) cc_final: 0.8493 (mp10) REVERT: G 335 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8116 (tm-30) REVERT: G 336 VAL cc_start: 0.9593 (m) cc_final: 0.8688 (m) REVERT: G 395 GLU cc_start: 0.8791 (mp0) cc_final: 0.8478 (mp0) REVERT: G 414 MET cc_start: 0.9223 (pmm) cc_final: 0.8925 (pmm) REVERT: G 482 MET cc_start: 0.9318 (tpp) cc_final: 0.8636 (tpp) REVERT: G 492 LYS cc_start: 0.8602 (pptt) cc_final: 0.8271 (pptt) REVERT: G 500 GLU cc_start: 0.9274 (pp20) cc_final: 0.8722 (pp20) REVERT: H 21 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8617 (tm-30) REVERT: H 33 ASN cc_start: 0.9114 (t0) cc_final: 0.8489 (t0) REVERT: H 70 MET cc_start: 0.8677 (mmt) cc_final: 0.7918 (mmp) REVERT: H 91 ILE cc_start: 0.9288 (tp) cc_final: 0.9046 (tp) REVERT: H 108 LYS cc_start: 0.9043 (tptm) cc_final: 0.8632 (tptp) REVERT: H 112 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8904 (tm-30) REVERT: H 150 MET cc_start: 0.7070 (tmm) cc_final: 0.6682 (tmm) REVERT: H 179 MET cc_start: 0.7576 (ppp) cc_final: 0.6970 (ppp) REVERT: H 215 ASP cc_start: 0.9521 (m-30) cc_final: 0.9037 (p0) REVERT: H 257 LYS cc_start: 0.9798 (ptpp) cc_final: 0.9546 (mmtm) REVERT: H 258 TYR cc_start: 0.9471 (t80) cc_final: 0.9146 (t80) REVERT: H 286 MET cc_start: 0.9626 (tpt) cc_final: 0.9279 (tpt) REVERT: H 289 TYR cc_start: 0.9400 (t80) cc_final: 0.9047 (t80) REVERT: H 290 ILE cc_start: 0.9768 (pt) cc_final: 0.9370 (pt) REVERT: H 315 ASP cc_start: 0.9405 (m-30) cc_final: 0.8887 (p0) REVERT: H 343 GLN cc_start: 0.8410 (pm20) cc_final: 0.8044 (pt0) REVERT: H 349 LYS cc_start: 0.9594 (mmtp) cc_final: 0.9253 (mmmm) REVERT: H 352 GLU cc_start: 0.9334 (tm-30) cc_final: 0.8980 (tm-30) REVERT: H 385 MET cc_start: 0.8764 (tpt) cc_final: 0.8167 (tpt) REVERT: H 410 LYS cc_start: 0.9336 (mptt) cc_final: 0.9023 (mmtm) REVERT: H 414 MET cc_start: 0.8681 (pmm) cc_final: 0.8247 (pmm) REVERT: H 418 ASP cc_start: 0.9393 (t70) cc_final: 0.9133 (t70) REVERT: H 465 GLN cc_start: 0.8812 (pp30) cc_final: 0.8235 (pp30) REVERT: H 468 CYS cc_start: 0.9253 (t) cc_final: 0.8965 (t) REVERT: H 469 GLN cc_start: 0.9049 (mm110) cc_final: 0.8793 (mm110) REVERT: H 478 GLN cc_start: 0.9418 (mt0) cc_final: 0.8816 (mt0) REVERT: H 482 MET cc_start: 0.9032 (tpt) cc_final: 0.8756 (tpt) REVERT: H 491 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7543 (tm-30) REVERT: H 493 ARG cc_start: 0.9109 (mtm110) cc_final: 0.8883 (mtm110) REVERT: K 1 MET cc_start: 0.8164 (mmt) cc_final: 0.7956 (mmp) REVERT: L 1 MET cc_start: 0.8551 (mpp) cc_final: 0.8103 (pmm) outliers start: 12 outliers final: 4 residues processed: 1446 average time/residue: 0.1877 time to fit residues: 443.3030 Evaluate side-chains 1185 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1179 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 363 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 221 optimal weight: 0.0970 chunk 330 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 chunk 373 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 466 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS E 466 HIS ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 507 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.088096 restraints weight = 72522.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.091956 restraints weight = 39890.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094691 restraints weight = 25991.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096624 restraints weight = 18812.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097914 restraints weight = 14718.034| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32220 Z= 0.143 Angle : 0.851 10.161 43712 Z= 0.418 Chirality : 0.053 0.363 4984 Planarity : 0.005 0.130 5452 Dihedral : 14.036 177.277 4572 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.34 % Favored : 91.63 % Rotamer: Outliers : 0.21 % Allowed : 5.44 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.12), residues: 3968 helix: -1.82 (0.13), residues: 1258 sheet: -2.46 (0.24), residues: 380 loop : -2.19 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 480 TYR 0.022 0.002 TYR F 233 PHE 0.033 0.002 PHE F 131 HIS 0.012 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (32212) covalent geometry : angle 0.85081 / 0.42 (43712) hydrogen bonds : bond 0.04258 / 2.76 ( 966) hydrogen bonds : angle 6.47651 / 4.42 ( 2655) Misc. bond : bond 0.00169 / 0.13 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1464 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.9247 (pm20) cc_final: 0.8879 (pm20) REVERT: A 28 ASP cc_start: 0.8869 (t70) cc_final: 0.8467 (t70) REVERT: A 36 LEU cc_start: 0.9152 (tp) cc_final: 0.8505 (tp) REVERT: A 38 LEU cc_start: 0.9568 (mm) cc_final: 0.8700 (mm) REVERT: A 48 GLN cc_start: 0.9270 (mt0) cc_final: 0.8922 (mt0) REVERT: A 105 ARG cc_start: 0.8994 (mmm160) cc_final: 0.8435 (tpm170) REVERT: A 108 LYS cc_start: 0.9502 (tptp) cc_final: 0.8879 (mmtt) REVERT: A 109 LYS cc_start: 0.9513 (ptpp) cc_final: 0.9234 (ptpt) REVERT: A 158 ILE cc_start: 0.8925 (mm) cc_final: 0.8393 (tp) REVERT: A 179 MET cc_start: 0.7296 (pmm) cc_final: 0.7023 (pmm) REVERT: A 203 ARG cc_start: 0.9367 (ttp-110) cc_final: 0.9162 (mtm110) REVERT: A 231 ARG cc_start: 0.9271 (ptm-80) cc_final: 0.9055 (ptm-80) REVERT: A 246 CYS cc_start: 0.9382 (t) cc_final: 0.9120 (t) REVERT: A 262 LEU cc_start: 0.9595 (pt) cc_final: 0.9341 (pt) REVERT: A 269 ASP cc_start: 0.8115 (m-30) cc_final: 0.7887 (m-30) REVERT: A 273 LEU cc_start: 0.9411 (tt) cc_final: 0.8276 (tt) REVERT: A 334 GLN cc_start: 0.9446 (mp10) cc_final: 0.8507 (mp10) REVERT: A 335 GLU cc_start: 0.8652 (mp0) cc_final: 0.8070 (mp0) REVERT: A 352 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8765 (tm-30) REVERT: A 375 LYS cc_start: 0.9620 (pttt) cc_final: 0.9416 (pttt) REVERT: A 386 MET cc_start: 0.8566 (ppp) cc_final: 0.8162 (ppp) REVERT: A 414 MET cc_start: 0.8017 (ptt) cc_final: 0.7787 (ptt) REVERT: A 420 MET cc_start: 0.8341 (mtm) cc_final: 0.7821 (mtp) REVERT: A 444 SER cc_start: 0.8505 (p) cc_final: 0.8185 (p) REVERT: A 480 ARG cc_start: 0.8841 (mpp80) cc_final: 0.8544 (mtm110) REVERT: A 507 HIS cc_start: 0.8621 (t-90) cc_final: 0.8290 (t70) REVERT: A 513 LEU cc_start: 0.9133 (mp) cc_final: 0.8856 (mp) REVERT: B 34 ASP cc_start: 0.8291 (m-30) cc_final: 0.8069 (m-30) REVERT: B 37 ILE cc_start: 0.9001 (mm) cc_final: 0.8643 (mm) REVERT: B 70 MET cc_start: 0.8243 (tpt) cc_final: 0.7681 (tpp) REVERT: B 82 MET cc_start: 0.9498 (ttm) cc_final: 0.9264 (ttm) REVERT: B 91 ILE cc_start: 0.9263 (mm) cc_final: 0.8591 (mm) REVERT: B 92 HIS cc_start: 0.9025 (p90) cc_final: 0.8083 (p-80) REVERT: B 106 LYS cc_start: 0.9413 (mtpt) cc_final: 0.9147 (mtpt) REVERT: B 108 LYS cc_start: 0.9346 (pttm) cc_final: 0.8660 (tptt) REVERT: B 131 PHE cc_start: 0.9180 (m-80) cc_final: 0.8768 (m-80) REVERT: B 132 GLU cc_start: 0.9564 (pt0) cc_final: 0.9213 (pt0) REVERT: B 165 PHE cc_start: 0.8700 (p90) cc_final: 0.8483 (p90) REVERT: B 166 LEU cc_start: 0.9423 (mm) cc_final: 0.9161 (tp) REVERT: B 181 LYS cc_start: 0.9221 (tppt) cc_final: 0.8831 (tppt) REVERT: B 185 LEU cc_start: 0.8968 (mt) cc_final: 0.8565 (mt) REVERT: B 238 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8549 (tppt) REVERT: B 250 ILE cc_start: 0.9256 (mp) cc_final: 0.8805 (tp) REVERT: B 287 ILE cc_start: 0.9536 (pt) cc_final: 0.9289 (pt) REVERT: B 289 TYR cc_start: 0.9452 (t80) cc_final: 0.9073 (t80) REVERT: B 291 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9052 (tppt) REVERT: B 334 GLN cc_start: 0.9293 (mt0) cc_final: 0.8723 (mm-40) REVERT: B 335 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 343 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 355 ARG cc_start: 0.8278 (ppt170) cc_final: 0.7857 (ttp-170) REVERT: B 364 ASP cc_start: 0.7029 (m-30) cc_final: 0.6418 (m-30) REVERT: B 372 HIS cc_start: 0.9023 (m170) cc_final: 0.8450 (m-70) REVERT: B 403 SER cc_start: 0.9299 (t) cc_final: 0.9091 (t) REVERT: B 404 ASP cc_start: 0.8530 (t0) cc_final: 0.8229 (t0) REVERT: B 491 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 506 LEU cc_start: 0.8776 (pp) cc_final: 0.8532 (pt) REVERT: C 16 ASP cc_start: 0.7888 (t0) cc_final: 0.7576 (t0) REVERT: C 32 TYR cc_start: 0.8821 (m-10) cc_final: 0.8320 (m-10) REVERT: C 33 ASN cc_start: 0.8839 (m110) cc_final: 0.8535 (m110) REVERT: C 47 ASP cc_start: 0.9580 (m-30) cc_final: 0.8929 (p0) REVERT: C 78 MET cc_start: 0.9174 (mmm) cc_final: 0.8902 (mmm) REVERT: C 82 MET cc_start: 0.9626 (tpp) cc_final: 0.9342 (tpp) REVERT: C 90 PHE cc_start: 0.9035 (m-80) cc_final: 0.8590 (m-80) REVERT: C 150 MET cc_start: 0.8466 (tpp) cc_final: 0.8140 (tpp) REVERT: C 199 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8681 (tp30) REVERT: C 200 ILE cc_start: 0.9273 (mm) cc_final: 0.8908 (mm) REVERT: C 203 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.8167 (mtm110) REVERT: C 229 LYS cc_start: 0.9375 (ptpp) cc_final: 0.9087 (mmmt) REVERT: C 274 ASP cc_start: 0.9365 (t0) cc_final: 0.8984 (t70) REVERT: C 287 ILE cc_start: 0.9693 (OUTLIER) cc_final: 0.9363 (tt) REVERT: C 289 TYR cc_start: 0.9389 (t80) cc_final: 0.9136 (t80) REVERT: C 290 ILE cc_start: 0.9465 (pt) cc_final: 0.9120 (pt) REVERT: C 291 LYS cc_start: 0.9111 (pttt) cc_final: 0.8783 (pttm) REVERT: C 331 CYS cc_start: 0.8965 (t) cc_final: 0.8703 (t) REVERT: C 333 THR cc_start: 0.9750 (p) cc_final: 0.9205 (p) REVERT: C 334 GLN cc_start: 0.9168 (mp10) cc_final: 0.8473 (mp10) REVERT: C 336 VAL cc_start: 0.9527 (m) cc_final: 0.9324 (m) REVERT: C 349 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8613 (mtpt) REVERT: C 362 ILE cc_start: 0.9400 (pt) cc_final: 0.9152 (mm) REVERT: C 441 GLN cc_start: 0.8551 (mp-120) cc_final: 0.8217 (mp-120) REVERT: C 482 MET cc_start: 0.9392 (tpp) cc_final: 0.8748 (tpp) REVERT: C 493 ARG cc_start: 0.8803 (mtm180) cc_final: 0.8523 (ptp90) REVERT: C 494 THR cc_start: 0.8870 (p) cc_final: 0.8600 (p) REVERT: C 500 GLU cc_start: 0.9210 (pp20) cc_final: 0.8565 (pp20) REVERT: D 12 TYR cc_start: 0.8231 (t80) cc_final: 0.6987 (m-80) REVERT: D 32 TYR cc_start: 0.9086 (m-80) cc_final: 0.8450 (m-10) REVERT: D 33 ASN cc_start: 0.9064 (t0) cc_final: 0.8492 (t0) REVERT: D 51 LEU cc_start: 0.9460 (pp) cc_final: 0.9257 (pp) REVERT: D 71 ASP cc_start: 0.9307 (t0) cc_final: 0.8577 (t0) REVERT: D 91 ILE cc_start: 0.9096 (tp) cc_final: 0.8874 (tp) REVERT: D 100 GLN cc_start: 0.9365 (mp10) cc_final: 0.8260 (pp30) REVERT: D 144 ILE cc_start: 0.9092 (mm) cc_final: 0.8773 (mp) REVERT: D 179 MET cc_start: 0.6782 (ppp) cc_final: 0.5787 (pmm) REVERT: D 215 ASP cc_start: 0.9538 (m-30) cc_final: 0.9026 (p0) REVERT: D 242 LYS cc_start: 0.9295 (mmpt) cc_final: 0.9084 (mmmt) REVERT: D 257 LYS cc_start: 0.9805 (ptpp) cc_final: 0.9484 (mmtm) REVERT: D 286 MET cc_start: 0.9650 (tpt) cc_final: 0.9298 (tpt) REVERT: D 289 TYR cc_start: 0.9404 (t80) cc_final: 0.8999 (t80) REVERT: D 290 ILE cc_start: 0.9733 (pt) cc_final: 0.9355 (pt) REVERT: D 315 ASP cc_start: 0.9338 (m-30) cc_final: 0.8924 (p0) REVERT: D 352 GLU cc_start: 0.9376 (tm-30) cc_final: 0.9033 (tm-30) REVERT: D 364 ASP cc_start: 0.6515 (m-30) cc_final: 0.5491 (m-30) REVERT: D 385 MET cc_start: 0.8547 (tpt) cc_final: 0.7340 (tpt) REVERT: D 386 MET cc_start: 0.8295 (ptm) cc_final: 0.7941 (ptm) REVERT: D 400 TYR cc_start: 0.7559 (m-80) cc_final: 0.7322 (m-80) REVERT: D 465 GLN cc_start: 0.8755 (pp30) cc_final: 0.8184 (pp30) REVERT: D 468 CYS cc_start: 0.9275 (t) cc_final: 0.8974 (t) REVERT: D 482 MET cc_start: 0.9218 (tpt) cc_final: 0.8876 (tpt) REVERT: D 489 LYS cc_start: 0.8854 (ptpt) cc_final: 0.8484 (ptpt) REVERT: O 1 MET cc_start: 0.8418 (mmp) cc_final: 0.8209 (mmm) REVERT: P 1 MET cc_start: 0.8601 (mpp) cc_final: 0.8217 (pmm) REVERT: E 21 GLN cc_start: 0.9229 (pm20) cc_final: 0.8764 (pm20) REVERT: E 32 TYR cc_start: 0.9368 (m-80) cc_final: 0.8735 (m-80) REVERT: E 36 LEU cc_start: 0.9045 (tp) cc_final: 0.8381 (tp) REVERT: E 38 LEU cc_start: 0.9597 (mm) cc_final: 0.8830 (mm) REVERT: E 48 GLN cc_start: 0.9286 (mt0) cc_final: 0.8916 (mt0) REVERT: E 82 MET cc_start: 0.9160 (ppp) cc_final: 0.8901 (ppp) REVERT: E 100 GLN cc_start: 0.9325 (mp10) cc_final: 0.9125 (mp10) REVERT: E 105 ARG cc_start: 0.8945 (mmm160) cc_final: 0.8008 (tpm170) REVERT: E 108 LYS cc_start: 0.9408 (tppt) cc_final: 0.8668 (tppt) REVERT: E 165 PHE cc_start: 0.8471 (p90) cc_final: 0.8244 (p90) REVERT: E 227 LEU cc_start: 0.9106 (tt) cc_final: 0.8835 (tt) REVERT: E 246 CYS cc_start: 0.9426 (t) cc_final: 0.8750 (p) REVERT: E 288 LYS cc_start: 0.9597 (mtmm) cc_final: 0.9282 (mttt) REVERT: E 319 ASP cc_start: 0.7591 (t70) cc_final: 0.7140 (t70) REVERT: E 325 MET cc_start: 0.8530 (ptm) cc_final: 0.7890 (ptm) REVERT: E 334 GLN cc_start: 0.9302 (mp10) cc_final: 0.8363 (mp10) REVERT: E 335 GLU cc_start: 0.8613 (mp0) cc_final: 0.8009 (mp0) REVERT: E 352 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8776 (tm-30) REVERT: E 353 TYR cc_start: 0.8855 (t80) cc_final: 0.8534 (t80) REVERT: E 357 PHE cc_start: 0.9285 (m-80) cc_final: 0.8946 (m-10) REVERT: E 364 ASP cc_start: 0.8518 (m-30) cc_final: 0.7087 (m-30) REVERT: E 375 LYS cc_start: 0.9662 (pttt) cc_final: 0.9458 (pttt) REVERT: E 385 MET cc_start: 0.8644 (ttp) cc_final: 0.8005 (ttp) REVERT: E 386 MET cc_start: 0.8531 (ppp) cc_final: 0.8217 (tmm) REVERT: E 420 MET cc_start: 0.8386 (mtm) cc_final: 0.7791 (mtp) REVERT: E 448 GLN cc_start: 0.8801 (mp10) cc_final: 0.8315 (mp10) REVERT: E 450 LYS cc_start: 0.9391 (mttp) cc_final: 0.9186 (mttp) REVERT: E 507 HIS cc_start: 0.8661 (t-90) cc_final: 0.8378 (t70) REVERT: E 513 LEU cc_start: 0.9036 (mp) cc_final: 0.8757 (mp) REVERT: F 18 LEU cc_start: 0.9500 (tp) cc_final: 0.9203 (tp) REVERT: F 36 LEU cc_start: 0.9334 (tp) cc_final: 0.9112 (tp) REVERT: F 37 ILE cc_start: 0.8973 (mm) cc_final: 0.8595 (mm) REVERT: F 70 MET cc_start: 0.8115 (tpp) cc_final: 0.6612 (tpt) REVERT: F 75 GLU cc_start: 0.7876 (pm20) cc_final: 0.7627 (pm20) REVERT: F 92 HIS cc_start: 0.9032 (p90) cc_final: 0.8723 (p-80) REVERT: F 103 GLU cc_start: 0.9597 (tp30) cc_final: 0.9153 (tp30) REVERT: F 106 LYS cc_start: 0.9407 (mtpt) cc_final: 0.9131 (mtpt) REVERT: F 108 LYS cc_start: 0.9206 (pttm) cc_final: 0.7992 (tppt) REVERT: F 131 PHE cc_start: 0.9141 (m-80) cc_final: 0.8807 (m-80) REVERT: F 132 GLU cc_start: 0.9488 (pt0) cc_final: 0.9175 (pt0) REVERT: F 185 LEU cc_start: 0.8951 (mt) cc_final: 0.8269 (mt) REVERT: F 238 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8465 (tppt) REVERT: F 250 ILE cc_start: 0.9379 (mp) cc_final: 0.8858 (tp) REVERT: F 287 ILE cc_start: 0.9517 (pt) cc_final: 0.9279 (pt) REVERT: F 291 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9080 (tppt) REVERT: F 322 ARG cc_start: 0.8677 (ttt-90) cc_final: 0.8275 (ttt90) REVERT: F 334 GLN cc_start: 0.9296 (mt0) cc_final: 0.8751 (mm-40) REVERT: F 343 GLN cc_start: 0.8524 (tm-30) cc_final: 0.7869 (tm-30) REVERT: F 355 ARG cc_start: 0.8384 (ppt170) cc_final: 0.7955 (ttp-170) REVERT: