Starting phenix.real_space_refine on Tue Aug 26 01:30:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ua2_20704/08_2025/6ua2_20704.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ua2_20704/08_2025/6ua2_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ua2_20704/08_2025/6ua2_20704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ua2_20704/08_2025/6ua2_20704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ua2_20704/08_2025/6ua2_20704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ua2_20704/08_2025/6ua2_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 8.23, per 1000 atoms: 0.26 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.23 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: 7.13 Time building geometry restraints manager: 3.77 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: 42598 4.49 - 8.97: 909 8.97 - 13.46: 117 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: 18923 34.69 - 69.39: 800 69.39 - 104.08: 79 104.08 - 138.78: 17 138.78 - 173.47: 13 Dihedral angle restraints: 19832 sinusoidal: 8424 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 19829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3845 0.091 - 0.181: 950 0.181 - 0.272: 152 0.272 - 0.362: 29 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: 0.02 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: 2.960 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.590 Find NCS groups from input model: 0.860 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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= 1.021 Angle : 1.745 22.429 43712 Z= 1.032 Chirality : 0.082 0.453 4984 Planarity : 0.008 0.081 5452 Dihedral : 19.048 173.474 12552 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 aren 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 covalent geometry : bond 0.01747 (32212) covalent geometry : angle 1.74453 (43712) hydrogen bonds : bond 0.21040 ( 966) hydrogen bonds : angle 9.28298 ( 2655) Misc. bond : bond 0.00086 ( 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 : 1.232 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: 0.8861 (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: 0.8420 (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: 0.9378 (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: 0.2075 time to fit residues: 491.9316 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 : 1.182 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 A 454 HIS A 466 HIS ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN 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 = 0.3691 r_free = 0.3691 target = 0.124203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088596 restraints weight = 71552.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.092526 restraints weight = 39281.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095184 restraints weight = 25421.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097216 restraints weight = 18469.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098455 restraints weight = 14299.433| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32220 Z= 0.160 Angle : 0.880 11.274 43712 Z= 0.442 Chirality : 0.052 0.331 4984 Planarity : 0.006 0.189 5452 Dihedral : 18.510 178.329 5344 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.79 % Favored : 92.16 % Rotamer: Outliers : 0.58 % Allowed : 7.55 % 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 aren not related in a simple way. whole: -3.85 (0.11), residues: 3968 helix: -2.49 (0.12), residues: 1250 sheet: -3.06 (0.22), residues: 402 loop : -2.56 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D 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 covalent geometry : bond 0.00341 (32212) covalent geometry : angle 0.87958 (43712) hydrogen bonds : bond 0.04926 ( 966) hydrogen bonds : angle 7.09604 ( 2655) Misc. bond : bond 0.00266 ( 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 1546 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 1527 time to evaluate : 1.278 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: A 21 GLN cc_start: 0.9249 (pm20) cc_final: 0.8758 (pm20) REVERT: A 28 ASP cc_start: 0.8875 (t70) cc_final: 0.8488 (t70) REVERT: A 32 TYR cc_start: 0.8961 (m-80) cc_final: 0.8470 (m-80) REVERT: A 36 LEU cc_start: 0.8931 (tp) cc_final: 0.8034 (tp) REVERT: A 38 LEU cc_start: 0.9613 (mm) cc_final: 0.8829 (mm) REVERT: A 69 PRO cc_start: 0.9456 (Cg_endo) cc_final: 0.9048 (Cg_exo) REVERT: A 105 ARG cc_start: 0.9004 (mmm160) cc_final: 0.8549 (tpm170) REVERT: A 108 LYS cc_start: 0.9477 (tptp) cc_final: 0.8992 (mmtt) REVERT: A 158 ILE cc_start: 0.8832 (mm) cc_final: 0.8278 (tp) REVERT: A 179 MET cc_start: 0.7330 (pmm) cc_final: 0.7072 (pmm) REVERT: A 224 ARG cc_start: 0.7577 (mmt180) cc_final: 0.6997 (mmt-90) REVERT: A 269 ASP cc_start: 0.7981 (m-30) cc_final: 0.7758 (m-30) REVERT: A 294 TYR cc_start: 0.9303 (m-80) cc_final: 0.9067 (m-80) REVERT: A 332 ILE cc_start: 0.9278 (pt) cc_final: 0.8714 (pt) REVERT: A 334 GLN cc_start: 0.9505 (mp10) cc_final: 0.8530 (mp10) REVERT: A 335 GLU cc_start: 0.8582 (mp0) cc_final: 0.7664 (mp0) REVERT: A 343 GLN cc_start: 0.8538 (pp30) cc_final: 0.7735 (pp30) REVERT: A 352 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8804 (tm-30) REVERT: A 364 ASP cc_start: 0.8062 (m-30) cc_final: 0.7571 (m-30) REVERT: A 372 HIS cc_start: 0.9298 (m170) cc_final: 0.8140 (m90) REVERT: A 386 MET cc_start: 0.8833 (ppp) cc_final: 0.8402 (ppp) REVERT: A 414 MET cc_start: 0.7993 (ptt) cc_final: 0.7627 (ptt) REVERT: A 420 MET cc_start: 0.8393 (mtm) cc_final: 0.7847 (mtp) REVERT: A 448 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: A 480 ARG cc_start: 0.9014 (mtm110) cc_final: 0.8512 (mtm110) REVERT: B 16 ASP cc_start: 0.7666 (t0) cc_final: 0.6557 (t0) REVERT: B 18 LEU cc_start: 0.9556 (tp) cc_final: 0.9277 (tp) REVERT: B 34 ASP cc_start: 0.8115 (m-30) cc_final: 0.7604 (m-30) REVERT: B 37 ILE cc_start: 0.9014 (mm) cc_final: 0.8623 (mm) REVERT: B 41 TYR cc_start: 0.9216 (t80) cc_final: 0.8950 (t80) REVERT: B 82 MET cc_start: 0.9485 (ttm) cc_final: 0.9271 (ttm) REVERT: B 100 GLN cc_start: 0.8794 (pm20) cc_final: 0.8562 (pt0) REVERT: B 106 LYS cc_start: 0.9344 (mtpt) cc_final: 0.9115 (mtpt) REVERT: B 108 LYS cc_start: 0.9393 (pttm) cc_final: 0.8386 (tppt) REVERT: B 131 PHE cc_start: 0.9174 (m-10) cc_final: 0.8202 (m-80) REVERT: B 132 GLU cc_start: 0.9532 (pt0) cc_final: 0.9107 (pt0) REVERT: B 172 ASP cc_start: 0.8511 (t0) cc_final: 0.8170 (t0) REVERT: B 216 ASP cc_start: 0.9403 (t70) cc_final: 0.9196 (t0) REVERT: B 224 ARG cc_start: 0.8844 (ttt-90) cc_final: 0.8618 (ttt180) REVERT: B 238 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8663 (tppt) REVERT: B 259 ARG cc_start: 0.9087 (mtp85) cc_final: 0.8464 (ttt90) REVERT: B 289 TYR cc_start: 0.9446 (t80) cc_final: 0.9149 (t80) REVERT: B 291 LYS cc_start: 0.9614 (mmmt) cc_final: 0.9051 (tppt) REVERT: B 334 GLN cc_start: 0.9233 (mt0) cc_final: 0.8897 (mm-40) REVERT: B 335 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 348 TYR cc_start: 0.9226 (t80) cc_final: 0.8858 (t80) REVERT: B 355 ARG cc_start: 0.8168 (ppt170) cc_final: 0.7881 (ttp-170) REVERT: B 372 HIS cc_start: 0.8917 (m170) cc_final: 0.8325 (m170) REVERT: B 400 TYR cc_start: 0.7655 (m-80) cc_final: 0.7050 (m-80) REVERT: B 404 ASP cc_start: 0.8467 (t0) cc_final: 0.8178 (t0) REVERT: B 491 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B 492 LYS cc_start: 0.8861 (ptpp) cc_final: 0.8642 (pttm) REVERT: C 16 ASP cc_start: 0.7482 (t0) cc_final: 0.6799 (t0) REVERT: C 32 TYR cc_start: 0.8951 (m-10) cc_final: 0.8626 (m-10) REVERT: C 43 ASP cc_start: 0.8190 (m-30) cc_final: 0.7937 (m-30) REVERT: C 74 THR cc_start: 0.6560 (t) cc_final: 0.6314 (t) REVERT: C 78 MET cc_start: 0.9051 (mmm) cc_final: 0.8825 (mmm) REVERT: C 82 MET cc_start: 0.9588 (tpp) cc_final: 0.9334 (tpp) REVERT: C 90 PHE cc_start: 0.8995 (m-80) cc_final: 0.8661 (m-80) REVERT: C 93 HIS cc_start: 0.8737 (p90) cc_final: 0.8477 (p-80) REVERT: C 102 ASN cc_start: 0.9150 (m-40) cc_final: 0.8887 (m-40) REVERT: C 110 TYR cc_start: 0.9026 (t80) cc_final: 0.8699 (t80) REVERT: C 111 GLU cc_start: 0.9166 (tp30) cc_final: 0.8887 (mp0) REVERT: C 175 LEU cc_start: 0.9155 (mt) cc_final: 0.8940 (mt) REVERT: C 199 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8571 (tp30) REVERT: C 200 ILE cc_start: 0.9233 (mm) cc_final: 0.8454 (mm) REVERT: C 203 ARG cc_start: 0.8598 (mtm-85) cc_final: 0.7605 (ptt90) REVERT: C 229 LYS cc_start: 0.9451 (ptpp) cc_final: 0.9165 (mmmt) REVERT: C 274 ASP cc_start: 0.9228 (t0) cc_final: 0.8797 (t70) REVERT: C 289 TYR cc_start: 0.9359 (t80) cc_final: 0.9010 (t80) REVERT: C 290 ILE cc_start: 0.9495 (pt) cc_final: 0.9144 (pt) REVERT: C 331 CYS cc_start: 0.8877 (t) cc_final: 0.8483 (t) REVERT: C 333 THR cc_start: 0.9739 (p) cc_final: 0.9250 (p) REVERT: C 334 GLN cc_start: 0.9084 (mp10) cc_final: 0.8521 (mp10) REVERT: C 335 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8000 (tm-30) REVERT: C 336 VAL cc_start: 0.9515 (m) cc_final: 0.8660 (m) REVERT: C 482 MET cc_start: 0.9280 (tpp) cc_final: 0.8768 (tpp) REVERT: C 487 GLU cc_start: 0.8726 (pm20) cc_final: 0.8395 (pm20) REVERT: C 492 LYS cc_start: 0.8507 (pptt) cc_final: 0.8176 (pptt) REVERT: C 494 THR cc_start: 0.8847 (p) cc_final: 0.8553 (p) REVERT: C 500 GLU cc_start: 0.9191 (pp20) cc_final: 0.8583 (pp20) REVERT: D 12 TYR cc_start: 0.8170 (t80) cc_final: 0.6637 (m-80) REVERT: D 21 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8469 (tp40) REVERT: D 25 ASN cc_start: 0.8648 (m110) cc_final: 0.7239 (m110) REVERT: D 33 ASN cc_start: 0.9103 (t0) cc_final: 0.8420 (t0) REVERT: D 71 ASP cc_start: 0.9393 (t0) cc_final: 0.8995 (t70) REVERT: D 91 ILE cc_start: 0.9267 (tp) cc_final: 0.9046 (tp) REVERT: D 112 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8743 (tm-30) REVERT: D 179 MET cc_start: 0.6889 (ppp) cc_final: 0.6052 (pmm) REVERT: D 192 ILE cc_start: 0.8211 (tp) cc_final: 0.7481 (tt) REVERT: D 215 ASP cc_start: 0.9516 (m-30) cc_final: 0.9036 (p0) REVERT: D 257 LYS cc_start: 0.9775 (ptpp) cc_final: 0.9479 (mmtm) REVERT: D 258 TYR cc_start: 0.9500 (t80) cc_final: 0.9255 (t80) REVERT: D 286 MET cc_start: 0.9648 (tpt) cc_final: 0.9294 (tpt) REVERT: D 289 TYR cc_start: 0.9427 (t80) cc_final: 0.9042 (t80) REVERT: D 290 ILE cc_start: 0.9726 (pt) cc_final: 0.9354 (pt) REVERT: D 311 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8562 (ttpp) REVERT: D 349 LYS cc_start: 0.9555 (mmtp) cc_final: 0.9312 (mmmm) REVERT: D 352 GLU cc_start: 0.9344 (tm-30) cc_final: 0.9011 (tm-30) REVERT: D 375 LYS cc_start: 0.9590 (pttt) cc_final: 0.9313 (pttt) REVERT: D 385 MET cc_start: 0.8392 (tpt) cc_final: 0.7359 (tpt) REVERT: D 386 MET cc_start: 0.8452 (ptm) cc_final: 0.8022 (ptm) REVERT: D 418 ASP cc_start: 0.9293 (t70) cc_final: 0.9081 (t70) REVERT: D 465 GLN cc_start: 0.8749 (pp30) cc_final: 0.7967 (pp30) REVERT: D 468 CYS cc_start: 0.9253 (t) cc_final: 0.8997 (t) REVERT: D 469 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8761 (mm-40) REVERT: D 482 MET cc_start: 0.8999 (tpt) cc_final: 0.8643 (tpt) REVERT: P 1 MET cc_start: 0.8673 (mpp) cc_final: 0.8219 (pmm) REVERT: E 28 ASP cc_start: 0.8914 (t70) cc_final: 0.8566 (t70) REVERT: E 32 TYR cc_start: 0.9375 (m-80) cc_final: 0.8821 (m-80) REVERT: E 36 LEU cc_start: 0.8944 (tp) cc_final: 0.8133 (tp) REVERT: E 38 LEU cc_start: 0.9605 (mm) cc_final: 0.8844 (mm) REVERT: E 69 PRO cc_start: 0.9579 (Cg_endo) cc_final: 0.9269 (Cg_exo) REVERT: E 82 MET cc_start: 0.9381 (ttp) cc_final: 0.9173 (tmm) REVERT: E 102 ASN cc_start: 0.9311 (t0) cc_final: 0.9060 (t0) REVERT: E 105 ARG cc_start: 0.8967 (mmm160) cc_final: 0.8591 (tpm170) REVERT: E 108 LYS cc_start: 0.9400 (tppt) cc_final: 0.9000 (mmtt) REVERT: E 165 PHE cc_start: 0.8569 (p90) cc_final: 