F 364 ASP cc_start: 0.7365 (m-30) cc_final: 0.6817 (m-30) REVERT: F 372 HIS cc_start: 0.9048 (m170) cc_final: 0.8509 (m170) REVERT: F 386 MET cc_start: 0.6776 (ptm) cc_final: 0.6216 (ppp) REVERT: F 399 GLU cc_start: 0.7564 (mp0) cc_final: 0.7350 (mp0) REVERT: F 404 ASP cc_start: 0.8495 (t0) cc_final: 0.8198 (t0) REVERT: F 455 LYS cc_start: 0.9415 (pttp) cc_final: 0.9142 (ptmm) REVERT: F 482 MET cc_start: 0.8910 (ptp) cc_final: 0.8504 (ptp) REVERT: F 491 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8196 (tm-30) REVERT: F 493 ARG cc_start: 0.8841 (ptt-90) cc_final: 0.8511 (ptt-90) REVERT: F 506 LEU cc_start: 0.8851 (pt) cc_final: 0.8581 (pt) REVERT: F 507 HIS cc_start: 0.8777 (t-90) cc_final: 0.8550 (t-90) REVERT: G 16 ASP cc_start: 0.7658 (t0) cc_final: 0.7293 (t0) REVERT: G 43 ASP cc_start: 0.8427 (m-30) cc_final: 0.8063 (m-30) REVERT: G 47 ASP cc_start: 0.9594 (m-30) cc_final: 0.8960 (p0) REVERT: G 78 MET cc_start: 0.9541 (tpp) cc_final: 0.9242 (tpp) REVERT: G 199 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8556 (tp30) REVERT: G 200 ILE cc_start: 0.9294 (mm) cc_final: 0.8827 (mm) REVERT: G 203 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8165 (mtm110) REVERT: G 229 LYS cc_start: 0.9355 (ptpp) cc_final: 0.9066 (mmmt) REVERT: G 243 GLN cc_start: 0.9258 (tp-100) cc_final: 0.8767 (tp-100) REVERT: G 274 ASP cc_start: 0.9267 (t0) cc_final: 0.8844 (t70) REVERT: G 287 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9223 (tt) REVERT: G 289 TYR cc_start: 0.9368 (t80) cc_final: 0.9066 (t80) REVERT: G 290 ILE cc_start: 0.9448 (pt) cc_final: 0.9176 (pt) REVERT: G 291 LYS cc_start: 0.9013 (ptpp) cc_final: 0.8626 (pttm) REVERT: G 331 CYS cc_start: 0.9086 (t) cc_final: 0.8879 (t) REVERT: G 332 ILE cc_start: 0.9591 (pt) cc_final: 0.9384 (pt) REVERT: G 333 THR cc_start: 0.9721 (p) cc_final: 0.9129 (p) REVERT: G 334 GLN cc_start: 0.9151 (mp10) cc_final: 0.8527 (mp10) REVERT: G 335 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8054 (tm-30) REVERT: G 336 VAL cc_start: 0.9526 (m) cc_final: 0.8661 (m) REVERT: G 349 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8694 (mtpt) REVERT: G 395 GLU cc_start: 0.8749 (mp0) cc_final: 0.8496 (mp0) REVERT: G 441 GLN cc_start: 0.8556 (mp-120) cc_final: 0.8203 (mp-120) REVERT: G 444 SER cc_start: 0.8489 (t) cc_final: 0.8177 (t) REVERT: G 482 MET cc_start: 0.9390 (tpp) cc_final: 0.8832 (tpp) REVERT: G 493 ARG cc_start: 0.8747 (mtm180) cc_final: 0.8121 (mtm-85) REVERT: G 500 GLU cc_start: 0.9236 (pp20) cc_final: 0.8667 (pp20) REVERT: H 21 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8346 (tp40) REVERT: H 25 ASN cc_start: 0.8505 (m110) cc_final: 0.7064 (m110) REVERT: H 63 THR cc_start: 0.8136 (t) cc_final: 0.7934 (t) REVERT: H 91 ILE cc_start: 0.9225 (tp) cc_final: 0.8931 (tp) REVERT: H 108 LYS cc_start: 0.9004 (tptm) cc_final: 0.8537 (tptp) REVERT: H 112 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8904 (tm-30) REVERT: H 179 MET cc_start: 0.7518 (ppp) cc_final: 0.6986 (ppp) REVERT: H 257 LYS cc_start: 0.9796 (ptpp) cc_final: 0.9489 (mmtm) REVERT: H 258 TYR cc_start: 0.9488 (t80) cc_final: 0.9259 (t80) REVERT: H 286 MET cc_start: 0.9656 (tpt) cc_final: 0.9289 (tpt) REVERT: H 289 TYR cc_start: 0.9397 (t80) cc_final: 0.9042 (t80) REVERT: H 290 ILE cc_start: 0.9745 (pt) cc_final: 0.9379 (pt) REVERT: H 315 ASP cc_start: 0.9276 (m-30) cc_final: 0.8881 (p0) REVERT: H 352 GLU cc_start: 0.9348 (tm-30) cc_final: 0.9003 (tm-30) REVERT: H 368 GLN cc_start: 0.8675 (mt0) cc_final: 0.8285 (mm-40) REVERT: H 385 MET cc_start: 0.7831 (tpt) cc_final: 0.6787 (tpt) REVERT: H 399 GLU cc_start: 0.7419 (pp20) cc_final: 0.7119 (pp20) REVERT: H 410 LYS cc_start: 0.9077 (mptt) cc_final: 0.8839 (mmtm) REVERT: H 414 MET cc_start: 0.8381 (pmm) cc_final: 0.7954 (pmm) REVERT: H 465 GLN cc_start: 0.8789 (pp30) cc_final: 0.8542 (tt0) REVERT: H 468 CYS cc_start: 0.9210 (t) cc_final: 0.8930 (t) REVERT: H 482 MET cc_start: 0.8910 (tpt) cc_final: 0.8681 (tpp) REVERT: K 1 MET cc_start: 0.8023 (mmt) cc_final: 0.7792 (mmp) REVERT: L 1 MET cc_start: 0.8571 (mpp) cc_final: 0.8176 (pmm) outliers start: 7 outliers final: 0 residues processed: 1467 average time/residue: 0.1860 time to fit residues: 445.3324 Evaluate side-chains 1234 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1232 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 59 optimal weight: 6.9990 chunk 314 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.079804 restraints weight = 76297.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.083230 restraints weight = 42416.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085527 restraints weight = 28050.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087345 restraints weight = 20784.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.088588 restraints weight = 16343.356| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 32220 Z= 0.327 Angle : 0.934 11.753 43712 Z= 0.475 Chirality : 0.055 0.339 4984 Planarity : 0.006 0.095 5452 Dihedral : 13.987 175.446 4572 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 25.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.12 % Allowed : 6.05 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.12), residues: 3968 helix: -1.77 (0.13), residues: 1246 sheet: -2.67 (0.22), residues: 426 loop : -2.13 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 322 TYR 0.028 0.003 TYR A 110 PHE 0.026 0.003 PHE H 131 HIS 0.021 0.002 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.33 (32212) covalent geometry : angle 0.93402 / 0.47 (43712) hydrogen bonds : bond 0.04752 / 3.12 ( 966) hydrogen bonds : angle 6.76985 / 4.63 ( 2655) Misc. bond : bond 0.00189 / 0.13 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1370 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.9370 (pm20) cc_final: 0.9053 (pm20) REVERT: A 36 LEU cc_start: 0.9109 (tp) cc_final: 0.8620 (tp) REVERT: A 38 LEU cc_start: 0.9650 (mm) cc_final: 0.8806 (mm) REVERT: A 48 GLN cc_start: 0.9232 (mt0) cc_final: 0.8737 (mt0) REVERT: A 78 MET cc_start: 0.9307 (tpp) cc_final: 0.8811 (tpp) REVERT: A 105 ARG cc_start: 0.9027 (mmm160) cc_final: 0.8299 (tpm170) REVERT: A 108 LYS cc_start: 0.9509 (tptp) cc_final: 0.9231 (tptp) REVERT: A 109 LYS cc_start: 0.9448 (ptpp) cc_final: 0.8929 (pttt) REVERT: A 110 TYR cc_start: 0.9225 (t80) cc_final: 0.8967 (t80) REVERT: A 129 ASP cc_start: 0.8686 (m-30) cc_final: 0.8475 (m-30) REVERT: A 158 ILE cc_start: 0.8960 (mm) cc_final: 0.8441 (tp) REVERT: A 179 MET cc_start: 0.7583 (pmm) cc_final: 0.7005 (pmm) REVERT: A 246 CYS cc_start: 0.9420 (t) cc_final: 0.8477 (p) REVERT: A 262 LEU cc_start: 0.9580 (pt) cc_final: 0.9335 (pp) REVERT: A 319 ASP cc_start: 0.7579 (t70) cc_final: 0.7113 (t70) REVERT: A 334 GLN cc_start: 0.9370 (mp10) cc_final: 0.8487 (mp10) REVERT: A 335 GLU cc_start: 0.8642 (mp0) cc_final: 0.8230 (mp0) REVERT: A 352 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8817 (tm-30) REVERT: A 355 ARG cc_start: 0.8690 (ptt90) cc_final: 0.8135 (ptt90) REVERT: A 375 LYS cc_start: 0.9660 (pttt) cc_final: 0.9289 (pttt) REVERT: A 386 MET cc_start: 0.8671 (ppp) cc_final: 0.8231 (ppp) REVERT: A 420 MET cc_start: 0.8397 (mtm) cc_final: 0.7924 (mtp) REVERT: A 454 HIS cc_start: 0.8940 (m90) cc_final: 0.8731 (m90) REVERT: A 480 ARG cc_start: 0.8939 (mpp80) cc_final: 0.8527 (mtm110) REVERT: A 482 MET cc_start: 0.9026 (ttt) cc_final: 0.8814 (ttt) REVERT: A 498 GLN cc_start: 0.9031 (pm20) cc_final: 0.8825 (pm20) REVERT: A 507 HIS cc_start: 0.8809 (t-90) cc_final: 0.8469 (t70) REVERT: A 510 GLU cc_start: 0.8426 (pp20) cc_final: 0.8206 (pp20) REVERT: B 16 ASP cc_start: 0.8053 (t0) cc_final: 0.6627 (t0) REVERT: B 18 LEU cc_start: 0.9598 (tp) cc_final: 0.9355 (tp) REVERT: B 31 THR cc_start: 0.8378 (m) cc_final: 0.8106 (m) REVERT: B 34 ASP cc_start: 0.8480 (m-30) cc_final: 0.8224 (m-30) REVERT: B 36 LEU cc_start: 0.9321 (tp) cc_final: 0.9053 (tp) REVERT: B 37 ILE cc_start: 0.9329 (mm) cc_final: 0.8919 (mm) REVERT: B 82 MET cc_start: 0.9500 (ttm) cc_final: 0.9253 (ttm) REVERT: B 106 LYS cc_start: 0.9421 (mtpt) cc_final: 0.9137 (mtpt) REVERT: B 108 LYS cc_start: 0.9446 (pttm) cc_final: 0.8665 (tppt) REVERT: B 132 GLU cc_start: 0.9569 (pt0) cc_final: 0.9254 (pt0) REVERT: B 166 LEU cc_start: 0.9418 (mm) cc_final: 0.8990 (tp) REVERT: B 181 LYS cc_start: 0.9249 (tppt) cc_final: 0.8819 (tppt) REVERT: B 185 LEU cc_start: 0.8882 (mt) cc_final: 0.8436 (mt) REVERT: B 291 LYS cc_start: 0.9616 (mmmt) cc_final: 0.9066 (tppt) REVERT: B 334 GLN cc_start: 0.9294 (mt0) cc_final: 0.8811 (mm-40) REVERT: B 335 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8380 (tm-30) REVERT: B 343 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8019 (tm-30) REVERT: B 349 LYS cc_start: 0.9435 (mttt) cc_final: 0.9207 (mmmm) REVERT: B 372 HIS cc_start: 0.9143 (m170) cc_final: 0.8444 (m170) REVERT: B 385 MET cc_start: 0.9113 (ttp) cc_final: 0.8758 (ttp) REVERT: B 404 ASP cc_start: 0.8744 (t0) cc_final: 0.8464 (t0) REVERT: C 32 TYR cc_start: 0.9003 (m-10) cc_final: 0.8624 (m-10) REVERT: C 35 PHE cc_start: 0.9400 (p90) cc_final: 0.9150 (p90) REVERT: C 47 ASP cc_start: 0.9599 (m-30) cc_final: 0.8977 (p0) REVERT: C 82 MET cc_start: 0.9639 (tpp) cc_final: 0.9266 (tpp) REVERT: C 90 PHE cc_start: 0.8983 (m-80) cc_final: 0.8645 (m-80) REVERT: C 140 CYS cc_start: 0.4386 (m) cc_final: 0.4143 (m) REVERT: C 175 LEU cc_start: 0.9315 (mt) cc_final: 0.9080 (mt) REVERT: C 199 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8651 (tp30) REVERT: C 200 ILE cc_start: 0.9287 (mm) cc_final: 0.8892 (mm) REVERT: C 203 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8200 (mtm110) REVERT: C 229 LYS cc_start: 0.9401 (ptpp) cc_final: 0.9098 (mmmt) REVERT: C 274 ASP cc_start: 0.9156 (t0) cc_final: 0.8930 (t0) REVERT: C 289 TYR cc_start: 0.9376 (t80) cc_final: 0.9128 (t80) REVERT: C 290 ILE cc_start: 0.9453 (pt) cc_final: 0.9148 (pt) REVERT: C 331 CYS cc_start: 0.8995 (t) cc_final: 0.8691 (t) REVERT: C 333 THR cc_start: 0.9702 (p) cc_final: 0.9177 (p) REVERT: C 334 GLN cc_start: 0.9190 (mp10) cc_final: 0.8471 (mp10) REVERT: C 349 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8749 (mtmt) REVERT: C 362 ILE cc_start: 0.9513 (pt) cc_final: 0.9218 (mm) REVERT: C 482 MET cc_start: 0.9350 (tpp) cc_final: 0.9002 (mmm) REVERT: C 500 GLU cc_start: 0.9207 (pp20) cc_final: 0.8637 (pp20) REVERT: D 12 TYR cc_start: 0.8536 (t80) cc_final: 0.7191 (m-80) REVERT: D 26 CYS cc_start: 0.8556 (t) cc_final: 0.8284 (t) REVERT: D 32 TYR cc_start: 0.9143 (m-80) cc_final: 0.8615 (m-10) REVERT: D 33 ASN cc_start: 0.9191 (t0) cc_final: 0.8872 (t0) REVERT: D 38 LEU cc_start: 0.9544 (mt) cc_final: 0.9298 (mt) REVERT: D 51 LEU cc_start: 0.9493 (pp) cc_final: 0.9228 (pp) REVERT: D 91 ILE cc_start: 0.9186 (tp) cc_final: 0.8960 (tp) REVERT: D 110 TYR cc_start: 0.9004 (t80) cc_final: 0.8804 (t80) REVERT: D 114 PHE cc_start: 0.9016 (m-80) cc_final: 0.8507 (m-80) REVERT: D 179 MET cc_start: 0.6231 (ppp) cc_final: 0.4836 (pmm) REVERT: D 215 ASP cc_start: 0.9567 (m-30) cc_final: 0.9020 (p0) REVERT: D 242 LYS cc_start: 0.9363 (mmpt) cc_final: 0.9139 (mmmt) REVERT: D 257 LYS cc_start: 0.9805 (ptpp) cc_final: 0.9575 (mmtm) REVERT: D 286 MET cc_start: 0.9623 (tpt) cc_final: 0.9332 (tpt) REVERT: D 289 TYR cc_start: 0.9380 (t80) cc_final: 0.9069 (t80) REVERT: D 290 ILE cc_start: 0.9775 (pt) cc_final: 0.9399 (pt) REVERT: D 315 ASP cc_start: 0.9353 (m-30) cc_final: 0.8808 (p0) REVERT: D 322 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7871 (ttt90) REVERT: D 349 LYS cc_start: 0.9691 (mmtp) cc_final: 0.9406 (mmmm) REVERT: D 352 GLU cc_start: 0.9398 (tm-30) cc_final: 0.9095 (tm-30) REVERT: D 364 ASP cc_start: 0.6388 (m-30) cc_final: 0.4654 (m-30) REVERT: D 385 MET cc_start: 0.8856 (tpt) cc_final: 0.8379 (tpt) REVERT: D 465 GLN cc_start: 0.8630 (pp30) cc_final: 0.7744 (pp30) REVERT: D 468 CYS cc_start: 0.9262 (t) cc_final: 0.8931 (t) REVERT: D 469 GLN cc_start: 0.8675 (mm110) cc_final: 0.8391 (mm110) REVERT: D 482 MET cc_start: 0.9261 (tpt) cc_final: 0.8834 (tpp) REVERT: D 492 LYS cc_start: 0.9320 (pttt) cc_final: 0.8820 (pttp) REVERT: N 12 TYR cc_start: 0.9089 (t80) cc_final: 0.8204 (t80) REVERT: P 1 MET cc_start: 0.8651 (mpp) cc_final: 0.8208 (pmm) REVERT: E 21 GLN cc_start: 0.9415 (pm20) cc_final: 0.9065 (pm20) REVERT: E 28 ASP cc_start: 0.9145 (t70) cc_final: 0.8864 (t70) REVERT: E 32 TYR cc_start: 0.9433 (m-80) cc_final: 0.8728 (m-80) REVERT: E 36 LEU cc_start: 0.9190 (tp) cc_final: 0.8765 (tp) REVERT: E 38 LEU cc_start: 0.9625 (mm) cc_final: 0.8883 (mm) REVERT: E 48 GLN cc_start: 0.9250 (mt0) cc_final: 0.8731 (mt0) REVERT: E 105 ARG cc_start: 0.8962 (mmm160) cc_final: 0.8729 (tpp80) REVERT: E 108 LYS cc_start: 0.9435 (tppt) cc_final: 0.9113 (tppt) REVERT: E 142 ILE cc_start: 0.8645 (tp) cc_final: 0.8408 (tp) REVERT: E 158 ILE cc_start: 0.9001 (mm) cc_final: 0.8747 (tp) REVERT: E 165 PHE cc_start: 0.8620 (p90) cc_final: 0.8410 (p90) REVERT: E 179 MET cc_start: 0.7539 (pmm) cc_final: 0.6978 (pmm) REVERT: E 227 LEU cc_start: 0.9224 (tt) cc_final: 0.8990 (tt) REVERT: E 228 LYS cc_start: 0.9518 (ptpp) cc_final: 0.9292 (ptpp) REVERT: E 246 CYS cc_start: 0.9460 (t) cc_final: 0.8456 (p) REVERT: E 256 ASP cc_start: 0.9048 (p0) cc_final: 0.8691 (m-30) REVERT: E 262 LEU cc_start: 0.9640 (pt) cc_final: 0.9419 (pt) REVERT: E 319 ASP cc_start: 0.7774 (t70) cc_final: 0.7279 (t70) REVERT: E 325 MET cc_start: 0.8922 (ptm) cc_final: 0.8330 (ptm) REVERT: E 332 ILE cc_start: 0.9515 (pt) cc_final: 0.9047 (pt) REVERT: E 334 GLN cc_start: 0.9250 (mp10) cc_final: 0.8404 (mp10) REVERT: E 335 GLU cc_start: 0.8637 (mp0) cc_final: 0.7834 (mp0) REVERT: E 352 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8775 (tm-30) REVERT: E 355 ARG cc_start: 0.8753 (ptt90) cc_final: 0.8498 (ptt90) REVERT: E 369 ASN cc_start: 0.9202 (p0) cc_final: 0.8776 (p0) REVERT: E 386 MET cc_start: 0.8597 (ppp) cc_final: 0.8207 (tmm) REVERT: E 414 MET cc_start: 0.8000 (ptp) cc_final: 0.7552 (ptp) REVERT: E 420 MET cc_start: 0.8458 (mtm) cc_final: 0.7940 (mtp) REVERT: E 448 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: E 454 HIS cc_start: 0.8972 (m90) cc_final: 0.8750 (m90) REVERT: E 456 PHE cc_start: 0.9538 (t80) cc_final: 0.9319 (t80) REVERT: E 460 LEU cc_start: 0.9720 (mp) cc_final: 0.9438 (mp) REVERT: E 480 ARG cc_start: 0.8975 (mpp80) cc_final: 0.8177 (mpp80) REVERT: E 482 MET cc_start: 0.8946 (ttt) cc_final: 0.8728 (ttt) REVERT: E 507 HIS cc_start: 0.8870 (t-90) cc_final: 0.8548 (t70) REVERT: F 34 ASP cc_start: 0.8454 (m-30) cc_final: 0.8246 (m-30) REVERT: F 36 LEU cc_start: 0.9320 (tp) cc_final: 0.9103 (tp) REVERT: F 37 ILE cc_start: 0.9297 (mm) cc_final: 0.8884 (mm) REVERT: F 70 MET cc_start: 0.8266 (tpp) cc_final: 0.7548 (mmm) REVERT: F 82 MET cc_start: 0.9467 (ttt) cc_final: 0.8850 (tmm) REVERT: F 106 LYS cc_start: 0.9458 (mtpt) cc_final: 0.9247 (mtpt) REVERT: F 108 LYS cc_start: 0.9336 (pttm) cc_final: 