0.8349 (p90) REVERT: E 224 ARG cc_start: 0.7489 (mmt180) cc_final: 0.6840 (mmt180) REVERT: E 273 LEU cc_start: 0.9160 (tt) cc_final: 0.8911 (tt) REVERT: E 281 ILE cc_start: 0.9647 (pt) cc_final: 0.9332 (pt) REVERT: E 284 ILE cc_start: 0.9341 (pt) cc_final: 0.9079 (pt) REVERT: E 285 ASN cc_start: 0.9422 (m-40) cc_final: 0.9175 (m-40) REVERT: E 287 ILE cc_start: 0.9813 (mt) cc_final: 0.9574 (mt) REVERT: E 288 LYS cc_start: 0.9613 (mtmm) cc_final: 0.9302 (ptpt) REVERT: E 294 TYR cc_start: 0.9316 (m-80) cc_final: 0.9054 (m-80) REVERT: E 303 ASN cc_start: 0.7931 (m-40) cc_final: 0.7626 (m110) REVERT: E 332 ILE cc_start: 0.9233 (pt) cc_final: 0.8950 (pt) REVERT: E 334 GLN cc_start: 0.9482 (mp10) cc_final: 0.8549 (mp10) REVERT: E 335 GLU cc_start: 0.8617 (mp0) cc_final: 0.7948 (mp0) REVERT: E 352 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8758 (tm-30) REVERT: E 355 ARG cc_start: 0.8636 (ptm-80) cc_final: 0.8064 (ptm-80) REVERT: E 364 ASP cc_start: 0.8177 (m-30) cc_final: 0.6619 (m-30) REVERT: E 368 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8018 (mm-40) REVERT: E 385 MET cc_start: 0.8423 (ttp) cc_final: 0.8043 (ttp) REVERT: E 386 MET cc_start: 0.8784 (ppp) cc_final: 0.8358 (ppp) REVERT: E 420 MET cc_start: 0.8418 (mtm) cc_final: 0.7836 (mtp) REVERT: E 441 GLN cc_start: 0.6877 (pp30) cc_final: 0.6652 (pp30) REVERT: E 448 GLN cc_start: 0.8698 (mp10) cc_final: 0.8406 (mp10) REVERT: E 469 GLN cc_start: 0.9267 (tp40) cc_final: 0.8668 (tt0) REVERT: E 507 HIS cc_start: 0.8790 (t-90) cc_final: 0.8396 (t70) REVERT: E 509 TYR cc_start: 0.9177 (p90) cc_final: 0.8973 (p90) REVERT: E 513 LEU cc_start: 0.9148 (mp) cc_final: 0.8824 (mt) REVERT: F 18 LEU cc_start: 0.9580 (tp) cc_final: 0.9322 (tp) REVERT: F 32 TYR cc_start: 0.8669 (m-80) cc_final: 0.8234 (m-80) REVERT: F 37 ILE cc_start: 0.9132 (mm) cc_final: 0.8711 (mm) REVERT: F 70 MET cc_start: 0.8054 (tpp) cc_final: 0.6999 (tpt) REVERT: F 103 GLU cc_start: 0.9654 (tp30) cc_final: 0.9289 (tp30) REVERT: F 106 LYS cc_start: 0.9432 (mtpt) cc_final: 0.9019 (mtpt) REVERT: F 108 LYS cc_start: 0.9309 (pttm) cc_final: 0.8204 (tppt) REVERT: F 131 PHE cc_start: 0.9175 (m-10) cc_final: 0.8185 (m-80) REVERT: F 132 GLU cc_start: 0.9462 (pt0) cc_final: 0.9018 (pt0) REVERT: F 136 ARG cc_start: 0.9273 (mmp-170) cc_final: 0.8764 (mmm160) REVERT: F 144 ILE cc_start: 0.9424 (tp) cc_final: 0.9153 (tp) REVERT: F 287 ILE cc_start: 0.9559 (pt) cc_final: 0.9320 (pt) REVERT: F 291 LYS cc_start: 0.9581 (mmmt) cc_final: 0.8974 (tppt) REVERT: F 334 GLN cc_start: 0.9246 (mt0) cc_final: 0.8917 (mm-40) REVERT: F 343 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7803 (tm-30) REVERT: F 355 ARG cc_start: 0.8208 (ppt170) cc_final: 0.7909 (ttp-170) REVERT: F 403 SER cc_start: 0.9150 (t) cc_final: 0.8941 (t) REVERT: F 404 ASP cc_start: 0.8409 (t0) cc_final: 0.8130 (t0) REVERT: F 455 LYS cc_start: 0.9342 (pttp) cc_final: 0.9141 (ptmm) REVERT: F 456 PHE