0.8183 (tppt) REVERT: F 117 ASP cc_start: 0.9395 (p0) cc_final: 0.9195 (p0) REVERT: F 132 GLU cc_start: 0.9512 (pt0) cc_final: 0.9267 (pt0) REVERT: F 185 LEU cc_start: 0.8843 (mt) cc_final: 0.8253 (mt) REVERT: F 287 ILE cc_start: 0.9578 (pt) cc_final: 0.9352 (pt) REVERT: F 289 TYR cc_start: 0.9509 (t80) cc_final: 0.9132 (t80) REVERT: F 291 LYS cc_start: 0.9584 (mmmt) cc_final: 0.9046 (tppt) REVERT: F 334 GLN cc_start: 0.9294 (mt0) cc_final: 0.8777 (mm-40) REVERT: F 335 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8336 (tm-30) REVERT: F 343 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8074 (tm-30) REVERT: F 355 ARG cc_start: 0.8585 (ppt170) cc_final: 0.7970 (ttp-170) REVERT: F 372 HIS cc_start: 0.9186 (m170) cc_final: 0.8618 (m170) REVERT: F 404 ASP cc_start: 0.8739 (t0) cc_final: 0.8506 (t0) REVERT: F 482 MET cc_start: 0.8905 (ptp) cc_final: 0.8672 (ptp) REVERT: F 491 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8237 (tm-30) REVERT: F 506 LEU cc_start: 0.9076 (pt) cc_final: 0.8789 (pt) REVERT: F 507 HIS cc_start: 0.8854 (t-90) cc_final: 0.8651 (t-90) REVERT: G 32 TYR cc_start: 0.9053 (m-10) cc_final: 0.8839 (m-10) REVERT: G 43 ASP cc_start: 0.8418 (m-30) cc_final: 0.8202 (m-30) REVERT: G 47 ASP cc_start: 0.9637 (m-30) cc_final: 0.9094 (p0) REVERT: G 78 MET cc_start: 0.9575 (tpp) cc_final: 0.9225 (tpp) REVERT: G 175 LEU cc_start: 0.9240 (mt) cc_final: 0.9028 (mt) REVERT: G 199 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8795 (tp30) REVERT: G 229 LYS cc_start: 0.9372 (ptpp) cc_final: 0.9037 (mmmt) REVERT: G 262 LEU cc_start: 0.9418 (pp) cc_final: 0.9163 (pp) REVERT: G 274 ASP cc_start: 0.9202 (t0) cc_final: 0.8918 (t0) REVERT: G 283 GLN cc_start: 0.9034 (mp10) cc_final: 0.8817 (mp10) REVERT: G 287 ILE cc_start: 0.9679 (mp) cc_final: 0.9245 (tt) REVERT: G 289 TYR cc_start: 0.9354 (t80) cc_final: 0.9057 (t80) REVERT: G 290 ILE cc_start: 0.9431 (pt) cc_final: 0.9166 (pt) REVERT: G 291 LYS cc_start: 0.9174 (ptpp) cc_final: 0.8827 (pttm) REVERT: G 331 CYS cc_start: 0.9033 (t) cc_final: 0.8776 (t) REVERT: G 332 ILE cc_start: 0.9652 (pt) cc_final: 0.9402 (pt) REVERT: G 333 THR cc_start: 0.9717 (p) cc_final: 0.9243 (p) REVERT: G 334 GLN cc_start: 0.9177 (mp10) cc_final: 0.8428 (mp10) REVERT: G 335 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8255 (tm-30) REVERT: G 336 VAL cc_start: 0.9584 (m) cc_final: 0.8616 (m) REVERT: G 349 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8600 (mtpt) REVERT: G 386 MET cc_start: 0.9013 (tmm) cc_final: 0.8729 (tmm) REVERT: G 390 LEU cc_start: 0.9316 (pt) cc_final: 0.9108 (pt) REVERT: G 395 GLU cc_start: 0.8783 (mp0) cc_final: 0.8442 (mp0) REVERT: G 482 MET cc_start: 0.9376 (tpp) cc_final: 0.9093 (tpt) REVERT: G 500 GLU cc_start: 0.9273 (pp20) cc_final: 0.8546 (pp20) REVERT: H 16 ASP cc_start: 0.8471 (m-30) cc_final: 0.8269 (m-30) REVERT: H 21 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8645 (tm-30) REVERT: H 33 ASN cc_start: 0.9209 (t0) cc_final: 0.8748 (t0) REVERT: H 63 THR cc_start: 0.8359 (t) cc_final: 0.8052 (t) REVERT: H 70 MET cc_start: 0.8897 (mmt) cc_final: 0.8508 (mmt) REVERT: H 91 ILE cc_start: 0.9234 (tp) cc_final: 0.8986 (tp) REVERT: H 93 HIS cc_start: 0.9142 (p-80) cc_final: 0.8721 (p-80) REVERT: H 112 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8887 (tm-30) REVERT: H 179 MET cc_start: 0.7352 (ppp) cc_final: 0.7016 (ppp) REVERT: H 215 ASP cc_start: 0.9527 (m-30) cc_final: 0.9046 (p0) REVERT: H 286 MET cc_start: 0.9632 (tpt) cc_final: 0.9203 (tpt) REVERT: H 290 ILE cc_start: 0.9773 (pt) cc_final: 0.9409 (pt) REVERT: H 315 ASP cc_start: 0.9311 (m-30) cc_final: 0.8829 (p0) REVERT: H 349 LYS cc_start: 0.9649 (mmtp) cc_final: 0.9308 (mmmm) REVERT: H 352 GLU cc_start: 0.9357 (tm-30) cc_final: 0.9043 (tm-30) REVERT: H 368 GLN cc_start: 0.8680 (mt0) cc_final: 0.8403 (mm-40) REVERT: H 385 MET cc_start: 0.8760 (tpt) cc_final: 0.8397 (tpt) REVERT: H 414 MET cc_start: 0.8641 (pmm) cc_final: 0.8375 (pmm) REVERT: H 465 GLN cc_start: 0.8665 (pp30) cc_final: 0.8358 (tt0) REVERT: H 468 CYS cc_start: 0.9264 (t) cc_final: 0.9018 (t) REVERT: H 482 MET cc_start: 0.9115 (tpt) cc_final: 0.8609 (tpp) REVERT: J 5 LEU cc_start: 0.9221 (mt) cc_final: 0.8899 (mt) REVERT: J 11 SER cc_start: 0.8576 (m) cc_final: 0.8357 (p) REVERT: J 12 TYR cc_start: 0.9149 (t80) cc_final: 0.8374 (t80) REVERT: L 1 MET cc_start: 0.8655 (mpp) cc_final: 0.8213 (pmm) outliers start: 4 outliers final: 2 residues processed: 1373 average time/residue: 0.1935 time to fit residues: 437.4793 Evaluate side-chains 1151 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1148 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 353 optimal weight: 0.1980 chunk 391 optimal weight: 9.9990 chunk 185 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 chunk 308 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 chunk 334 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS A 504 HIS B 171 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 93 HIS ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.085615 restraints weight = 73162.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.089373 restraints weight = 40140.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092002 restraints weight = 26228.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093679 restraints weight = 19092.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095126 restraints weight = 15255.215| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32220 Z= 0.163 Angle : 0.877 11.524 43712 Z= 0.430 Chirality : 0.054 0.506 4984 Planarity : 0.005 0.106 5452 Dihedral : 13.486 175.291 4572 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.85 % Favored : 91.13 % Rotamer: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.12), residues: 3968 helix: -1.75 (0.13), residues: 1246 sheet: -2.50 (0.22), residues: 402 loop : -1.97 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 203 TYR 0.031 0.002 TYR B 233 PHE 0.032 0.002 PHE A 456 HIS 0.012 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (32212) covalent geometry : angle 0.87713 / 0.43 (43712) hydrogen bonds : bond 0.04225 / 2.73 ( 966) hydrogen bonds : angle 6.53052 / 4.46 ( 2655) Misc. bond : bond 0.00262 / 0.21 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1447 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.9204 (pm20) cc_final: 0.8892 (pm20) REVERT: A 28 ASP cc_start: 0.9045 (t70) cc_final: 0.8463 (t70) REVERT: A 32 TYR cc_start: 0.8698 (m-10) cc_final: 0.8084 (m-80) REVERT: A 36 LEU cc_start: 0.9119 (tp) cc_final: 0.8354 (tp) REVERT: A 38 LEU cc_start: 0.9622 (mm) cc_final: 0.8759 (mm) REVERT: A 48 GLN cc_start: 0.9263 (mt0) cc_final: 0.8894 (mt0) REVERT: A 75 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 78 MET cc_start: 0.9225 (tpp) cc_final: 0.8793 (tpp) REVERT: A 105 ARG cc_start: 0.9005 (mmm160) cc_final: 0.8348 (tpm170) REVERT: A 108 LYS cc_start: 0.9491 (tptp) cc_final: 0.9223 (tptp) REVERT: A 109 LYS cc_start: 0.9410 (ptpp) cc_final: 0.8856 (pttt) REVERT: A 129 ASP cc_start: 0.8730 (m-30) cc_final: 0.8528 (m-30) REVERT: A 150 MET cc_start: 0.7740 (tpt) cc_final: 0.7200 (tpt) REVERT: A 158 ILE cc_start: 0.8982 (mm) cc_final: 0.8489 (tp) REVERT: A 179 MET cc_start: 0.7494 (pmm) cc_final: 0.6988 (pmm) REVERT: A 246 CYS cc_start: 0.9401 (t) cc_final: 0.8528 (p) REVERT: A 250 ILE cc_start: 0.9673 (pt) cc_final: 0.9472 (pt) REVERT: A 262 LEU cc_start: 0.9562 (pt) cc_final: 0.9314 (pp) REVERT: A 273 LEU cc_start: 0.9645 (tp) cc_final: 0.9340 (tp) REVERT: A 319 ASP cc_start: 0.7560 (t70) cc_final: 0.7161 (t70) REVERT: A 325 MET cc_start: 0.9076 (ptm) cc_final: 0.8259 (ptm) REVERT: A 332 ILE cc_start: 0.9443 (pt) cc_final: 0.9090 (pt) REVERT: A 334 GLN cc_start: 0.9412 (mp10) cc_final: 0.8450 (mp10) REVERT: A 335 GLU cc_start: 0.8659 (mp0) cc_final: 0.7819 (mp0) REVERT: A 343 GLN cc_start: 0.8345 (pp30) cc_final: 0.7314 (pp30) REVERT: A 352 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8767 (tm-30) REVERT: A 355 ARG cc_start: 0.8603 (ptt90) cc_final: 0.8059 (ptt90) REVERT: A 375 LYS cc_start: 0.9555 (pttt) cc_final: 0.9338 (pttt) REVERT: A 385 MET cc_start: 0.8764 (ttp) cc_final: 0.7850 (ttp) REVERT: A 386 MET cc_start: 0.8495 (ppp) cc_final: 0.8208 (ppp) REVERT: A 420 MET cc_start: 0.8335 (mtm) cc_final: 0.7853 (mtp) REVERT: A 454 HIS cc_start: 0.8926 (m90) cc_final: 0.8704 (m90) REVERT: A 480 ARG cc_start: 0.8870 (mpp80) cc_final: 0.8077 (mpp80) REVERT: A 482 MET cc_start: 0.8965 (ttt) cc_final: 0.8725 (ttt) REVERT: A 498 GLN cc_start: 0.8914 (pm20) cc_final: 0.8635 (pm20) REVERT: A 507 HIS cc_start: 0.8559 (t-90) cc_final: 0.8255 (t70) REVERT: A 510 GLU cc_start: 0.8530 (pp20) cc_final: 0.8322 (pp20) REVERT: B 18 LEU cc_start: 0.9451 (tp) cc_final: 0.9189 (tp) REVERT: B 36 LEU cc_start: 0.9300 (tp) cc_final: 0.9014 (tp) REVERT: B 37 ILE cc_start: 0.9190 (mm) cc_final: 0.8793 (mm) REVERT: B 82 MET cc_start: 0.9509 (ttm) cc_final: 0.9306 (ttm) REVERT: B 106 LYS cc_start: 0.9388 (mtpt) cc_final: 0.9128 (mtpt) REVERT: B 108 LYS cc_start: 0.9402 (pttm) cc_final: 0.8596 (tppt) REVERT: B 131 PHE cc_start: 0.9187 (m-80) cc_final: 0.8937 (m-80) REVERT: B 132 GLU cc_start: 0.9574 (pt0) cc_final: 0.9283 (pt0) REVERT: B 166 LEU cc_start: 0.9388 (mm) cc_final: 0.9049 (tp) REVERT: B 181 LYS cc_start: 0.9210 (tppt) cc_final: 0.8818 (tppt) REVERT: B 183 GLU cc_start: 0.8985 (pm20) cc_final: 0.8645 (pm20) REVERT: B 185 LEU cc_start: 0.8954 (mt) cc_final: 0.8484 (mt) REVERT: B 192 ILE cc_start: 0.9330 (mt) cc_final: 0.9129 (mt) REVERT: B 200 ILE cc_start: 0.9743 (mt) cc_final: 0.9375 (mm) REVERT: B 238 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8466 (tppt) REVERT: B 287 ILE cc_start: 0.9548 (pt) cc_final: 0.9333 (pt) REVERT: B 291 LYS cc_start: 0.9600 (mmmt) cc_final: 0.9050 (tppt) REVERT: B 322 ARG cc_start: 0.9151 (ttt90) cc_final: 0.8776 (ttt90) REVERT: B 334 GLN cc_start: 0.9238 (mt0) cc_final: 0.8682 (mm-40) REVERT: B 335 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 349 LYS cc_start: 0.9451 (mttt) cc_final: 0.9244 (mmmm) REVERT: B 372 HIS cc_start: 0.9078 (m170) cc_final: 0.8610 (m170) REVERT: B 385 MET cc_start: 0.8688 (ttp) cc_final: 0.8352 (ttp) REVERT: B 404 ASP cc_start: 0.8715 (t0) cc_final: 0.8406 (t0) REVERT: B 414 MET cc_start: 0.8970 (mpp) cc_final: 0.8528 (mpp) REVERT: B 482 MET cc_start: 0.8725 (ptp) cc_final: 0.8502 (ptp) REVERT: B 491 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 493 ARG cc_start: 0.8678 (ptt-90) cc_final: 0.8442 (ptt-90) REVERT: C 43 ASP cc_start: 0.8543 (m-30) cc_final: 0.8267 (m-30) REVERT: C 47 ASP cc_start: 0.9585 (m-30) cc_final: 0.8910 (p0) REVERT: C 82 MET cc_start: 0.9632 (tpp) cc_final: 0.9331 (tpp) REVERT: C 90 PHE cc_start: 0.9124 (m-80) cc_final: 0.8750 (m-80) REVERT: C 92 HIS cc_start: 0.8285 (p90) cc_final: 0.8056 (p90) REVERT: C 103 GLU cc_start: 0.9688 (mp0) cc_final: 0.9481 (mp0) REVERT: C 140 CYS cc_start: 0.4220 (m) cc_final: 0.3988 (m) REVERT: C 175 LEU cc_start: 0.9305 (mt) cc_final: 0.9058 (mt) REVERT: C 199 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8678 (tp30) REVERT: C 200 ILE cc_start: 0.9310 (mm) cc_final: 0.8859 (mm) REVERT: C 203 ARG cc_start: 0.8757 (mtm-85) cc_final: 0.8190 (mtm110) REVERT: C 229 LYS cc_start: 0.9390 (ptpp) cc_final: 0.9074 (mmmt) REVERT: C 274 ASP cc_start: 0.9271 (t0) cc_final: 0.8921 (t70) REVERT: C 289 TYR cc_start: 0.9390 (t80) cc_final: 0.9159 (t80) REVERT: C 311 LYS cc_start: 0.8921 (tttt) cc_final: 0.8708 (ttmt) REVERT: C 322 ARG cc_start: 0.8438 (ttt90) cc_final: 0.8052 (ttt90) REVERT: C 331 CYS cc_start: 0.9038 (t) cc_final: 0.8525 (t) REVERT: C 333 THR cc_start: 0.9715 (p) cc_final: 0.9191 (p) REVERT: C 334 GLN cc_start: 0.9165 (mp10) cc_final: 0.8351 (mp10) REVERT: C 349 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8845 (mtpt) REVERT: C 362 ILE cc_start: 0.9457 (pt) cc_final: 0.9193 (mm) REVERT: C 386 MET cc_start: 0.9005 (tmm) cc_final: 0.8790 (tmm) REVERT: C 390 LEU cc_start: 0.9449 (pt) cc_final: 0.9116 (pt) REVERT: C 441 GLN cc_start: 0.8593 (mp-120) cc_final: 0.8237 (mp-120) REVERT: C 482 MET cc_start: 0.9356 (tpp) cc_final: 0.9105 (mmm) REVERT: C 500 GLU cc_start: 0.9230 (pp20) cc_final: 0.8506 (pp20) REVERT: D 12 TYR cc_start: 0.8360 (t80) cc_final: 0.7064 (m-80) REVERT: D 21 GLN cc_start: 0.9043 (tp40) cc_final: 0.8709 (tp40) REVERT: D 26 CYS cc_start: 0.8661 (t) cc_final: 0.8443 (t) REVERT: D 33 ASN cc_start: 0.9162 (t0) cc_final: 0.8829 (t0) REVERT: D 51 LEU cc_start: 0.9461 (pp) cc_final: 0.9210 (pp) REVERT: D 71 ASP cc_start: 0.9083 (t0) cc_final: 0.8812 (t0) REVERT: D 91 ILE cc_start: 0.9135 (tp) cc_final: 0.8879 (tp) REVERT: D 93 HIS cc_start: 0.9448 (p-80) cc_final: 0.9191 (p-80) REVERT: D 114 PHE cc_start: 0.9029 (m-80) cc_final: 0.8658 (m-10) REVERT: D 144 ILE cc_start: 0.9112 (mm) cc_final: 0.8909 (tp) REVERT: D 170 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8040 (mp0) REVERT: D 179 MET cc_start: 0.6226 (ppp) cc_final: 0.4893 (pmm) REVERT: D 215 ASP cc_start: 0.9586 (m-30) cc_final: 0.9051 (p0) REVERT: D 229 LYS cc_start: 0.8964 (tmtt) cc_final: 0.8558 (mmtt) REVERT: D 242 LYS cc_start: 0.9318 (mmpt) cc_final: 0.9078 (mmmt) REVERT: D 257 LYS cc_start: 0.9814 (ptpp) cc_final: 0.9555 (mmtm) REVERT: D 286 MET cc_start: 0.9627 (tpt) cc_final: 0.9314 (tpt) REVERT: D 289 TYR cc_start: 0.9374 (t80) cc_final: 0.9022 (t80) REVERT: D 290 ILE cc_start: 0.9751 (pt) cc_final: 0.9415 (pt) REVERT: D 315 ASP cc_start: 0.9251 (m-30) cc_final: 0.8811 (p0) REVERT: D 349 LYS cc_start: 0.9656 (mmtp) cc_final: 0.9289 (mmmm) REVERT: D 352 GLU cc_start: 0.9376 (tm-30) cc_final: 0.9032 (tm-30) REVERT: D 379 LEU cc_start: 0.9631 (mm) cc_final: 0.9373 (mm) REVERT: D 385 MET cc_start: 0.8309 (tpt) cc_final: 0.7715 (tpt) REVERT: D 400 TYR cc_start: 0.7370 (m-80) cc_final: 0.7120 (m-80) REVERT: D 465 GLN cc_start: 0.8661 (pp30) cc_final: 0.8346 (tt0) REVERT: D 468 CYS cc_start: 0.9210 (t) cc_final: 0.8889 (t) REVERT: D 478 GLN cc_start: 0.9610 (tt0) cc_final: 0.9196 (tt0) REVERT: N 5 LEU cc_start: 0.9520 (mt) cc_final: 0.9043 (mt) REVERT: N 12 TYR cc_start: 0.9056 (t80) cc_final: 0.8395 (t80) REVERT: P 1 MET cc_start: 0.8550 (mpp) cc_final: 0.8211 (pmm) REVERT: E 21 GLN cc_start: 0.9234 (pm20) cc_final: 0.8836 (pm20) REVERT: E 28 ASP cc_start: 0.9279 (t70) cc_final: 0.8537 (t70) REVERT: E 32 TYR cc_start: 0.9329 (m-80) cc_final: 0.8739 (m-80) REVERT: E 36 LEU cc_start: 0.8997 (tp) cc_final: 0.8535 (tp) REVERT: E 38 LEU cc_start: 0.9586 (mm) cc_final: 0.8785 (mm) REVERT: E 48 GLN cc_start: 0.9324 (mt0) cc_final: 0.8903 (mt0) REVERT: E 105 ARG cc_start: 0.8985 (mmm160) cc_final: 0.8410 (tpm170) REVERT: E 150 MET cc_start: 0.7858 (tpt) cc_final: 0.7066 (tpt) REVERT: E 179 MET cc_start: 0.7543 (pmm) cc_final: 0.7303 (pmm) REVERT: E 228 LYS cc_start: 0.9519 (ptpp) cc_final: 0.9294 (ptpp) REVERT: E 246 CYS cc_start: 0.9455 (t) cc_final: 0.8649 (p) REVERT: E 256 ASP cc_start: 0.9012 (p0) cc_final: 0.8764 (m-30) REVERT: E 288 LYS cc_start: 0.9533 (mtmm) cc_final: 0.9264 (mttt) REVERT: E 319 ASP cc_start: 0.7733 (t70) cc_final: 0.7275 (t70) REVERT: E 325 MET cc_start: 0.8961 (ptm) cc_final: 0.8611 (ptm) REVERT: E 332 ILE cc_start: 0.9438 (pt) cc_final: 0.9081 (pt) REVERT: E 334 GLN cc_start: 0.9304 (mp10) cc_final: 0.8404 (mp10) REVERT: E 335 GLU cc_start: 0.8646 (mp0) cc_final: 0.7843 (mp0) REVERT: E 352 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8802 (tm-30) REVERT: E 353 TYR cc_start: 0.8942 (t80) cc_final: 0.8680 (t80) REVERT: E 364 ASP cc_start: 0.8749 (m-30) cc_final: 0.7383 (m-30) REVERT: E 375 LYS cc_start: 0.9699 (pttt) cc_final: 0.9466 (pttt) REVERT: E 385 MET cc_start: 0.8917 (ttp) cc_final: 0.8097 (ttp) REVERT: E 386 MET cc_start: 0.8612 (ppp) cc_final: 0.8008 (tmm) REVERT: E 420 MET cc_start: 0.8355 (mtm) cc_final: 0.7802 (mtp) REVERT: E 454 HIS cc_start: 0.8926 (m90) cc_final: 0.8693 (m90) REVERT: E 460 LEU cc_start: 0.9707 (mp) cc_final: 0.9479 (mp) REVERT: E 482 MET cc_start: 0.8921 (ttt) cc_final: 0.8711 (ttt) REVERT: E 507 HIS cc_start: 0.8569 (t-90) cc_final: 0.8307 (t70) REVERT: F 18 LEU cc_start: 0.9442 (tp) cc_final: 0.9214 (tp) REVERT: F 34 ASP cc_start: 0.8275 (m-30) cc_final: 0.8052 (m-30) REVERT: F 36 LEU cc_start: 0.9355 (tp) cc_final: 0.9098 (tp) REVERT: F 37 ILE cc_start: 0.9216 (mm) cc_final: 0.8791 (mm) REVERT: F 66 VAL cc_start: 0.9185 (p) cc_final: 0.8956 (p) REVERT: F 70 MET cc_start: 0.8233 (tpp) cc_final: 0.7522 (mmm) REVERT: F 82 MET cc_start: 0.9473 (ttt) cc_final: 0.8878 (tmm) REVERT: F 106 LYS cc_start: 0.9433 (mtpt) cc_final: 0.9144 (mtpt) REVERT: F 108 LYS cc_start: 0.9248 (pttm) cc_final: 0.8052 (tppt) REVERT: F 131 PHE cc_start: 0.9296 (m-10) cc_final: 0.8800 (m-80) REVERT: F 132 GLU cc_start: 0.9482 (pt0) cc_final: 0.9186 (pt0) REVERT: F 134 LYS cc_start: 0.9323 (ptpp) cc_final: 0.9078 (pttt) REVERT: F 178 ILE cc_start: 0.8991 (pt) cc_final: 0.8751 (pt) REVERT: F 185 LEU cc_start: 0.8844 (mt) cc_final: 0.8218 (mt) REVERT: F 199 GLU cc_start: 0.9516 (mt-10) cc_final: 0.9273 (mt-10) REVERT: F 233 TYR cc_start: 0.9435 (m-10) cc_final: 0.9233 (m-80) REVERT: F 250 ILE cc_start: 0.9343 (mp) cc_final: 0.8836 (tp) REVERT: F 287 ILE cc_start: 0.9531 (pt) cc_final: 0.9259 (pt) REVERT: F 289 TYR cc_start: 0.9478 (t80) cc_final: 0.9105 (t80) REVERT: F 291 LYS cc_start: 0.9529 (mmmt) cc_final: 0.8974 (tppt) REVERT: F 334 GLN cc_start: 0.9251 (mt0) cc_final: 0.8741 (mm-40) REVERT: F 337 LEU cc_start: 0.9259 (mm) cc_final: 0.9046 (mm) REVERT: F 343 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: F 351 SER cc_start: 0.9375 (p) cc_final: 0.9047 (p) REVERT: F 355 ARG cc_start: 0.8414 (ppt170) cc_final: 0.8135 (ttp-170) REVERT: F 372 HIS cc_start: 0.9126 (m170) cc_final: 0.8689 (m-70) REVERT: F 386 MET cc_start: 0.6954 (ptm) cc_final: 0.6251 (ppp) REVERT: F 400 TYR cc_start: 0.7536 (m-80) cc_final: 0.7013 (m-80) REVERT: F 404 ASP cc_start: 0.8589 (t0) cc_final: 0.8336 (t0) REVERT: F 491 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8265 (tm-30) REVERT: F 506 LEU cc_start: 0.8727 (pt) cc_final: 0.8448 (pt) REVERT: G 43 ASP cc_start: 0.8469 (m-30) cc_final: 0.8216 (m-30) REVERT: G 47 ASP cc_start: 0.9606 (m-30) cc_final: 0.9008 (p0) REVERT: G 78 MET cc_start: 0.9578 (tpp) cc_final: 0.9205 (tpp) REVERT: G 229 LYS cc_start: 0.9379 (ptpp) cc_final: 0.9070 (mmmt) REVERT: G 262 LEU cc_start: 0.9452 (pp) cc_final: 0.9205 (pp) REVERT: G 274 ASP cc_start: 0.9242 (t0) cc_final: 0.8944 (t70) REVERT: G 283 GLN cc_start: 0.8976 (mp10) cc_final: 0.8765 (mp10) REVERT: G 287 ILE cc_start: 0.9693 (mp) cc_final: 0.9230 (tt) REVERT: G 289 TYR cc_start: 0.9380 (t80) cc_final: 0.9082 (t80) REVERT: G 291 LYS cc_start: 0.9003 (ptpp) cc_final: 0.8573 (pttm) REVERT: G 331 CYS cc_start: 0.9094 (t) cc_final: 0.8703 (t) REVERT: G 332 ILE cc_start: 0.9629 (pt) cc_final: 0.9403 (pt) REVERT: G 333 THR cc_start: 0.9721 (p) cc_final: 0.9077 (p) REVERT: G 334 GLN cc_start: 0.9160 (mp10) cc_final: 0.8330 (mp10) REVERT: G 335 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8138 (tm-30) REVERT: G 336 VAL cc_start: 0.9536 (m) cc_final: 0.8612 (m) REVERT: G 386 MET cc_start: 0.9072 (tmm) cc_final: 0.8817 (tmm) REVERT: G 390 LEU cc_start: 0.9251 (pt) cc_final: 0.8904 (pt) REVERT: G 395 GLU cc_start: 0.8745 (mp0) cc_final: 0.8479 (mp0) REVERT: G 444 SER cc_start: 0.8610 (t) cc_final: 0.8135 (t) REVERT: G 482 MET cc_start: 0.9308 (tpp) cc_final: 0.8919 (mmm) REVERT: G 500 GLU cc_start: 0.9267 (pp20) cc_final: 0.8559 (pp20) REVERT: H 21 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8572 (tm-30) REVERT: H 51 LEU cc_start: 0.9479 (pp) cc_final: 0.9260 (pp) REVERT: H 63 THR cc_start: 0.8309 (t) cc_final: 0.8090 (t) REVERT: H 91 ILE cc_start: 0.9300 (tp) cc_final: 0.9019 (tp) REVERT: H 108 LYS cc_start: 0.9050 (tptm) cc_final: 0.8714 (tptp) REVERT: H 112 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8921 (tm-30) REVERT: H 179 MET cc_start: 0.7545 (ppp) cc_final: 0.7089 (ppp) REVERT: H 208 LYS cc_start: 0.8829 (tmtt) cc_final: 0.8568 (tmtt) REVERT: H 209 LEU cc_start: 0.8985 (tp) cc_final: 0.8630 (pp) REVERT: H 215 ASP cc_start: 0.9529 (m-30) cc_final: 0.9037 (p0) REVERT: H 229 LYS cc_start: 0.8870 (pttt) cc_final: 0.8643 (mmtt) REVERT: H 242 LYS cc_start: 0.9420 (mmpt) cc_final: 0.9206 (mmmt) REVERT: H 286 MET cc_start: 0.9656 (tpt) cc_final: 0.9188 (tpt) REVERT: H 290 ILE cc_start: 0.9745 (pt) cc_final: 0.9426 (pt) REVERT: H 315 ASP cc_start: 0.9222 (m-30) cc_final: 0.8786 (p0) REVERT: H 349 LYS cc_start: 0.9610 (mmtp) cc_final: 0.9247 (mmmm) REVERT: H 352 GLU cc_start: 0.9364 (tm-30) cc_final: 0.8992 (tm-30) REVERT: H 368 GLN cc_start: 0.8660 (mt0) cc_final: 0.8282 (mm-40) REVERT: H 379 LEU cc_start: 0.9616 (mm) cc_final: 0.9369 (mm) REVERT: H 385 MET cc_start: 0.8205 (tpt) cc_final: 0.7788 (tpt) REVERT: H 410 LYS cc_start: 0.9087 (mptt) cc_final: 0.8844 (mptt) REVERT: H 414 MET cc_start: 0.8684 (pmm) cc_final: 0.8249 (pmm) REVERT: H 465 GLN cc_start: 0.8640 (pp30) cc_final: 0.8306 (tt0) REVERT: H 468 CYS cc_start: 0.9169 (t) cc_final: 0.8846 (t) REVERT: H 478 GLN cc_start: 0.9615 (tt0) cc_final: 0.9222 (tt0) REVERT: H 482 MET cc_start: 0.8985 (tpt) cc_final: 0.8679 (tpp) REVERT: J 4 TYR cc_start: 0.9567 (t80) cc_final: 0.9358 (t80) REVERT: J 12 TYR cc_start: 0.9053 (t80) cc_final: 0.8361 (t80) REVERT: L 1 MET cc_start: 0.8601 (mpp) cc_final: 0.8255 (pmm) outliers start: 1 outliers final: 0 residues processed: 1447 average time/residue: 0.1939 time to fit residues: 460.2748 Evaluate side-chains 1222 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1221 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 8 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 282 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 368 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 377 optimal weight: 0.9980 chunk 336 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN E 309 GLN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 466 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.084148 restraints weight = 74358.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.087785 restraints weight = 41283.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.090313 restraints weight = 27072.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.092217 restraints weight = 19831.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093462 restraints weight = 15522.942| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 32220 Z= 0.201 Angle : 0.886 10.551 43712 Z= 0.438 Chirality : 0.053 0.426 4984 Planarity : 0.005 0.148 5452 Dihedral : 13.208 173.743 4572 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.68 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.12), residues: 3968 helix: -1.73 (0.13), residues: 1246 sheet: -2.45 (0.22), residues: 422 loop : -1.96 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 512 TYR 0.028 0.002 TYR E 110 PHE 0.025 0.002 PHE F 456 HIS 0.014 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (32212) covalent geometry : angle 0.88648 / 0.44 (43712) hydrogen bonds : bond 0.04289 / 2.77 ( 966) hydrogen bonds : angle 6.58203 / 4.51 ( 2655) Misc. bond : bond 0.00179 / 0.14 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1418 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7855 (t80) cc_final: 0.6883 (m-80) REVERT: A 21 GLN cc_start: 0.9209 (pm20) cc_final: 0.8956 (pm20) REVERT: A 28 ASP cc_start: 0.9023 (t70) cc_final: 0.8563 (t70) REVERT: A 32 TYR cc_start: 0.8762 (m-10) cc_final: 0.8222 (m-80) REVERT: A 36 LEU cc_start: 0.8778 (tp) cc_final: 0.8433 (tp) REVERT: A 38 LEU cc_start: 0.9655 (mm) cc_final: 0.8822 (mm) REVERT: A 48 GLN cc_start: 0.9263 (mt0) cc_final: 0.8796 (mt0) REVERT: A 68 SER cc_start: 0.9442 (t) cc_final: 0.9211 (t) REVERT: A 78 MET cc_start: 0.9085 (tpp) cc_final: 0.8731 (tpp) REVERT: A 105 ARG cc_start: 0.8971 (mmm160) cc_final: 0.8234 (tpm170) REVERT: A 108 LYS cc_start: 0.9496 (tptp) cc_final: 0.8991 (mmmt) REVERT: A 109 LYS cc_start: 0.9315 (ptpp) cc_final: 0.8887 (ptpt) REVERT: A 150 MET cc_start: 0.7779 (tpt) cc_final: 0.7229 (tpt) REVERT: A 158 ILE cc_start: 0.9017 (mm) cc_final: 0.8518 (tp) REVERT: A 179 MET cc_start: 0.7346 (pmm) cc_final: 0.7103 (pmm) REVERT: A 224 ARG cc_start: 0.7885 (mmt180) cc_final: 0.7598 (mpt-90) REVERT: A 246 CYS cc_start: 0.9379 (t) cc_final: 0.8382 (p) REVERT: A 262 LEU cc_start: 0.9570 (pt) cc_final: 0.9288 (pp) REVERT: A 273 LEU cc_start: 0.9581 (tp) cc_final: 0.9283 (tp) REVERT: A 319 ASP cc_start: 0.7758 (t70) cc_final: 0.7494 (t70) REVERT: A 334 GLN cc_start: 0.9364 (mp10) cc_final: 0.8316 (mp10) REVERT: A 335 GLU cc_start: 0.8593 (mp0) cc_final: 0.8158 (mp0) REVERT: A 343 GLN cc_start: 0.8353 (pp30) cc_final: 0.7441 (pp30) REVERT: A 353 TYR cc_start: 0.8986 (t80) cc_final: 0.8760 (t80) REVERT: A 385 MET cc_start: 0.8625 (ttp) cc_final: 0.8319 (ttt) REVERT: A 386 MET cc_start: 0.8664 (ppp) cc_final: 0.8276 (ppp) REVERT: A 420 MET cc_start: 0.8252 (mtm) cc_final: 0.7821 (mtp) REVERT: A 454 HIS cc_start: 0.8907 (m90) cc_final: 0.8707 (m90) REVERT: A 482 MET cc_start: 0.8995 (ttt) cc_final: 0.8742 (ttt) REVERT: A 507 HIS cc_start: 0.8656 (t-90) cc_final: 0.8334 (t70) REVERT: A 509 TYR cc_start: 0.9042 (p90) cc_final: 0.8681 (p90) REVERT: B 18 LEU cc_start: 0.9477 (tp) cc_final: 0.9224 (tp) REVERT: B 34 ASP cc_start: 0.8422 (m-30) cc_final: 0.8219 (m-30) REVERT: B 36 LEU cc_start: 0.9305 (tp) cc_final: 0.9017 (tp) REVERT: B 37 ILE cc_start: 0.9095 (mm) cc_final: 0.8737 (mm) REVERT: B 70 MET cc_start: 0.8142 (tpp) cc_final: 0.7712 (tpp) REVERT: B 82 MET cc_start: 0.9485 (ttm) cc_final: 0.9255 (ttm) REVERT: B 106 LYS cc_start: 0.9388 (mtpt) cc_final: 0.9125 (mtpt) REVERT: B 108 LYS cc_start: 0.9429 (pttm) cc_final: 0.8460 (tppt) REVERT: B 131 PHE cc_start: 0.9467 (m-80) cc_final: 0.8917 (m-80) REVERT: B 132 GLU cc_start: 0.9558 (pt0) cc_final: 0.9252 (pt0) REVERT: B 167 LYS cc_start: 0.9121 (mppt) cc_final: 0.8910 (mmtt) REVERT: B 181 LYS cc_start: 0.9192 (tppt) cc_final: 0.8781 (tppt) REVERT: B 185 LEU cc_start: 0.8899 (mt) cc_final: 0.8424 (mt) REVERT: B 200 ILE cc_start: 0.9758 (mt) cc_final: 0.9545 (mt) REVERT: B 224 ARG cc_start: 0.9146 (ttt180) cc_final: 0.8932 (ttt180) REVERT: B 242 LYS cc_start: 0.8692 (tttt) cc_final: 0.8232 (tttt) REVERT: B 291 LYS cc_start: 0.9592 (mmmt) cc_final: 0.9060 (tppt) REVERT: B 322 ARG cc_start: 0.9116 (ttt90) cc_final: 0.8793 (ttt90) REVERT: B 334 GLN cc_start: 0.9324 (mt0) cc_final: 0.8855 (mm-40) REVERT: B 335 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 343 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 351 SER cc_start: 0.9342 (p) cc_final: 0.9096 (p) REVERT: B 352 GLU cc_start: 0.8830 (pm20) cc_final: 0.8622 (pm20) REVERT: B 372 HIS cc_start: 0.9164 (m170) cc_final: 0.8369 (m170) REVERT: B 386 MET cc_start: 0.8132 (tpp) cc_final: 0.7913 (tpp) REVERT: B 404 ASP cc_start: 0.8713 (t0) cc_final: 0.8417 (t0) REVERT: B 414 MET cc_start: 0.9061 (mpp) cc_final: 0.8717 (mpp) REVERT: B 491 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 506 LEU cc_start: 0.8971 (pp) cc_final: 0.8733 (pt) REVERT: C 47 ASP cc_start: 0.9595 (m-30) cc_final: 0.8945 (p0) REVERT: C 74 THR cc_start: 0.6840 (t) cc_final: 0.6605 (t) REVERT: C 82 MET cc_start: 0.9637 (tpp) cc_final: 0.9301 (tpp) REVERT: C 90 PHE cc_start: 0.9081 (m-80) cc_final: 0.8732 (m-80) REVERT: C 140 CYS cc_start: 0.4317 (m) cc_final: 0.4099 (m) REVERT: C 175 LEU cc_start: 0.9246 (mt) cc_final: 0.9033 (mt) REVERT: C 199 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8592 (tp30) REVERT: C 200 ILE cc_start: 0.9319 (mm) cc_final: 0.8901 (mm) REVERT: C 203 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8288 (mtm110) REVERT: C 229 LYS cc_start: 0.9389 (ptpp) cc_final: 0.9070 (mmmt) REVERT: C 274 ASP cc_start: 0.9232 (t0) cc_final: 0.8979 (t0) REVERT: C 289 TYR cc_start: 0.9408 (t80) cc_final: 0.9178 (t80) REVERT: C 321 LEU cc_start: 0.9412 (tp) cc_final: 0.9199 (tp) REVERT: C 331 CYS cc_start: 0.9033 (t) cc_final: 0.8626 (t) REVERT: C 333 THR cc_start: 0.9702 (p) cc_final: 0.9183 (p) REVERT: C 334 GLN cc_start: 0.9140 (mp10) cc_final: 0.8341 (mp10) REVERT: C 342 PRO cc_start: 0.9481 (Cg_exo) cc_final: 0.9251 (Cg_endo) REVERT: C 349 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8854 (mtpt) REVERT: C 362 ILE cc_start: 0.9518 (pt) cc_final: 0.9246 (mm) REVERT: C 386 MET cc_start: 0.8999 (tmm) cc_final: 0.8774 (tmm) REVERT: C 390 LEU cc_start: 0.9363 (pt) cc_final: 0.9044 (pt) REVERT: C 482 MET cc_start: 0.9394 (tpp) cc_final: 0.8968 (tpp) REVERT: C 487 GLU cc_start: 0.8751 (pm20) cc_final: 0.8460 (pm20) REVERT: C 500 GLU cc_start: 0.9223 (pp20) cc_final: 0.8375 (pp20) REVERT: C 504 HIS cc_start: 0.8715 (p90) cc_final: 0.7948 (p90) REVERT: D 12 TYR cc_start: 0.8462 (t80) cc_final: 0.7194 (m-80) REVERT: D 32 TYR cc_start: 0.9049 (m-10) cc_final: 0.8743 (m-10) REVERT: D 33 ASN cc_start: 0.9179 (t0) cc_final: 0.8756 (t0) REVERT: D 63 THR cc_start: 0.8083 (t) cc_final: 0.7844 (t) REVERT: D 91 ILE cc_start: 0.9195 (tp) cc_final: 0.8943 (tp) REVERT: D 93 HIS cc_start: 0.9389 (p-80) cc_final: 0.8951 (p-80) REVERT: D 114 PHE cc_start: 0.9109 (m-80) cc_final: 0.8808 (m-10) REVERT: D 144 ILE cc_start: 0.9126 (mm) cc_final: 0.8791 (mp) REVERT: D 179 MET cc_start: 0.6168 (ppp) cc_final: 0.5010 (pmm) REVERT: D 215 ASP cc_start: 0.9574 (m-30) cc_final: 0.9031 (p0) REVERT: D 242 LYS cc_start: 0.9340 (mmpt) cc_final: 0.9088 (mmmt) REVERT: D 257 LYS cc_start: 0.9813 (ptpp) cc_final: 0.9543 (mmtm) REVERT: D 286 MET cc_start: 0.9623 (tpt) cc_final: 0.9330 (tpt) REVERT: D 289 TYR cc_start: 0.9381 (t80) cc_final: 0.9016 (t80) REVERT: D 290 ILE cc_start: 0.9753 (pt) cc_final: 0.9438 (pt) REVERT: D 315 ASP cc_start: 0.9225 (m-30) cc_final: 0.8801 (p0) REVERT: D 352 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9105 (tm-30) REVERT: D 379 LEU cc_start: 0.9667 (mm) cc_final: 0.9423 (mm) REVERT: D 385 MET cc_start: 0.8649 (tpt) cc_final: 0.7834 (tpt) REVERT: D 386 MET cc_start: 0.8476 (ptm) cc_final: 0.8198 (ptm) REVERT: D 400 TYR cc_start: 0.7445 (m-80) cc_final: 0.7195 (m-80) REVERT: D 414 MET cc_start: 0.8681 (pmm) cc_final: 0.8480 (pmm) REVERT: D 465 GLN cc_start: 0.8642 (pp30) cc_final: 0.8341 (tt0) REVERT: D 468 CYS cc_start: 0.9199 (t) cc_final: 0.8854 (t) REVERT: D 478 GLN cc_start: 0.9629 (tt0) cc_final: 0.9202 (tt0) REVERT: D 482 MET cc_start: 0.8978 (tpt) cc_final: 0.8723 (tpp) REVERT: N 12 TYR cc_start: 0.8953 (t80) cc_final: 0.8025 (t80) REVERT: P 1 MET cc_start: 0.8431 (mpp) cc_final: 0.8173 (pmm) REVERT: E 12 TYR cc_start: 0.7450 (t80) cc_final: 0.6859 (m-80) REVERT: E 21 GLN cc_start: 0.9241 (pm20) cc_final: 0.8931 (pm20) REVERT: E 32 TYR cc_start: 0.9363 (m-80) cc_final: 0.8798 (m-80) REVERT: E 36 LEU cc_start: 0.8608 (tp) cc_final: 0.8371 (tp) REVERT: E 38 LEU cc_start: 0.9581 (mm) cc_final: 0.8824 (mm) REVERT: E 48 GLN cc_start: 0.9296 (mt0) cc_final: 0.8840 (mt0) REVERT: E 105 ARG cc_start: 0.8939 (mmm160) cc_final: 0.8495 (tpm170) REVERT: E 108 LYS cc_start: 0.9485 (tppt) cc_final: 0.8897 (mmtt) REVERT: E 150 MET cc_start: 0.7826 (tpt) cc_final: 0.7063 (tpt) REVERT: E 228 LYS cc_start: 0.9504 (ptpp) cc_final: 0.9277 (ptpp) REVERT: E 246 CYS cc_start: 0.9418 (t) cc_final: 0.9186 (t) REVERT: E 254 GLU cc_start: 0.9348 (tp30) cc_final: 0.8690 (pm20) REVERT: E 256 ASP cc_start: 0.9051 (p0) cc_final: 0.8775 (m-30) REVERT: E 262 LEU cc_start: 0.9641 (pt) cc_final: 0.9393 (pt) REVERT: E 269 ASP cc_start: 0.7998 (m-30) cc_final: 0.7655 (m-30) REVERT: E 319 ASP cc_start: 0.7706 (t70) cc_final: 0.7269 (t70) REVERT: E 332 ILE cc_start: 0.9452 (pt) cc_final: 0.9037 (pt) REVERT: E 334 GLN cc_start: 0.9273 (mp10) cc_final: 0.8302 (mp10) REVERT: E 335 GLU cc_start: 0.8668 (mp0) cc_final: 0.7825 (mp0) REVERT: E 352 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8801 (tm-30) REVERT: E 353 TYR cc_start: 0.8929 (t80) cc_final: 0.8615 (t80) REVERT: E 364 ASP cc_start: 0.8680 (m-30) cc_final: 0.7483 (m-30) REVERT: E 375 LYS cc_start: 0.9704 (pttt) cc_final: 0.9501 (pttt) REVERT: E 385 MET cc_start: 0.8908 (ttp) cc_final: 0.8264 (ttp) REVERT: E 386 MET cc_start: 0.8589 (ppp) cc_final: 0.8070 (ppp) REVERT: E 390 LEU cc_start: 0.9124 (pt) cc_final: 0.8868 (pt) REVERT: E 420 MET cc_start: 0.8373 (mtm) cc_final: 0.7811 (mtp) REVERT: E 454 HIS cc_start: 0.8960 (m90) cc_final: 0.8744 (m90) REVERT: E 480 ARG cc_start: 0.8958 (mpp80) cc_final: 0.8264 (mpp80) REVERT: E 482 MET cc_start: 0.9033 (ttt) cc_final: 0.8799 (ttt) REVERT: E 483 MET cc_start: 0.9727 (tmm) cc_final: 0.9475 (tmm) REVERT: E 507 HIS cc_start: 0.8624 (t-90) cc_final: 0.8341 (t70) REVERT: E 509 TYR cc_start: 0.9060 (p90) cc_final: 0.8763 (p90) REVERT: F 34 ASP cc_start: 0.8344 (m-30) cc_final: 0.8064 (m-30) REVERT: F 36 LEU cc_start: 0.9265 (tp) cc_final: 0.8959 (tp) REVERT: F 37 ILE cc_start: 0.9038 (mm) cc_final: 0.8645 (mm) REVERT: F 70 MET cc_start: 0.8205 (tpp) cc_final: 0.7233 (tpp) REVERT: F 103 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9230 (mm-30) REVERT: F 108 LYS cc_start: 0.9285 (pttm) cc_final: 0.8018 (tppt) REVERT: F 131 PHE cc_start: 0.9295 (m-10) cc_final: 0.8871 (m-80) REVERT: F 132 GLU cc_start: 0.9504 (pt0) cc_final: 0.9214 (pt0) REVERT: F 134 LYS cc_start: 0.9379 (ptpp) cc_final: 0.9119 (pttt) REVERT: F 185 LEU cc_start: 0.8863 (mt) cc_final: 0.8348 (mt) REVERT: F 199 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9262 (mt-10) REVERT: F 233 TYR cc_start: 0.9480 (m-10) cc_final: 0.9244 (m-10) REVERT: F 238 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8405 (tppt) REVERT: F 250 ILE cc_start: 0.9365 (mp) cc_final: 0.8852 (tp) REVERT: F 287 ILE cc_start: 0.9554 (pt) cc_final: 0.9262 (pt) REVERT: F 291 LYS cc_start: 0.9570 (mmmt) cc_final: 0.9064 (tppt) REVERT: F 334 GLN cc_start: 0.9334 (mt0) cc_final: 0.8897 (mm-40) REVERT: F 335 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8186 (tm-30) REVERT: F 337 LEU cc_start: 0.9236 (mm) cc_final: 0.8995 (mm) REVERT: F 343 GLN cc_start: 0.8256 (tm130) cc_final: 0.7838 (tm-30) REVERT: F 355 ARG cc_start: 0.8508 (ppt170) cc_final: 0.8285 (ptt90) REVERT: F 372 HIS cc_start: 0.9141 (m170) cc_final: 0.8693 (m-70) REVERT: F 386 MET cc_start: 0.7515 (ptm) cc_final: 0.6773 (ppp) REVERT: F 400 TYR cc_start: 0.7511 (m-80) cc_final: 0.6948 (m-80) REVERT: F 404 ASP cc_start: 0.8610 (t0) cc_final: 0.8358 (t0) REVERT: F 414 MET cc_start: 0.9168 (mpp) cc_final: 0.8869 (mpp) REVERT: F 491 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8495 (tm-30) REVERT: F 506 LEU cc_start: 0.8810 (pt) cc_final: 0.8536 (pt) REVERT: G 47 ASP cc_start: 0.9624 (m-30) cc_final: 0.9059 (p0) REVERT: G 78 MET cc_start: 0.9564 (tpp) cc_final: 0.9121 (tpp) REVERT: G 229 LYS cc_start: 0.9376 (ptpp) cc_final: 0.9043 (mmmt) REVERT: G 262 LEU cc_start: 0.9465 (pp) cc_final: 0.9251 (pp) REVERT: G 274 ASP cc_start: 0.9270 (t0) cc_final: 0.8911 (t70) REVERT: G 289 TYR cc_start: 0.9406 (t80) cc_final: 0.9136 (t80) REVERT: G 331 CYS cc_start: 0.9058 (t) cc_final: 0.8695 (t) REVERT: G 332 ILE cc_start: 0.9634 (pt) cc_final: 0.9400 (pt) REVERT: G 333 THR cc_start: 0.9722 (p) cc_final: 0.9103 (p) REVERT: G 334 GLN cc_start: 0.9159 (mp10) cc_final: 0.8310 (mp10) REVERT: G 335 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8123 (tm-30) REVERT: G 336 VAL cc_start: 0.9504 (m) cc_final: 0.8524 (m) REVERT: G 395 GLU cc_start: 0.8794 (mp0) cc_final: 0.8447 (mp0) REVERT: G 482 MET cc_start: 0.9331 (tpp) cc_final: 0.8946 (mmm) REVERT: G 500 GLU cc_start: 0.9255 (pp20) cc_final: 0.8419 (pp20) REVERT: G 504 HIS cc_start: 0.8633 (p90) cc_final: 0.7784 (p90) REVERT: H 21 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8513 (tm-30) REVERT: H 63 THR cc_start: 0.8274 (t) cc_final: 0.8011 (t) REVERT: H 91 ILE cc_start: 0.9303 (tp) cc_final: 0.9012 (tp) REVERT: H 93 HIS cc_start: 0.9156 (p-80) cc_final: 0.8948 (p-80) REVERT: H 108 LYS cc_start: 0.9070 (tptm) cc_final: 0.8724 (tptp) REVERT: H 112 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8929 (tm-30) REVERT: H 179 MET cc_start: 0.7159 (ppp) cc_final: 0.6607 (ppp) REVERT: H 208 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8559 (tmtt) REVERT: H 209 LEU cc_start: 0.9031 (tp) cc_final: 0.8701 (pp) REVERT: H 215 ASP cc_start: 0.9504 (m-30) cc_final: 0.8984 (p0) REVERT: H 242 LYS cc_start: 0.9415 (mmpt) cc_final: 0.9205 (mmmt) REVERT: H 286 MET cc_start: 0.9634 (tpt) cc_final: 0.9177 (tpt) REVERT: H 290 ILE cc_start: 0.9736 (pt) cc_final: 0.9403 (pt) REVERT: H 315 ASP cc_start: 0.9221 (m-30) cc_final: 0.8783 (p0) REVERT: H 335 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8337 (tm-30) REVERT: H 349 LYS cc_start: 0.9647 (mmtp) cc_final: 0.9269 (mmmm) REVERT: H 352 GLU cc_start: 0.9394 (tm-30) cc_final: 0.9078 (tm-30) REVERT: H 368 GLN cc_start: 0.8715 (mt0) cc_final: 0.8487 (mm-40) REVERT: H 379 LEU cc_start: 0.9639 (mm) cc_final: 0.9424 (mm) REVERT: H 385 MET cc_start: 0.7987 (tpt) cc_final: 0.7779 (tpt) REVERT: H 386 MET cc_start: 0.7515 (ptm) cc_final: 0.6993 (ppp) REVERT: H 400 TYR cc_start: 0.7510 (m-80) cc_final: 0.7197 (m-10) REVERT: H 414 MET cc_start: 0.8733 (pmm) cc_final: 0.8328 (pmm) REVERT: H 465 GLN cc_start: 0.8656 (pp30) cc_final: 0.8366 (tt0) REVERT: H 468 CYS cc_start: 0.9202 (t) cc_final: 0.8864 (t) REVERT: H 478 GLN cc_start: 0.9622 (tt0) cc_final: 0.9218 (tt0) REVERT: H 492 LYS cc_start: 0.9320 (pttt) cc_final: 0.8919 (pttp) REVERT: J 4 TYR cc_start: 0.9578 (t80) cc_final: 0.9363 (t80) REVERT: J 5 LEU cc_start: 0.9528 (mt) cc_final: 0.9118 (mt) REVERT: J 12 TYR cc_start: 0.9086 (t80) cc_final: 0.8417 (t80) REVERT: L 1 MET cc_start: 0.8539 (mpp) cc_final: 0.8255 (pmm) outliers start: 0 outliers final: 0 residues processed: 1418 average time/residue: 0.1924 time to fit residues: 450.9378 Evaluate side-chains 1209 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1209 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 271 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 291 optimal weight: 0.6980 chunk 308 optimal weight: 5.9990 chunk 266 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 367 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 205 optimal weight: 7.9990 chunk 384 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 466 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN H 498 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.088753 restraints weight = 72519.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092666 restraints weight = 40010.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095413 restraints weight = 26080.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097404 restraints weight = 18930.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098811 restraints weight = 14793.353| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32220 Z= 0.151 Angle : 0.887 12.876 43712 Z= 0.432 Chirality : 0.053 0.420 4984 Planarity : 0.005 0.112 5452 Dihedral : 12.780 174.347 4572 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.72 % Favored : 91.26 % Rotamer: Outliers : 0.06 % Allowed : 1.89 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.12), residues: 3968 helix: -1.70 (0.13), residues: 1232 sheet: -2.43 (0.23), residues: 376 loop : -1.84 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 407 TYR 0.021 0.002 TYR B 233 PHE 0.036 0.002 PHE E 456 HIS 0.007 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (32212) covalent geometry : angle 0.88706 / 0.43 (43712) hydrogen bonds : bond 0.04195 / 2.72 ( 966) hydrogen bonds : angle 6.53204 / 4.47 ( 2655) Misc. bond : bond 0.00148 / 0.11 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1447 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1445 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.9128 (pm20) cc_final: 0.8912 (pm20) REVERT: A 28 ASP cc_start: 0.9130 (t70) cc_final: 0.8591 (t70) REVERT: A 32 TYR cc_start: 0.8741 (m-10) cc_final: 0.8269 (m-80) REVERT: A 36 LEU cc_start: 0.8651 (tp) cc_final: 0.7955 (tp) REVERT: A 38 LEU cc_start: 0.9581 (mm) cc_final: 0.8851 (mm) REVERT: A 48 GLN cc_start: 0.9273 (mt0) cc_final: 0.8868 (mt0) REVERT: A 78 MET cc_start: 0.9009 (tpp) cc_final: 0.8786 (tpp) REVERT: A 105 ARG cc_start: 0.8964 (mmm160) cc_final: 0.8272 (tpm170) REVERT: A 108 LYS cc_start: 0.9469 (tptp) cc_final: 0.8922 (mmmt) REVERT: A 109 LYS cc_start: 0.9315 (ptpp) cc_final: 0.8912 (ptpt) REVERT: A 150 MET cc_start: 0.7783 (tpt) cc_final: 0.7205 (tpt) REVERT: A 246 CYS cc_start: 0.9395 (t) cc_final: 0.8492 (p) REVERT: A 262 LEU cc_start: 0.9577 (pt) cc_final: 0.9314 (pp) REVERT: A 273 LEU cc_start: 0.9618 (tp) cc_final: 0.9330 (tp) REVERT: A 291 LYS cc_start: 0.9502 (tppt) cc_final: 0.9296 (tptp) REVERT: A 319 ASP cc_start: 0.7808 (t70) cc_final: 0.7538 (t70) REVERT: A 325 MET cc_start: 0.8810 (ptm) cc_final: 0.8427 (ptm) REVERT: A 332 ILE cc_start: 0.9330 (pt) cc_final: 0.8933 (pt) REVERT: A 334 GLN cc_start: 0.9365 (mp10) cc_final: 0.8334 (mp10) REVERT: A 335 GLU cc_start: 0.8563 (mp0) cc_final: 0.7708 (mp0) REVERT: A 343 GLN cc_start: 0.8333 (pp30) cc_final: 0.7556 (pp30) REVERT: A 352 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8687 (tm-30) REVERT: A 375 LYS cc_start: 0.9572 (pttt) cc_final: 0.9341 (pttt) REVERT: A 386 MET cc_start: 0.8762 (ppp) cc_final: 0.8109 (ppp) REVERT: A 420 MET cc_start: 0.8198 (mtm) cc_final: 0.7759 (mtp) REVERT: A 454 HIS cc_start: 0.8845 (m90) cc_final: 0.8591 (m90) REVERT: A 480 ARG cc_start: 0.8914 (mpp80) cc_final: 0.8378 (mtm110) REVERT: A 482 MET cc_start: 0.9039 (ttt) cc_final: 0.8832 (ttt) REVERT: A 496 SER cc_start: 0.9320 (t) cc_final: 0.9117 (t) REVERT: A 507 HIS cc_start: 0.8514 (t-90) cc_final: 0.8218 (t70) REVERT: B 18 LEU cc_start: 0.9349 (tp) cc_final: 0.9138 (tp) REVERT: B 31 THR cc_start: 0.8052 (m) cc_final: 0.7802 (m) REVERT: B 36 LEU cc_start: 0.9364 (tp) cc_final: 0.9064 (tp) REVERT: B 37 ILE cc_start: 0.8999 (mm) cc_final: 0.8596 (mm) REVERT: B 42 ILE cc_start: 0.9327 (pt) cc_final: 0.9103 (pt) REVERT: B 70 MET cc_start: 0.8150 (tpp) cc_final: 0.7517 (mmm) REVERT: B 82 MET cc_start: 0.9505 (ttm) cc_final: 0.9269 (ttm) REVERT: B 106 LYS cc_start: 0.9366 (mtpt) cc_final: 0.9136 (mtpt) REVERT: B 108 LYS cc_start: 0.9390 (pttm) cc_final: 0.8593 (tppt) REVERT: B 131 PHE cc_start: 0.9516 (m-80) cc_final: 0.8411 (m-80) REVERT: B 132 GLU cc_start: 0.9561 (pt0) cc_final: 0.9236 (pt0) REVERT: B 134 LYS cc_start: 0.9433 (pttt) cc_final: 0.9070 (tttp) REVERT: B 167 LYS cc_start: 0.9119 (mppt) cc_final: 0.8905 (mmtt) REVERT: B 176 GLU cc_start: 0.8207 (mp0) cc_final: 0.7863 (mp0) REVERT: B 181 LYS cc_start: 0.9114 (tppt) cc_final: 0.8686 (tppt) REVERT: B 185 LEU cc_start: 0.8929 (mt) cc_final: 0.8427 (mt) REVERT: B 199 GLU cc_start: 0.9371 (pp20) cc_final: 0.8820 (pp20) REVERT: B 200 ILE cc_start: 0.9662 (mt) cc_final: 0.9361 (mm) REVERT: B 238 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8523 (tppt) REVERT: B 242 LYS cc_start: 0.8646 (tttt) cc_final: 0.8083 (tptt) REVERT: B 291 LYS cc_start: 0.9584 (mmmt) cc_final: 0.9069 (tppt) REVERT: B 294 TYR cc_start: 0.9429 (m-80) cc_final: 0.9087 (m-80) REVERT: B 334 GLN cc_start: 0.9280 (mt0) cc_final: 0.8772 (mm-40) REVERT: B 343 GLN cc_start: 0.8387 (tm130) cc_final: 0.7878 (tm-30) REVERT: B 372 HIS cc_start: 0.8946 (m170) cc_final: 0.8646 (m90) REVERT: B 400 TYR cc_start: 0.6787 (m-80) cc_final: 0.6093 (m-10) REVERT: B 403 SER cc_start: 0.9327 (t) cc_final: 0.9123 (t) REVERT: B 404 ASP cc_start: 0.8590 (t0) cc_final: 0.8316 (t0) REVERT: B 449 ASP cc_start: 0.8818 (t70) cc_final: 0.8585 (t70) REVERT: B 487 GLU cc_start: 0.8522 (pp20) cc_final: 0.8306 (pp20) REVERT: B 491 GLU cc_start: 0.8556 (tm-30) cc_final: 0.7726 (tm-30) REVERT: C 47 ASP cc_start: 0.9593 (m-30) cc_final: 0.8929 (p0) REVERT: C 78 MET cc_start: 0.9422 (mmp) cc_final: 0.9142 (mmt) REVERT: C 82 MET cc_start: 0.9632 (tpp) cc_final: 0.9339 (tpp) REVERT: C 90 PHE cc_start: 0.9114 (m-80) cc_final: 0.8700 (m-80) REVERT: C 99 PHE cc_start: 0.9562 (t80) cc_final: 0.9306 (t80) REVERT: C 199 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8572 (tp30) REVERT: C 200 ILE cc_start: 0.9318 (mm) cc_final: 0.8845 (mm) REVERT: C 203 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8291 (mtm110) REVERT: C 229 LYS cc_start: 0.9355 (ptpp) cc_final: 0.9025 (mmmt) REVERT: C 274 ASP cc_start: 0.9306 (t0) cc_final: 0.9039 (t70) REVERT: C 291 LYS cc_start: 0.9095 (pttt) cc_final: 0.8843 (pttt) REVERT: C 331 CYS cc_start: 0.9088 (t) cc_final: 0.8601 (t) REVERT: C 333 THR cc_start: 0.9726 (p) cc_final: 0.9132 (p) REVERT: C 334 GLN cc_start: 0.9130 (mp10) cc_final: 0.8277 (mp10) REVERT: C 342 PRO cc_start: 0.9467 (Cg_exo) cc_final: 0.9216 (Cg_endo) REVERT: C 349 LYS cc_start: 0.9149 (mtpt) cc_final: 0.8860 (mtpt) REVERT: C 357 PHE cc_start: 0.9077 (m-80) cc_final: 0.8835 (m-80) REVERT: C 362 ILE cc_start: 0.9430 (pt) cc_final: 0.9221 (mm) REVERT: C 386 MET cc_start: 0.8970 (tmm) cc_final: 0.8770 (tmm) REVERT: C 456 PHE cc_start: 0.9737 (t80) cc_final: 0.9470 (t80) REVERT: C 482 MET cc_start: 0.9397 (tpp) cc_final: 0.8902 (tpp) REVERT: C 500 GLU cc_start: 0.9231 (pp20) cc_final: 0.8679 (pp20) REVERT: D 12 TYR cc_start: 0.8347 (t80) cc_final: 0.7038 (m-80) REVERT: D 21 GLN cc_start: 0.9050 (tp40) cc_final: 0.8369 (tp40) REVERT: D 25 ASN cc_start: 0.8481 (m110) cc_final: 0.7719 (m110) REVERT: D 32 TYR cc_start: 0.9040 (m-10) cc_final: 0.8772 (m-10) REVERT: D 33 ASN cc_start: 0.9161 (t0) cc_final: 0.8765 (t0) REVERT: D 91 ILE cc_start: 0.9161 (tp) cc_final: 0.8863 (tp) REVERT: D 93 HIS cc_start: 0.9432 (p-80) cc_final: 0.8997 (p-80) REVERT: D 94 ASN cc_start: 0.9007 (m110) cc_final: 0.8583 (t0) REVERT: D 114 PHE cc_start: 0.9025 (m-80) cc_final: 0.8817 (m-10) REVERT: D 144 ILE cc_start: 0.9133 (mm) cc_final: 0.8810 (mp) REVERT: D 179 MET cc_start: 0.5402 (ppp) cc_final: 0.3798 (pmm) REVERT: D 215 ASP cc_start: 0.9574 (m-30) cc_final: 0.8779 (t70) REVERT: D 242 LYS cc_start: 0.9310 (mmpt) cc_final: 0.9056 (mmmt) REVERT: D 257 LYS cc_start: 0.9813 (ptpp) cc_final: 0.9533 (mmtm) REVERT: D 281 ILE cc_start: 0.9719 (mm) cc_final: 0.9487 (mm) REVERT: D 285 ASN cc_start: 0.9745 (m110) cc_final: 0.9383 (p0) REVERT: D 286 MET cc_start: 0.9627 (tpt) cc_final: 0.9405 (tpt) REVERT: D 289 TYR cc_start: 0.9405 (t80) cc_final: 0.9029 (t80) REVERT: D 290 ILE cc_start: 0.9740 (pt) cc_final: 0.9455 (pt) REVERT: D 315 ASP cc_start: 0.9118 (m-30) cc_final: 0.8667 (p0) REVERT: D 352 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9023 (tm-30) REVERT: D 379 LEU cc_start: 0.9638 (mm) cc_final: 0.9354 (mm) REVERT: D 385 MET cc_start: 0.8548 (tpt) cc_final: 0.7392 (tpt) REVERT: D 386 MET cc_start: 0.8409 (ptm) cc_final: 0.8006 (ptm) REVERT: D 465 GLN cc_start: 0.8580 (pp30) cc_final: 0.8263 (tt0) REVERT: D 468 CYS cc_start: 0.9143 (t) cc_final: 0.8858 (t) REVERT: D 478 GLN cc_start: 0.9608 (tt0) cc_final: 0.9208 (tt0) REVERT: D 482 MET cc_start: 0.8952 (tpt) cc_final: 0.8673 (tpp) REVERT: N 12 TYR cc_start: 0.8645 (t80) cc_final: 0.8277 (t80) REVERT: E 12 TYR cc_start: 0.7524 (t80) cc_final: 0.6969 (m-80) REVERT: E 21 GLN cc_start: 0.9151 (pm20) cc_final: 0.8866 (pm20) REVERT: E 32 TYR cc_start: 0.9318 (m-80) cc_final: 0.8609 (m-80) REVERT: E 36 LEU cc_start: 0.8656 (tp) cc_final: 0.8049 (tp) REVERT: E 38 LEU cc_start: 0.9591 (mm) cc_final: 0.8879 (mm) REVERT: E 48 GLN cc_start: 0.9272 (mt0) cc_final: 0.8803 (mt0) REVERT: E 105 ARG cc_start: 0.8967 (mmm160) cc_final: 0.7969 (tpm170) REVERT: E 108 LYS cc_start: 0.9494 (tppt) cc_final: 0.8973 (mmtt) REVERT: E 109 LYS cc_start: 0.9265 (ptpp) cc_final: 0.8610 (ptpp) REVERT: E 112 GLN cc_start: 0.8946 (mp-120) cc_final: 0.8501 (mp10) REVERT: E 150 MET cc_start: 0.7832 (tpt) cc_final: 0.7070 (tpt) REVERT: E 179 MET cc_start: 0.7359 (pmm) cc_final: 0.6981 (pmm) REVERT: E 228 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9283 (ptpp) REVERT: E 246 CYS cc_start: 0.9444 (t) cc_final: 0.9138 (t) REVERT: E 250 ILE cc_start: 0.9546 (pt) cc_final: 0.9326 (pt) REVERT: E 254 GLU cc_start: 0.9339 (tp30) cc_final: 0.8735 (pm20) REVERT: E 256 ASP cc_start: 0.9024 (p0) cc_final: 0.8763 (m-30) REVERT: E 262 LEU cc_start: 0.9662 (pt) cc_final: 0.9406 (pt) REVERT: E 319 ASP cc_start: 0.7857 (t70) cc_final: 0.7527 (t70) REVERT: E 332 ILE cc_start: 0.9405 (pt) cc_final: 0.9039 (pt) REVERT: E 334 GLN cc_start: 0.9314 (mp10) cc_final: 0.8291 (mp10) REVERT: E 335 GLU cc_start: 0.8721 (mp0) cc_final: 0.7910 (mp0) REVERT: E 341 ARG cc_start: 0.9422 (ptm160) cc_final: 0.8904 (ptm160) REVERT: E 352 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8818 (tm-30) REVERT: E 353 TYR cc_start: 0.8858 (t80) cc_final: 0.8620 (t80) REVERT: E 364 ASP cc_start: 0.8761 (m-30) cc_final: 0.7494 (m-30) REVERT: E 385 MET cc_start: 0.8744 (ttp) cc_final: 0.7921 (ttp) REVERT: E 386 MET cc_start: 0.8361 (ppp) cc_final: 0.7896 (ppp) REVERT: E 420 MET cc_start: 0.8245 (mtm) cc_final: 0.7668 (mtp) REVERT: E 483 MET cc_start: 0.9706 (tmm) cc_final: 0.9481 (tmm) REVERT: E 507 HIS cc_start: 0.8463 (t-90) cc_final: 0.8221 (t70) REVERT: F 18 LEU cc_start: 0.9282 (tp) cc_final: 0.9002 (tp) REVERT: F 34 ASP cc_start: 0.8256 (m-30) cc_final: 0.8020 (m-30) REVERT: F 36 LEU cc_start: 0.9325 (tp) cc_final: 0.9016 (tp) REVERT: F 37 ILE cc_start: 0.8967 (mm) cc_final: 0.8574 (mm) REVERT: F 70 MET cc_start: 0.8107 (tpp) cc_final: 0.7378 (mmm) REVERT: F 103 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9017 (mm-30) REVERT: F 108 LYS cc_start: 0.9247 (pttm) cc_final: 0.8051 (tppt) REVERT: F 131 PHE cc_start: 0.9254 (m-10) cc_final: 0.8828 (m-80) REVERT: F 132 GLU cc_start: 0.9488 (pt0) cc_final: 0.9192 (pt0) REVERT: F 134 LYS cc_start: 0.9393 (ptpp) cc_final: 0.9098 (pttt) REVERT: F 185 LEU cc_start: 0.8920 (mt) cc_final: 0.8272 (mt) REVERT: F 233 TYR cc_start: 0.9433 (m-10) cc_final: 0.9202 (m-10) REVERT: F 238 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8347 (tppt) REVERT: F 250 ILE cc_start: 0.9340 (mp) cc_final: 0.8856 (tp) REVERT: F 291 LYS cc_start: 0.9579 (mmmt) cc_final: 0.9032 (tppt) REVERT: F 334 GLN cc_start: 0.9329 (mt0) cc_final: 0.8760 (mm-40) REVERT: F 335 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8136 (tm-30) REVERT: F 351 SER cc_start: 0.9327 (p) cc_final: 0.9048 (p) REVERT: F 355 ARG cc_start: 0.8483 (ppt170) cc_final: 0.8113 (ttp-170) REVERT: F 372 HIS cc_start: 0.9025 (m170) cc_final: 0.8687 (m90) REVERT: F 386 MET cc_start: 0.6794 (ptm) cc_final: 0.6157 (ppp) REVERT: F 399 GLU cc_start: 0.7712 (mp0) cc_final: 0.7443 (mp0) REVERT: F 400 TYR cc_start: 0.7507 (m-80) cc_final: 0.7085 (m-80) REVERT: F 491 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8403 (tm-30) REVERT: F 506 LEU cc_start: 0.8737 (pt) cc_final: 0.8424 (pt) REVERT: G 43 ASP cc_start: 0.8510 (m-30) cc_final: 0.8277 (m-30) REVERT: G 47 ASP cc_start: 0.9617 (m-30) cc_final: 0.9006 (p0) REVERT: G 78 MET cc_start: 0.9561 (tpp) cc_final: 0.9076 (tpp) REVERT: G 229 LYS cc_start: 0.9367 (ptpp) cc_final: 0.9035 (mmmt) REVERT: G 274 ASP cc_start: 0.9271 (t0) cc_final: 0.8878 (t70) REVERT: G 331 CYS cc_start: 0.9097 (t) cc_final: 0.8683 (t) REVERT: G 332 ILE cc_start: 0.9592 (pt) cc_final: 0.9386 (pt) REVERT: G 333 THR cc_start: 0.9729 (p) cc_final: 0.9118 (p) REVERT: G 334 GLN cc_start: 0.9103 (mp10) cc_final: 0.8245 (mp10) REVERT: G 335 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8049 (tm-30) REVERT: G 336 VAL cc_start: 0.9429 (m) cc_final: 0.8510 (m) REVERT: G 349 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8218 (mtmt) REVERT: G 386 MET cc_start: 0.8979 (tmm) cc_final: 0.8746 (tmm) REVERT: G 395 GLU cc_start: 0.8760 (mp0) cc_final: 0.8476 (mp0) REVERT: G 482 MET cc_start: 0.9295 (tpp) cc_final: 0.9041 (tpt) REVERT: G 500 GLU cc_start: 0.9268 (pp20) cc_final: 0.8311 (pp20) REVERT: G 504 HIS cc_start: 0.8530 (p90) cc_final: 0.7486 (p90) REVERT: H 25 ASN cc_start: 0.8674 (m110) cc_final: 0.8440 (m110) REVERT: H 33 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8486 (t0) REVERT: H 91 ILE cc_start: 0.9326 (tp) cc_final: 0.9032 (tp) REVERT: H 108 LYS cc_start: 0.9072 (tptm) cc_final: 0.8265 (tptt) REVERT: H 112 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8868 (tm-30) REVERT: H 179 MET cc_start: 0.6993 (ppp) cc_final: 0.6168 (tmm) REVERT: H 208 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8605 (tmtt) REVERT: H 209 LEU cc_start: 0.9087 (tp) cc_final: 0.8747 (pp) REVERT: H 215 ASP cc_start: 0.9432 (m-30) cc_final: 0.9033 (p0) REVERT: H 229 LYS cc_start: 0.8845 (pttt) cc_final: 0.8624 (mmtt) REVERT: H 242 LYS cc_start: 0.9378 (mmpt) cc_final: 0.9158 (mmmt) REVERT: H 286 MET cc_start: 0.9645 (tpt) cc_final: 0.9170 (tpt) REVERT: H 290 ILE cc_start: 0.9725 (pt) cc_final: 0.9405 (pt) REVERT: H 315 ASP cc_start: 0.9150 (m-30) cc_final: 0.8733 (p0) REVERT: H 352 GLU cc_start: 0.9389 (tm-30) cc_final: 0.9033 (tm-30) REVERT: H 368 GLN cc_start: 0.8721 (mt0) cc_final: 0.8334 (mm-40) REVERT: H 375 LYS cc_start: 0.9443 (ptmt) cc_final: 0.9200 (ptmt) REVERT: H 379 LEU cc_start: 0.9646 (mm) cc_final: 0.9426 (mm) REVERT: H 400 TYR cc_start: 0.7540 (m-80) cc_final: 0.7189 (m-10) REVERT: H 414 MET cc_start: 0.8631 (pmm) cc_final: 0.8272 (pmm) REVERT: H 465 GLN cc_start: 0.8579 (pp30) cc_final: 0.8295 (tt0) REVERT: H 468 CYS cc_start: 0.9111 (t) cc_final: 0.8824 (t) REVERT: H 478 GLN cc_start: 0.9596 (tt0) cc_final: 0.9190 (tt0) REVERT: H 482 MET cc_start: 0.8747 (tpp) cc_final: 0.8342 (tpp) REVERT: H 487 GLU cc_start: 0.9017 (pm20) cc_final: 0.8750 (pm20) REVERT: H 492 LYS cc_start: 0.9251 (pttt) cc_final: 0.8844 (pttp) REVERT: J 4 TYR cc_start: 0.9571 (t80) cc_final: 0.9366 (t80) REVERT: J 12 TYR cc_start: 0.8885 (t80) cc_final: 0.8267 (t80) outliers start: 2 outliers final: 1 residues processed: 1446 average time/residue: 0.1954 time to fit residues: 462.2927 Evaluate side-chains 1187 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1185 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 322 optimal weight: 8.9990 chunk 342 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 380 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 260 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 158 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS E 469 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS H 279 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.088890 restraints weight = 73444.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092746 restraints weight = 41033.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095452 restraints weight = 27036.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097470 restraints weight = 19894.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098923 restraints weight = 15592.429| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32220 Z= 0.153 Angle : 0.910 13.449 43712 Z= 0.446 Chirality : 0.054 0.418 4984 Planarity : 0.005 0.160 5452 Dihedral : 12.373 176.165 4572 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.05 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.12), residues: 3968 helix: -1.72 (0.13), residues: 1240 sheet: -2.29 (0.23), residues: 388 loop : -1.82 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 322 TYR 0.040 0.002 TYR A 110 PHE 0.025 0.002 PHE G 131 HIS 0.005 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (32212) covalent geometry : angle 0.90965 / 0.45 (43712) hydrogen bonds : bond 0.04295 / 2.79 ( 966) hydrogen bonds : angle 6.54710 / 4.49 ( 2655) Misc. bond : bond 0.00120 / 0.08 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1412 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1412 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.9147 (t70) cc_final: 0.8580 (t70) REVERT: A 32 TYR cc_start: 0.8741 (m-10) cc_final: 0.8205 (m-80) REVERT: A 36 LEU cc_start: 0.8666 (tp) cc_final: 0.7947 (tp) REVERT: A 38 LEU cc_start: 0.9553 (mm) cc_final: 0.8860 (mm) REVERT: A 48 GLN cc_start: 0.9250 (mt0) cc_final: 0.8852 (mt0) REVERT: A 100 GLN cc_start: 0.9396 (mp10) cc_final: 0.9071 (mp10) REVERT: A 108 LYS cc_start: 0.9482 (tptp) cc_final: 0.9176 (pttp) REVERT: A 137 HIS cc_start: 0.9454 (m90) cc_final: 0.8617 (m90) REVERT: A 150 MET cc_start: 0.7824 (tpt) cc_final: 0.7314 (tpt) REVERT: A 165 PHE cc_start: 0.8732 (p90) cc_final: 0.8381 (p90) REVERT: A 246 CYS cc_start: 0.9422 (t) cc_final: 0.8631 (p) REVERT: A 262 LEU cc_start: 0.9579 (pt) cc_final: 0.9308 (pp) REVERT: A 273 LEU cc_start: 0.9524 (tp) cc_final: 0.9233 (tp) REVERT: A 291 LYS cc_start: 0.9550 (tppt) cc_final: 0.9312 (tptp) REVERT: A 319 ASP cc_start: 0.7816 (t70) cc_final: 0.7543 (t70) REVERT: A 325 MET cc_start: 0.8296 (ptm) cc_final: 0.8013 (ptm) REVERT: A 335 GLU cc_start: 0.8684 (mp0) cc_final: 0.8273 (mp0) REVERT: A 343 GLN cc_start: 0.8203 (pp30) cc_final: 0.7229 (pp30) REVERT: A 352 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 353 TYR cc_start: 0.8894 (t80) cc_final: 0.8627 (t80) REVERT: A 375 LYS cc_start: 0.9590 (pttt) cc_final: 0.9332 (pttt) REVERT: A 385 MET cc_start: 0.8536 (ttp) cc_final: 0.8328 (ttp) REVERT: A 386 MET cc_start: 0.8660 (ppp) cc_final: 0.8141 (ppp) REVERT: A 414 MET cc_start: 0.7564 (ppp) cc_final: 0.6808 (ppp) REVERT: A 420 MET cc_start: 0.8178 (mtm) cc_final: 0.7732 (mtp) REVERT: A 480 ARG cc_start: 0.8944 (mpp80) cc_final: 0.8408 (mtm110) REVERT: A 507 HIS cc_start: 0.8516 (t-90) cc_final: 0.8196 (t70) REVERT: B 16 ASP cc_start: 0.7261 (t0) cc_final: 0.6180 (t0) REVERT: B 18 LEU cc_start: 0.9371 (tp) cc_final: 0.9144 (tp) REVERT: B 31 THR cc_start: 0.8270 (m) cc_final: 0.7875 (m) REVERT: B 34 ASP cc_start: 0.8601 (m-30) cc_final: 0.7888 (m-30) REVERT: B 36 LEU cc_start: 0.9405 (tp) cc_final: 0.9068 (tp) REVERT: B 37 ILE cc_start: 0.9047 (mm) cc_final: 0.8708 (mm) REVERT: B 70 MET cc_start: 0.8209 (tpp) cc_final: 0.7765 (mmm) REVERT: B 82 MET cc_start: 0.9496 (ttm) cc_final: 0.9206 (ttm) REVERT: B 108 LYS cc_start: 0.9353 (pttm) cc_final: 0.8388 (tppt) REVERT: B 131 PHE cc_start: 0.9527 (m-80) cc_final: 0.8454 (m-80) REVERT: B 132 GLU cc_start: 0.9567 (pt0) cc_final: 0.9249 (pt0) REVERT: B 134 LYS cc_start: 0.9388 (pttt) cc_final: 0.9028 (tttp) REVERT: B 167 LYS cc_start: 0.9132 (mppt) cc_final: 0.8906 (mmtt) REVERT: B 181 LYS cc_start: 0.9069 (tppt) cc_final: 0.8710 (tppt) REVERT: B 185 LEU cc_start: 0.8938 (mt) cc_final: 0.8463 (mt) REVERT: B 238 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8459 (tppt) REVERT: B 242 LYS cc_start: 0.8656 (tttt) cc_final: 0.8260 (tptt) REVERT: B 250 ILE cc_start: 0.9313 (mp) cc_final: 0.8783 (tp) REVERT: B 291 LYS cc_start: 0.9584 (mmmt) cc_final: 0.9073 (tppt) REVERT: B 334 GLN cc_start: 0.9334 (mt0) cc_final: 0.8819 (mm-40) REVERT: B 355 ARG cc_start: 0.8188 (ppt170) cc_final: 0.7340 (ptm-80) REVERT: B 372 HIS cc_start: 0.8990 (m170) cc_final: 0.8476 (m90) REVERT: B 400 TYR cc_start: 0.6655 (m-80) cc_final: 0.5763 (m-10) REVERT: B 404 ASP cc_start: 0.8581 (t0) cc_final: 0.8347 (t0) REVERT: B 414 MET cc_start: 0.8923 (mpp) cc_final: 0.8587 (mpp) REVERT: B 449 ASP cc_start: 0.8820 (t70) cc_final: 0.8081 (t0) REVERT: B 487 GLU cc_start: 0.8599 (pp20) cc_final: 0.8229 (pp20) REVERT: B 491 GLU cc_start: 0.8638 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 506 LEU cc_start: 0.8657 (pt) cc_final: 0.8369 (pt) REVERT: C 47 ASP cc_start: 0.9574 (m-30) cc_final: 0.8875 (p0) REVERT: C 78 MET cc_start: 0.9383 (mmp) cc_final: 0.9144 (mmt) REVERT: C 82 MET cc_start: 0.9640 (tpp) cc_final: 0.9312 (tpp) REVERT: C 90 PHE cc_start: 0.9168 (m-80) cc_final: 0.8675 (m-80) REVERT: C 99 PHE cc_start: 0.9583 (t80) cc_final: 0.9360 (t80) REVERT: C 108 LYS cc_start: 0.9273 (tptt) cc_final: 0.9061 (pttp) REVERT: C 140 CYS cc_start: 0.4487 (m) cc_final: 0.4269 (m) REVERT: C 199 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8554 (tp30) REVERT: C 200 ILE cc_start: 0.9304 (mm) cc_final: 0.8825 (mm) REVERT: C 203 ARG cc_start: 0.8824 (mtm-85) cc_final: 0.8410 (mtm110) REVERT: C 229 LYS cc_start: 0.9378 (ptpp) cc_final: 0.9055 (mmmt) REVERT: C 274 ASP cc_start: 0.9329 (t0) cc_final: 0.8978 (t70) REVERT: C 306 THR cc_start: 0.8777 (t) cc_final: 0.8302 (t) REVERT: C 319 ASP cc_start: 0.8339 (t0) cc_final: 0.8120 (t0) REVERT: C 331 CYS cc_start: 0.9041 (t) cc_final: 0.8533 (t) REVERT: C 333 THR cc_start: 0.9713 (p) cc_final: 0.9173 (p) REVERT: C 334 GLN cc_start: 0.9128 (mp10) cc_final: 0.8311 (mp10) REVERT: C 335 GLU cc_start: 0.8602 (tm-30) cc_final: 0.7972 (tm-30) REVERT: C 349 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8701 (mtmt) REVERT: C 362 ILE cc_start: 0.9422 (pt) cc_final: 0.9204 (mm) REVERT: C 441 GLN cc_start: 0.8561 (mp-120) cc_final: 0.8097 (mp-120) REVERT: C 482 MET cc_start: 0.9401 (tpp) cc_final: 0.9023 (tpp) REVERT: C 493 ARG cc_start: 0.8892 (mtm180) cc_final: 0.8116 (mtm-85) REVERT: C 500 GLU cc_start: 0.9198 (pp20) cc_final: 0.8537 (pp20) REVERT: D 12 TYR cc_start: 0.8374 (t80) cc_final: 0.7096 (m-80) REVERT: D 21 GLN cc_start: 0.9064 (tp40) cc_final: 0.8421 (tp40) REVERT: D 25 ASN cc_start: 0.8513 (m110) cc_final: 0.7721 (m110) REVERT: D 32 TYR cc_start: 0.9064 (m-10) cc_final: 0.8740 (m-10) REVERT: D 33 ASN cc_start: 0.9271 (t0) cc_final: 0.8740 (t0) REVERT: D 38 LEU cc_start: 0.9431 (mt) cc_final: 0.9192 (mt) REVERT: D 91 ILE cc_start: 0.9196 (tp) cc_final: 0.8922 (tp) REVERT: D 93 HIS cc_start: 0.9225 (p-80) cc_final: 0.8989 (p-80) REVERT: D 144 ILE cc_start: 0.9114 (mm) cc_final: 0.8673 (mp) REVERT: D 179 MET cc_start: 0.5339 (ppp) cc_final: 0.3870 (pmm) REVERT: D 215 ASP cc_start: 0.9542 (m-30) cc_final: 0.9063 (p0) REVERT: D 242 LYS cc_start: 0.9281 (mmpt) cc_final: 0.9016 (mmmt) REVERT: D 257 LYS cc_start: 0.9813 (ptpp) cc_final: 0.9548 (mmtm) REVERT: D 286 MET cc_start: 0.9636 (tpt) cc_final: 0.9334 (tpt) REVERT: D 289 TYR cc_start: 0.9410 (t80) cc_final: 0.9060 (t80) REVERT: D 290 ILE cc_start: 0.9754 (pt) cc_final: 0.9429 (pt) REVERT: D 315 ASP cc_start: 0.9055 (m-30) cc_final: 0.8615 (p0) REVERT: D 352 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9071 (tm-30) REVERT: D 375 LYS cc_start: 0.9491 (pttt) cc_final: 0.9245 (pttt) REVERT: D 379 LEU cc_start: 0.9684 (mm) cc_final: 0.9427 (mm) REVERT: D 385 MET cc_start: 0.8517 (tpt) cc_final: 0.7302 (tpt) REVERT: D 386 MET cc_start: 0.8478 (ptm) cc_final: 0.8058 (ptm) REVERT: D 400 TYR cc_start: 0.7216 (m-80) cc_final: 0.6571 (m-80) REVERT: D 414 MET cc_start: 0.8468 (pmm) cc_final: 0.8164 (pmm) REVERT: D 441 GLN cc_start: 0.7511 (mp-120) cc_final: 0.7307 (mp-120) REVERT: D 453 ILE cc_start: 0.9617 (pt) cc_final: 0.9210 (pt) REVERT: D 465 GLN cc_start: 0.8551 (pp30) cc_final: 0.8156 (tt0) REVERT: D 468 CYS cc_start: 0.9163 (t) cc_final: 0.8853 (t) REVERT: D 482 MET cc_start: 0.8722 (tpt) cc_final: 0.7979 (tpp) REVERT: D 487 GLU cc_start: 0.8825 (pm20) cc_final: 0.8529 (pm20) REVERT: N 12 TYR cc_start: 0.8555 (t80) cc_final: 0.8274 (t80) REVERT: O 1 MET cc_start: 0.7960 (mmm) cc_final: 0.7469 (mmp) REVERT: P 1 MET cc_start: 0.8342 (pmm) cc_final: 0.8032 (pmm) REVERT: E 12 TYR cc_start: 0.7577 (t80) cc_final: 0.6828 (m-80) REVERT: E 32 TYR cc_start: 0.9163 (m-80) cc_final: 0.8767 (m-80) REVERT: E 36 LEU cc_start: 0.8568 (tp) cc_final: 0.8137 (tp) REVERT: E 38 LEU cc_start: 0.9554 (mm) cc_final: 0.8848 (mm) REVERT: E 48 GLN cc_start: 0.9230 (mt0) cc_final: 0.8744 (mt0) REVERT: E 100 GLN cc_start: 0.9366 (mp10) cc_final: 0.9136 (mp10) REVERT: E 105 ARG cc_start: 0.8975 (mmm160) cc_final: 0.7942 (tpm170) REVERT: E 109 LYS cc_start: 0.9294 (ptpp) cc_final: 0.8659 (ptpp) REVERT: E 112 GLN cc_start: 0.8895 (mp-120) cc_final: 0.8527 (mp10) REVERT: E 137 HIS cc_start: 0.9364 (m90) cc_final: 0.8696 (m90) REVERT: E 150 MET cc_start: 0.7818 (tpt) cc_final: 0.7045 (tpt) REVERT: E 165 PHE cc_start: 0.8438 (p90) cc_final: 0.8194 (p90) REVERT: E 179 MET cc_start: 0.7523 (pmm) cc_final: 0.7150 (pmm) REVERT: E 203 ARG cc_start: 0.9031 (mtm110) cc_final: 0.8778 (mtm110) REVERT: E 228 LYS cc_start: 0.9524 (ptpp) cc_final: 0.9281 (ptpp) REVERT: E 246 CYS cc_start: 0.9421 (t) cc_final: 0.8616 (p) REVERT: E 250 ILE cc_start: 0.9484 (pt) cc_final: 0.9241 (pt) REVERT: E 254 GLU cc_start: 0.9336 (tp30) cc_final: 0.8749 (pm20) REVERT: E 256 ASP cc_start: 0.9008 (p0) cc_final: 0.8714 (m-30) REVERT: E 262 LEU cc_start: 0.9646 (pt) cc_final: 0.9387 (pt) REVERT: E 319 ASP cc_start: 0.7778 (t70) cc_final: 0.7484 (t70) REVERT: E 334 GLN cc_start: 0.9288 (mp10) cc_final: 0.8349 (mp10) REVERT: E 335 GLU cc_start: 0.8729 (mp0) cc_final: 0.8169 (mp0) REVERT: E 341 ARG cc_start: 0.9352 (ptm160) cc_final: 0.8769 (ptm160) REVERT: E 352 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8790 (tm-30) REVERT: E 353 TYR cc_start: 0.8897 (t80) cc_final: 0.8622 (t80) REVERT: E 364 ASP cc_start: 0.8712 (m-30) cc_final: 0.7475 (m-30) REVERT: E 385 MET cc_start: 0.8660 (ttp) cc_final: 0.7828 (ttp) REVERT: E 420 MET cc_start: 0.8190 (mtm) cc_final: 0.7608 (mtp) REVERT: E 480 ARG cc_start: 0.8958 (mpp80) cc_final: 0.8285 (mpp80) REVERT: E 483 MET cc_start: 0.9719 (tmm) cc_final: 0.9480 (tmm) REVERT: E 507 HIS cc_start: 0.8470 (t-90) cc_final: 0.8189 (t70) REVERT: F 18 LEU cc_start: 0.9244 (tp) cc_final: 0.9007 (tp) REVERT: F 36 LEU cc_start: 0.9349 (tp) cc_final: 0.9142 (tp) REVERT: F 37 ILE cc_start: 0.9023 (mm) cc_final: 0.8623 (mm) REVERT: F 41 TYR cc_start: 0.9088 (t80) cc_final: 0.8719 (t80) REVERT: F 70 MET cc_start: 0.8164 (tpp) cc_final: 0.7620 (mmm) REVERT: F 103 GLU cc_start: 0.9504 (mm-30) cc_final: 0.9053 (mm-30) REVERT: F 106 LYS cc_start: 0.9403 (mtpt) cc_final: 0.9185 (mtpt) REVERT: F 131 PHE cc_start: 0.9227 (m-10) cc_final: 0.8794 (m-80) REVERT: F 132 GLU cc_start: 0.9499 (pt0) cc_final: 0.9206 (pt0) REVERT: F 134 LYS cc_start: 0.9352 (ptpp) cc_final: 0.9050 (pttt) REVERT: F 185 LEU cc_start: 0.8963 (mt) cc_final: 0.8433 (mt) REVERT: F 233 TYR cc_start: 0.9429 (m-10) cc_final: 0.9192 (m-10) REVERT: F 238 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8309 (tppt) REVERT: F 250 ILE cc_start: 0.9412 (mp) cc_final: 0.9098 (tp) REVERT: F 291 LYS cc_start: 0.9587 (mmmt) cc_final: 0.9061 (tppt) REVERT: F 294 TYR cc_start: 0.9438 (m-80) cc_final: 0.9090 (m-80) REVERT: F 322 ARG cc_start: 0.8488 (ttt90) cc_final: 0.7737 (tpt-90) REVERT: F 334 GLN cc_start: 0.9312 (mt0) cc_final: 0.8749 (mm-40) REVERT: F 335 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7950 (tm-30) REVERT: F 337 LEU cc_start: 0.9130 (mm) cc_final: 0.8918 (mm) REVERT: F 348 TYR cc_start: 0.9338 (t80) cc_final: 0.8996 (t80) REVERT: F 351 SER cc_start: 0.9304 (p) cc_final: 0.9056 (p) REVERT: F 372 HIS cc_start: 0.8962 (m170) cc_final: 0.8673 (m90) REVERT: F 399 GLU cc_start: 0.7658 (mp0) cc_final: 0.7343 (mp0) REVERT: F 400 TYR cc_start: 0.7583 (m-80) cc_final: 0.7158 (m-80) REVERT: F 456 PHE cc_start: 0.9577 (t80) cc_final: 0.9377 (t80) REVERT: F 491 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8275 (tm-30) REVERT: F 493 ARG cc_start: 0.8736 (ptt-90) cc_final: 0.8208 (ptt-90) REVERT: F 506 LEU cc_start: 0.8664 (pt) cc_final: 0.8393 (pt) REVERT: G 47 ASP cc_start: 0.9623 (m-30) cc_final: 0.9034 (p0) REVERT: G 78 MET cc_start: 0.9572 (tpp) cc_final: 0.9056 (tpp) REVERT: G 222 ILE cc_start: 0.7286 (mm) cc_final: 0.7068 (mm) REVERT: G 229 LYS cc_start: 0.9363 (ptpp) cc_final: 0.9026 (mmmt) REVERT: G 274 ASP cc_start: 0.9107 (t0) cc_final: 0.8677 (t70) REVERT: G 331 CYS cc_start: 0.9124 (t) cc_final: 0.8738 (t) REVERT: G 333 THR cc_start: 0.9729 (p) cc_final: 0.9120 (p) REVERT: G 334 GLN cc_start: 0.9093 (mp10) cc_final: 0.8231 (mp10) REVERT: G 335 GLU cc_start: 0.8582 (tm-30) cc_final: 0.7968 (tm-30) REVERT: G 336 VAL cc_start: 0.9413 (m) cc_final: 0.8591 (m) REVERT: G 353 TYR cc_start: 0.8761 (t80) cc_final: 0.8107 (t80) REVERT: G 386 MET cc_start: 0.8955 (tmm) cc_final: 0.8749 (tmm) REVERT: G 395 GLU cc_start: 0.8740 (mp0) cc_final: 0.8433 (mp0) REVERT: G 482 MET cc_start: 0.9263 (tpp) cc_final: 0.8857 (mmm) REVERT: G 493 ARG cc_start: 0.8886 (mtm180) cc_final: 0.8141 (mtm-85) REVERT: G 500 GLU cc_start: 0.9270 (pp20) cc_final: 0.8610 (pp20) REVERT: H 16 ASP cc_start: 0.8018 (m-30) cc_final: 0.7783 (m-30) REVERT: H 21 GLN cc_start: 0.8800 (tm-30) cc_final: 0.7999 (tm-30) REVERT: H 25 ASN cc_start: 0.8734 (m110) cc_final: 0.8103 (m110) REVERT: H 91 ILE cc_start: 0.9362 (tp) cc_final: 0.9079 (tp) REVERT: H 108 LYS cc_start: 0.9051 (tptm) cc_final: 0.8600 (tptp) REVERT: H 112 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8884 (tm-30) REVERT: H 179 MET cc_start: 0.6834 (ppp) cc_final: 0.6037 (tmm) REVERT: H 208 LYS cc_start: 0.8808 (tmtt) cc_final: 0.8558 (tmtt) REVERT: H 209 LEU cc_start: 0.9069 (tp) cc_final: 0.8727 (pp) REVERT: H 215 ASP cc_start: 0.9442 (m-30) cc_final: 0.8824 (t70) REVERT: H 229 LYS cc_start: 0.8858 (pttt) cc_final: 0.8614 (mmtt) REVERT: H 242 LYS cc_start: 0.9367 (mmpt) cc_final: 0.9147 (mmmt) REVERT: H 286 MET cc_start: 0.9656 (tpt) cc_final: 0.9204 (tpt) REVERT: H 290 ILE cc_start: 0.9720 (pt) cc_final: 0.9402 (pt) REVERT: H 315 ASP cc_start: 0.9086 (m-30) cc_final: 0.8650 (p0) REVERT: H 352 GLU cc_start: 0.9389 (tm-30) cc_final: 0.9015 (tm-30) REVERT: H 364 ASP cc_start: 0.8588 (t70) cc_final: 0.8306 (t0) REVERT: H 368 GLN cc_start: 0.8668 (mt0) cc_final: 0.8239 (mm-40) REVERT: H 375 LYS cc_start: 0.9379 (ptmt) cc_final: 0.9106 (ptmt) REVERT: H 379 LEU cc_start: 0.9644 (mm) cc_final: 0.9410 (mm) REVERT: H 385 MET cc_start: 0.8112 (tpt) cc_final: 0.7558 (tpt) REVERT: H 409 LYS cc_start: 0.7996 (ttmm) cc_final: 0.7781 (tppt) REVERT: H 410 LYS cc_start: 0.8938 (mptt) cc_final: 0.8667 (mmtm) REVERT: H 414 MET cc_start: 0.8728 (pmm) cc_final: 0.8484 (pmm) REVERT: H 453 ILE cc_start: 0.9556 (pt) cc_final: 0.9147 (pt) REVERT: H 465 GLN cc_start: 0.8579 (pp30) cc_final: 0.8299 (tt0) REVERT: H 468 CYS cc_start: 0.9139 (t) cc_final: 0.8811 (t) REVERT: H 478 GLN cc_start: 0.9612 (tt0) cc_final: 0.9209 (tt0) REVERT: H 482 MET cc_start: 0.8772 (tpp) cc_final: 0.8367 (tpp) REVERT: H 492 LYS cc_start: 0.9171 (pttt) cc_final: 0.8740 (pttp) REVERT: J 4 TYR cc_start: 0.9581 (t80) cc_final: 0.9350 (t80) REVERT: J 5 LEU cc_start: 0.9501 (mt) cc_final: 0.9048 (mt) REVERT: J 12 TYR cc_start: 0.8758 (t80) cc_final: 0.8375 (t80) REVERT: K 1 MET cc_start: 0.7964 (mmm) cc_final: 0.7420 (mmp) REVERT: K 4 TYR cc_start: 0.7403 (p90) cc_final: 0.7123 (p90) REVERT: L 1 MET cc_start: 0.8422 (pmm) cc_final: 0.8220 (pmm) outliers start: 0 outliers final: 0 residues processed: 1412 average time/residue: 0.1914 time to fit residues: 444.6649 Evaluate side-chains 1194 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1194 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 300 optimal weight: 1.9990 chunk 18 optimal weight: 0.0050 chunk 114 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 372 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 249 optimal weight: 3.9990 chunk 390 optimal weight: 0.1980 chunk 326 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 507 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN H 498 GLN ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.127769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090881 restraints weight = 72809.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094830 restraints weight = 40864.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097567 restraints weight = 26932.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099540 restraints weight = 19715.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100688 restraints weight = 15520.279| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32220 Z= 0.151 Angle : 0.906 14.035 43712 Z= 0.442 Chirality : 0.053 0.333 4984 Planarity : 0.004 0.073 5452 Dihedral : 11.819 164.167 4572 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.49 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.12), residues: 3968 helix: -1.71 (0.13), residues: 1242 sheet: -2.28 (0.23), residues: 382 loop : -1.73 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 407 TYR 0.041 0.002 TYR E 110 PHE 0.039 0.002 PHE B 456 HIS 0.007 0.001 HIS H 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (32212) covalent geometry : angle 0.90559 / 0.44 (43712) hydrogen bonds : bond 0.04318 / 2.82 ( 966) hydrogen bonds : angle 6.55868 / 4.49 ( 2655) Misc. bond : bond 0.00088 / 0.06 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1397 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1397 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7967 (t80) cc_final: 0.6765 (m-80) REVERT: A 28 ASP cc_start: 0.9149 (t70) cc_final: 0.8622 (t70) REVERT: A 32 TYR cc_start: 0.8611 (m-10) cc_final: 0.8123 (m-80) REVERT: A 36 LEU cc_start: 0.8634 (tp) cc_final: 0.8302 (tp) REVERT: A 38 LEU cc_start: 0.9576 (mm) cc_final: 0.8793 (mm) REVERT: A 48 GLN cc_start: 0.9265 (mt0) cc_final: 0.8898 (mt0) REVERT: A 108 LYS cc_start: 0.9522 (tptp) cc_final: 0.9175 (pttm) REVERT: A 117 ASP cc_start: 0.8885 (p0) cc_final: 0.8488 (p0) REVERT: A 137 HIS cc_start: 0.9453 (m90) cc_final: 0.8624 (m90) REVERT: A 150 MET cc_start: 0.7817 (tpt) cc_final: 0.7294 (tpt) REVERT: A 179 MET cc_start: 0.7289 (pmm) cc_final: 0.6773 (pmm) REVERT: A 246 CYS cc_start: 0.9402 (t) cc_final: 0.8689 (p) REVERT: A 273 LEU cc_start: 0.9498 (tp) cc_final: 0.9215 (tp) REVERT: A 291 LYS cc_start: 0.9578 (tppt) cc_final: 0.9332 (tptp) REVERT: A 319 ASP cc_start: 0.7830 (t70) cc_final: 0.7509 (t0) REVERT: A 335 GLU cc_start: 0.8679 (mp0) cc_final: 0.8207 (mp0) REVERT: A 341 ARG cc_start: 0.9376 (ptm160) cc_final: 0.8973 (ptm160) REVERT: A 343 GLN cc_start: 0.8202 (pp30) cc_final: 0.7197 (pp30) REVERT: A 352 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8732 (tm-30) REVERT: A 353 TYR cc_start: 0.8879 (t80) cc_final: 0.8375 (t80) REVERT: A 355 ARG cc_start: 0.8544 (ppt170) cc_final: 0.8282 (ppt170) REVERT: A 375 LYS cc_start: 0.9577 (pttt) cc_final: 0.9259 (pttt) REVERT: A 385 MET cc_start: 0.8467 (ttp) cc_final: 0.7844 (ttp) REVERT: A 386 MET cc_start: 0.8325 (ppp) cc_final: 0.7846 (ppp) REVERT: A 414 MET cc_start: 0.7560 (ppp) cc_final: 0.6851 (ppp) REVERT: A 420 MET cc_start: 0.8189 (mtm) cc_final: 0.7713 (mtp) REVERT: A 460 LEU cc_start: 0.9712 (mp) cc_final: 0.9493 (mp) REVERT: A 480 ARG cc_start: 0.8885 (mpp80) cc_final: 0.8267 (mtm110) REVERT: A 483 MET cc_start: 0.9731 (tmm) cc_final: 0.9473 (tmm) REVERT: A 507 HIS cc_start: 0.8474 (t-90) cc_final: 0.8149 (t70) REVERT: B 16 ASP cc_start: 0.7167 (t0) cc_final: 0.6058 (t0) REVERT: B 18 LEU cc_start: 0.9408 (tp) cc_final: 0.9080 (tp) REVERT: B 31 THR cc_start: 0.8188 (m) cc_final: 0.7799 (m) REVERT: B 37 ILE cc_start: 0.9056 (mm) cc_final: 0.8700 (mm) REVERT: B 70 MET cc_start: 0.8241 (tpp) cc_final: 0.7751 (mmm) REVERT: B 82 MET cc_start: 0.9474 (ttm) cc_final: 0.9242 (ttm) REVERT: B 100 GLN cc_start: 0.9242 (mt0) cc_final: 0.8893 (mm-40) REVERT: B 105 ARG cc_start: 0.9160 (mtm110) cc_final: 0.8631 (mtm110) REVERT: B 106 LYS cc_start: 0.9306 (mtpt) cc_final: 0.9060 (mtpt) REVERT: B 108 LYS cc_start: 0.9273 (pttm) cc_final: 0.8250 (tppt) REVERT: B 131 PHE cc_start: 0.9526 (m-80) cc_final: 0.8888 (m-80) REVERT: B 132 GLU cc_start: 0.9567 (pt0) cc_final: 0.9275 (pt0) REVERT: B 134 LYS cc_start: 0.9385 (pttt) cc_final: 0.9180 (pttp) REVERT: B 179 MET cc_start: 0.7430 (tmm) cc_final: 0.7069 (tmm) REVERT: B 185 LEU cc_start: 0.8847 (mt) cc_final: 0.8402 (mt) REVERT: B 238 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8436 (tppt) REVERT: B 242 LYS cc_start: 0.8613 (tttt) cc_final: 0.8274 (tptt) REVERT: B 250 ILE cc_start: 0.9350 (mp) cc_final: 0.8869 (tp) REVERT: B 322 ARG cc_start: 0.8923 (ttt90) cc_final: 0.8346 (tpt-90) REVERT: B 334 GLN cc_start: 0.9319 (mt0) cc_final: 0.8815 (mm-40) REVERT: B 348 TYR cc_start: 0.9234 (t80) cc_final: 0.8925 (t80) REVERT: B 352 GLU cc_start: 0.8752 (pm20) cc_final: 0.8420 (mp0) REVERT: B 355 ARG cc_start: 0.8165 (ppt170) cc_final: 0.7362 (ptm-80) REVERT: B 364 ASP cc_start: 0.7351 (m-30) cc_final: 0.5474 (m-30) REVERT: B 372 HIS cc_start: 0.8928 (m170) cc_final: 0.8437 (m90) REVERT: B 400 TYR cc_start: 0.6896 (m-80) cc_final: 0.5684 (m-10) REVERT: B 404 ASP cc_start: 0.8565 (t0) cc_final: 0.8351 (t0) REVERT: B 414 MET cc_start: 0.8886 (mpp) cc_final: 0.8589 (mpp) REVERT: B 449 ASP cc_start: 0.8808 (t70) cc_final: 0.8081 (t70) REVERT: B 491 GLU cc_start: 0.8690 (tm-30) cc_final: 0.7881 (tm-30) REVERT: B 493 ARG cc_start: 0.8640 (ptt-90) cc_final: 0.8259 (ptt-90) REVERT: C 30 LEU cc_start: 0.9335 (mm) cc_final: 0.8878 (mm) REVERT: C 47 ASP cc_start: 0.9596 (m-30) cc_final: 0.8895 (p0) REVERT: C 82 MET cc_start: 0.9634 (tpp) cc_final: 0.9323 (tpp) REVERT: C 90 PHE cc_start: 0.9209 (m-80) cc_final: 0.8685 (m-80) REVERT: C 99 PHE cc_start: 0.9584 (t80) cc_final: 0.9354 (t80) REVERT: C 108 LYS cc_start: 0.9252 (tptt) cc_final: 0.9033 (pttp) REVERT: C 140 CYS cc_start: 0.4406 (m) cc_final: 0.4177 (m) REVERT: C 199 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8585 (tp30) REVERT: C 200 ILE cc_start: 0.9338 (mm) cc_final: 0.8888 (mm) REVERT: C 203 ARG cc_start: 0.8789 (mtm-85) cc_final: 0.8359 (mtm110) REVERT: C 229 LYS cc_start: 0.9380 (ptpp) cc_final: 0.9083 (mmmt) REVERT: C 243 GLN cc_start: 0.9303 (tp-100) cc_final: 0.8772 (tp40) REVERT: C 274 ASP cc_start: 0.9239 (t0) cc_final: 0.8826 (t70) REVERT: C 319 ASP cc_start: 0.8336 (t0) cc_final: 0.8124 (t0) REVERT: C 331 CYS cc_start: 0.9094 (t) cc_final: 0.8770 (t) REVERT: C 333 THR cc_start: 0.9713 (p) cc_final: 0.9103 (p) REVERT: C 334 GLN cc_start: 0.9174 (mp10) cc_final: 0.8384 (mp10) REVERT: C 335 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7910 (tm-30) REVERT: C 349 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8641 (mtmt) REVERT: C 357 PHE cc_start: 0.9225 (m-80) cc_final: 0.9017 (m-80) REVERT: C 362 ILE cc_start: 0.9323 (pt) cc_final: 0.9093 (mm) REVERT: C 386 MET cc_start: 0.8964 (tmm) cc_final: 0.8552 (tmm) REVERT: C 441 GLN cc_start: 0.8462 (mp-120) cc_final: 0.8130 (mp10) REVERT: C 456 PHE cc_start: 0.9637 (t80) cc_final: 0.9411 (t80) REVERT: C 482 MET cc_start: 0.9385 (tpp) cc_final: 0.9015 (tpp) REVERT: C 493 ARG cc_start: 0.8852 (mtm180) cc_final: 0.8496 (ptp90) REVERT: C 500 GLU cc_start: 0.9134 (pp20) cc_final: 0.8430 (pp20) REVERT: D 12 TYR cc_start: 0.8229 (t80) cc_final: 0.6974 (m-80) REVERT: D 21 GLN cc_start: 0.9063 (tp40) cc_final: 0.8409 (tp40) REVERT: D 25 ASN cc_start: 0.8528 (m110) cc_final: 0.7793 (m110) REVERT: D 32 TYR cc_start: 0.9030 (m-10) cc_final: 0.8664 (m-10) REVERT: D 33 ASN cc_start: 0.9258 (t0) cc_final: 0.8650 (t0) REVERT: D 91 ILE cc_start: 0.9214 (tp) cc_final: 0.8929 (tp) REVERT: D 93 HIS cc_start: 0.9325 (p-80) cc_final: 0.8860 (p-80) REVERT: D 94 ASN cc_start: 0.9033 (m110) cc_final: 0.8678 (t0) REVERT: D 144 ILE cc_start: 0.9073 (mm) cc_final: 0.8739 (mp) REVERT: D 179 MET cc_start: 0.5223 (ppp) cc_final: 0.3578 (pmm) REVERT: D 215 ASP cc_start: 0.9538 (m-30) cc_final: 0.8799 (t70) REVERT: D 242 LYS cc_start: 0.9285 (mmpt) cc_final: 0.9016 (mmmt) REVERT: D 257 LYS cc_start: 0.9815 (ptpp) cc_final: 0.9554 (mmtm) REVERT: D 286 MET cc_start: 0.9651 (tpt) cc_final: 0.9358 (tpt) REVERT: D 289 TYR cc_start: 0.9431 (t80) cc_final: 0.9093 (t80) REVERT: D 290 ILE cc_start: 0.9745 (pt) cc_final: 0.9472 (pt) REVERT: D 315 ASP cc_start: 0.9060 (m-30) cc_final: 0.8517 (p0) REVERT: D 352 GLU cc_start: 0.9411 (tm-30) cc_final: 0.9044 (tm-30) REVERT: D 379 LEU cc_start: 0.9673 (mm) cc_final: 0.9420 (mm) REVERT: D 385 MET cc_start: 0.8647 (tpt) cc_final: 0.7513 (tpt) REVERT: D 386 MET cc_start: 0.8367 (ptm) cc_final: 0.8005 (ptm) REVERT: D 441 GLN cc_start: 0.7509 (mp-120) cc_final: 0.7169 (mp-120) REVERT: D 468 CYS cc_start: 0.9136 (t) cc_final: 0.8768 (t) REVERT: D 482 MET cc_start: 0.8724 (tpt) cc_final: 0.8263 (tpt) REVERT: M 1 MET cc_start: 0.6920 (mtt) cc_final: 0.6554 (ttm) REVERT: O 1 MET cc_start: 0.7886 (mmm) cc_final: 0.7399 (mmp) REVERT: P 1 MET cc_start: 0.8282 (pmm) cc_final: 0.7966 (pmm) REVERT: E 32 TYR cc_start: 0.9216 (m-80) cc_final: 0.8753 (m-80) REVERT: E 36 LEU cc_start: 0.8754 (tp) cc_final: 0.8225 (tp) REVERT: E 38 LEU cc_start: 0.9563 (mm) cc_final: 0.8816 (mm) REVERT: E 48 GLN cc_start: 0.9219 (mt0) cc_final: 0.8794 (mt0) REVERT: E 100 GLN cc_start: 0.9311 (mp10) cc_final: 0.9099 (mp10) REVERT: E 105 ARG cc_start: 0.8970 (mmm160) cc_final: 0.8104 (tpm170) REVERT: E 108 LYS cc_start: 0.9451 (tppt) cc_final: 0.8904 (mmtt) REVERT: E 109 LYS cc_start: 0.9265 (ptpp) cc_final: 0.8764 (ptpp) REVERT: E 112 GLN cc_start: 0.8799 (mp-120) cc_final: 0.8424 (mp10) REVERT: E 137 HIS cc_start: 0.9367 (m90) cc_final: 0.8787 (m90) REVERT: E 142 ILE cc_start: 0.8711 (tp) cc_final: 0.8456 (tp) REVERT: E 150 MET cc_start: 0.7809 (tpt) cc_final: 0.7041 (tpt) REVERT: E 158 ILE cc_start: 0.9133 (mm) cc_final: 0.8851 (tp) REVERT: E 165 PHE cc_start: 0.8432 (p90) cc_final: 0.8129 (p90) REVERT: E 179 MET cc_start: 0.7477 (pmm) cc_final: 0.6862 (pmm) REVERT: E 203 ARG cc_start: 0.9088 (mtm110) cc_final: 0.8803 (mtm110) REVERT: E 228 LYS cc_start: 0.9490 (ptpp) cc_final: 0.9253 (ptpp) REVERT: E 246 CYS cc_start: 0.9363 (t) cc_final: 0.8931 (t) REVERT: E 250 ILE cc_start: 0.9431 (pt) cc_final: 0.9202 (pt) REVERT: E 254 GLU cc_start: 0.9330 (tp30) cc_final: 0.9043 (pm20) REVERT: E 319 ASP cc_start: 0.7878 (t70) cc_final: 0.7601 (t70) REVERT: E 334 GLN cc_start: 0.9292 (mp10) cc_final: 0.8371 (mp10) REVERT: E 335 GLU cc_start: 0.8767 (mp0) cc_final: 0.8192 (mp0) REVERT: E 341 ARG cc_start: 0.9349 (ptm160) cc_final: 0.8796 (ptm160) REVERT: E 352 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8725 (tm-30) REVERT: E 353 TYR cc_start: 0.8896 (t80) cc_final: 0.8668 (t80) REVERT: E 355 ARG cc_start: 0.8531 (ptt90) cc_final: 0.8171 (ptt90) REVERT: E 364 ASP cc_start: 0.8712 (m-30) cc_final: 0.7253 (m-30) REVERT: E 375 LYS cc_start: 0.9711 (pttt) cc_final: 0.9395 (pttt) REVERT: E 385 MET cc_start: 0.8457 (ttp) cc_final: 0.7591 (ttp) REVERT: E 420 MET cc_start: 0.8151 (mtm) cc_final: 0.7539 (mtp) REVERT: E 460 LEU cc_start: 0.9719 (mp) cc_final: 0.9495 (mp) REVERT: E 480 ARG cc_start: 0.8912 (mpp80) cc_final: 0.8232 (mpp80) REVERT: E 483 MET cc_start: 0.9706 (tmm) cc_final: 0.9468 (tmm) REVERT: E 507 HIS cc_start: 0.8354 (t-90) cc_final: 0.8101 (t70) REVERT: F 18 LEU cc_start: 0.9226 (tp) cc_final: 0.8882 (tp) REVERT: F 36 LEU cc_start: 0.9355 (tp) cc_final: 0.9122 (tp) REVERT: F 37 ILE cc_start: 0.8995 (mm) cc_final: 0.8590 (mm) REVERT: F 41 TYR cc_start: 0.9118 (t80) cc_final: 0.8736 (t80) REVERT: F 70 MET cc_start: 0.8103 (tpp) cc_final: 0.7574 (mmm) REVERT: F 103 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9016 (mm-30) REVERT: F 108 LYS cc_start: 0.9052 (pttm) cc_final: 0.7857 (tppt) REVERT: F 131 PHE cc_start: 0.9209 (m-10) cc_final: 0.8789 (m-80) REVERT: F 132 GLU cc_start: 0.9483 (pt0) cc_final: 0.9190 (pt0) REVERT: F 134 LYS cc_start: 0.9351 (ptpp) cc_final: 0.9058 (pttt) REVERT: F 199 GLU cc_start: 0.9508 (mt-10) cc_final: 0.9294 (mt-10) REVERT: F 233 TYR cc_start: 0.9398 (m-10) cc_final: 0.9187 (m-10) REVERT: F 238 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8272 (tppt) REVERT: F 250 ILE cc_start: 0.9400 (mp) cc_final: 0.9177 (tp) REVERT: F 322 ARG cc_start: 0.8421 (ttt90) cc_final: 0.7527 (tpt-90) REVERT: F 334 GLN cc_start: 0.9287 (mt0) cc_final: 0.8760 (mm-40) REVERT: F 335 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8184 (tm-30) REVERT: F 343 GLN cc_start: 0.8194 (tm130) cc_final: 0.7804 (tm-30) REVERT: F 352 GLU cc_start: 0.8807 (pm20) cc_final: 0.8599 (pm20) REVERT: F 364 ASP cc_start: 0.6384 (m-30) cc_final: 0.4997 (m-30) REVERT: F 372 HIS cc_start: 0.8972 (m170) cc_final: 0.8714 (m90) REVERT: F 399 GLU cc_start: 0.7416 (mp0) cc_final: 0.7133 (mp0) REVERT: F 400 TYR cc_start: 0.7715 (m-80) cc_final: 0.7273 (m-80) REVERT: F 482 MET cc_start: 0.8864 (ptp) cc_final: 0.8624 (pmm) REVERT: F 491 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8186 (tm-30) REVERT: F 493 ARG cc_start: 0.8763 (ptt-90) cc_final: 0.8355 (ptt-90) REVERT: F 506 LEU cc_start: 0.8701 (pt) cc_final: 0.8463 (pt) REVERT: G 47 ASP cc_start: 0.9622 (m-30) cc_final: 0.9013 (p0) REVERT: G 74 THR cc_start: 0.7281 (t) cc_final: 0.6850 (t) REVERT: G 78 MET cc_start: 0.9556 (tpp) cc_final: 0.9046 (tpp) REVERT: G 229 LYS cc_start: 0.9368 (ptpp) cc_final: 0.9018 (mmmt) REVERT: G 274 ASP cc_start: 0.9057 (t0) cc_final: 0.8656 (t70) REVERT: G 291 LYS cc_start: 0.9061 (pttm) cc_final: 0.8744 (pttm) REVERT: G 331 CYS cc_start: 0.9057 (t) cc_final: 0.8721 (t) REVERT: G 333 THR cc_start: 0.9727 (p) cc_final: 0.9136 (p) REVERT: G 334 GLN cc_start: 0.9083 (mp10) cc_final: 0.8243 (mp10) REVERT: G 335 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7916 (tm-30) REVERT: G 336 VAL cc_start: 0.9370 (m) cc_final: 0.8604 (m) REVERT: G 353 TYR cc_start: 0.8816 (t80) cc_final: 0.8157 (t80) REVERT: G 395 GLU cc_start: 0.8755 (mp0) cc_final: 0.8475 (mp0) REVERT: G 482 MET cc_start: 0.9237 (tpp) cc_final: 0.8852 (mmm) REVERT: G 493 ARG cc_start: 0.8852 (mtm180) cc_final: 0.8496 (ptp90) REVERT: G 500 GLU cc_start: 0.9180 (pp20) cc_final: 0.8295 (pp20) REVERT: G 504 HIS cc_start: 0.8454 (p90) cc_final: 0.7468 (p-80) REVERT: H 16 ASP cc_start: 0.8045 (m-30) cc_final: 0.7808 (m-30) REVERT: H 21 GLN cc_start: 0.8787 (tm-30) cc_final: 0.7928 (tm-30) REVERT: H 25 ASN cc_start: 0.8729 (m110) cc_final: 0.8057 (m110) REVERT: H 33 ASN cc_start: 0.8891 (t0) cc_final: 0.8319 (t0) REVERT: H 62 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8841 (mtpp) REVERT: H 91 ILE cc_start: 0.9383 (tp) cc_final: 0.9072 (tp) REVERT: H 100 GLN cc_start: 0.9283 (mp10) cc_final: 0.9058 (mp10) REVERT: H 108 LYS cc_start: 0.9072 (tptm) cc_final: 0.8684 (tptp) REVERT: H 112 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8885 (tm-30) REVERT: H 179 MET cc_start: 0.6787 (ppp) cc_final: 0.6178 (ppp) REVERT: H 208 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8414 (tmtt) REVERT: H 209 LEU cc_start: 0.9101 (tp) cc_final: 0.8786 (pp) REVERT: H 215 ASP cc_start: 0.9446 (m-30) cc_final: 0.8835 (t70) REVERT: H 229 LYS cc_start: 0.8888 (pttt) cc_final: 0.8654 (mmtt) REVERT: H 286 MET cc_start: 0.9660 (tpt) cc_final: 0.9206 (tpt) REVERT: H 290 ILE cc_start: 0.9732 (pt) cc_final: 0.9423 (pt) REVERT: H 315 ASP cc_start: 0.9061 (m-30) cc_final: 0.8587 (p0) REVERT: H 343 GLN cc_start: 0.7710 (tm130) cc_final: 0.6485 (tm130) REVERT: H 345 THR cc_start: 0.9152 (p) cc_final: 0.8945 (p) REVERT: H 349 LYS cc_start: 0.9604 (mmtp) cc_final: 0.9213 (mmmm) REVERT: H 352 GLU cc_start: 0.9385 (tm-30) cc_final: 0.9072 (tm-30) REVERT: H 368 GLN cc_start: 0.8711 (mt0) cc_final: 0.8384 (mm-40) REVERT: H 375 LYS cc_start: 0.9321 (ptmt) cc_final: 0.9030 (ptmt) REVERT: H 379 LEU cc_start: 0.9639 (mm) cc_final: 0.9395 (mm) REVERT: H 410 LYS cc_start: 0.8852 (mptt) cc_final: 0.8555 (mmtm) REVERT: H 414 MET cc_start: 0.8723 (pmm) cc_final: 0.8421 (pmm) REVERT: H 465 GLN cc_start: 0.8566 (pp30) cc_final: 0.8233 (tt0) REVERT: H 468 CYS cc_start: 0.9099 (t) cc_final: 0.8778 (t) REVERT: H 478 GLN cc_start: 0.9614 (tt0) cc_final: 0.9235 (tt0) REVERT: H 492 LYS cc_start: 0.9143 (pttt) cc_final: 0.8731 (pttp) REVERT: I 1 MET cc_start: 0.7123 (mtp) cc_final: 0.6363 (ttm) REVERT: J 4 TYR cc_start: 0.9584 (t80) cc_final: 0.9367 (t80) REVERT: J 5 LEU cc_start: 0.9503 (mt) cc_final: 0.9046 (mt) REVERT: J 11 SER cc_start: 0.7770 (p) cc_final: 0.7566 (p) REVERT: J 12 TYR cc_start: 0.8594 (t80) cc_final: 0.8262 (t80) REVERT: K 1 MET cc_start: 0.7879 (mmm) cc_final: 0.7244 (mmp) REVERT: L 1 MET cc_start: 0.8311 (pmm) cc_final: 0.8014 (pmm) outliers start: 0 outliers final: 0 residues processed: 1397 average time/residue: 0.1896 time to fit residues: 436.5664 Evaluate side-chains 1202 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1202 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 271 optimal weight: 4.9990 chunk 385 optimal weight: 0.8980 chunk 265 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 264 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 100 optimal weight: 0.0070 chunk 180 optimal weight: 0.7980 chunk 268 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS E 466 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 507 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.128164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091803 restraints weight = 72542.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095792 restraints weight = 40658.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098591 restraints weight = 26640.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100576 restraints weight = 19365.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102069 restraints weight = 15165.158| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32220 Z= 0.153 Angle : 0.909 16.136 43712 Z= 0.446 Chirality : 0.053 0.413 4984 Planarity : 0.005 0.103 5452 Dihedral : 11.553 160.252 4572 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.62 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.12), residues: 3968 helix: -1.66 (0.13), residues: 1238 sheet: -2.24 (0.22), residues: 390 loop : -1.75 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 322 TYR 0.040 0.002 TYR A 110 PHE 0.020 0.001 PHE A 35 HIS 0.005 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (32212) covalent geometry : angle 0.90905 / 0.45 (43712) hydrogen bonds : bond 0.04335 / 2.83 ( 966) hydrogen bonds : angle 6.54562 / 4.47 ( 2655) Misc. bond : bond 0.00360 / 0.18 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8245.81 seconds wall clock time: 142 minutes 58.08 seconds (8578.08 seconds total)