cc_start: 0.9559 (t80) cc_final: 0.9350 (t80) REVERT: F 491 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8155 (tm-30) REVERT: F 493 ARG cc_start: 0.8103 (pmt-80) cc_final: 0.7566 (pmt-80) REVERT: F 507 HIS cc_start: 0.8655 (t-90) cc_final: 0.8413 (t-90) REVERT: G 43 ASP cc_start: 0.8561 (m-30) cc_final: 0.8307 (m-30) REVERT: G 47 ASP cc_start: 0.9581 (m-30) cc_final: 0.8973 (p0) REVERT: G 78 MET cc_start: 0.9506 (tpp) cc_final: 0.9262 (tpp) REVERT: G 106 LYS cc_start: 0.7832 (mttp) cc_final: 0.7589 (mttp) REVERT: G 154 LEU cc_start: 0.9082 (tt) cc_final: 0.8155 (mm) REVERT: G 175 LEU cc_start: 0.9217 (mt) cc_final: 0.8948 (mt) REVERT: G 199 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8653 (tp30) REVERT: G 200 ILE cc_start: 0.9199 (mm) cc_final: 0.8739 (mm) REVERT: G 203 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8134 (mtm110) REVERT: G 216 ASP cc_start: 0.9235 (m-30) cc_final: 0.8918 (t0) REVERT: G 229 LYS cc_start: 0.9424 (ptpp) cc_final: 0.9147 (mmmt) REVERT: G 274 ASP cc_start: 0.9250 (t0) cc_final: 0.8948 (t70) REVERT: G 287 ILE cc_start: 0.9692 (OUTLIER) cc_final: 0.9345 (tt) REVERT: G 289 TYR cc_start: 0.9346 (t80) cc_final: 0.8931 (t80) REVERT: G 290 ILE cc_start: 0.9464 (pt) cc_final: 0.9128 (pt) REVERT: G 291 LYS cc_start: 0.9021 (ptpp) cc_final: 0.8701 (pttt) REVERT: G 331 CYS cc_start: 0.8987 (t) cc_final: 0.8541 (t) REVERT: G 332 ILE cc_start: 0.9551 (pt) cc_final: 0.9296 (pt) REVERT: G 333 THR cc_start: 0.9738 (p) cc_final: 0.9210 (p) REVERT: G 334 GLN cc_start: 0.9088 (mp10) cc_final: 0.8430 (mp10) REVERT: G 335 GLU cc_start: 0.8699 (tm-30) cc_final: 0.7961 (tm-30) REVERT: G 336 VAL cc_start: 0.9540 (m) cc_final: 0.8612 (m) REVERT: G 339 CYS cc_start: 0.9080 (t) cc_final: 0.8850 (t) REVERT: G 418 ASP cc_start: 0.9332 (t70) cc_final: 0.9031 (t0) REVERT: G 482 MET cc_start: 0.9245 (tpp) cc_final: 0.8620 (tpp) REVERT: G 487 GLU cc_start: 0.8751 (pm20) cc_final: 0.8538 (pm20) REVERT: G 492 LYS cc_start: 0.8531 (pptt) cc_final: 0.8179 (pptt) REVERT: G 494 THR cc_start: 0.8843 (p) cc_final: 0.8612 (p) REVERT: G 500 GLU cc_start: 0.9203 (pp20) cc_final: 0.8634 (pp20) REVERT: H 16 ASP cc_start: 0.8183 (m-30) cc_final: 0.7927 (m-30) REVERT: H 21 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8571 (tp40) REVERT: H 25 ASN cc_start: 0.8672 (m110) cc_final: 0.7328 (m110) REVERT: H 33 ASN cc_start: 0.9115 (t0) cc_final: 0.8518 (t0) REVERT: H 63 THR cc_start: 0.8153 (t) cc_final: 0.7942 (t) REVERT: H 91 ILE cc_start: 0.9214 (tp) cc_final: 0.8926 (tp) REVERT: H 93 HIS cc_start: 0.9139 (p-80) cc_final: 0.8902 (p-80) REVERT: H 108 LYS cc_start: 0.8888 (tptm) cc_final: 0.8520 (tptp) REVERT: H 112 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8780 (tm-30) REVERT: H 144 ILE cc_start: 0.8634 (mm) cc_final: 0.8417 (mm) REVERT: H 192 ILE cc_start: 0.8111 (tp) cc_final: 0.7671 (tt) REVERT: H 257 LYS cc_start: 0.9774 (ptpp) cc_final: 0.9497 (mmtm) REVERT: H 258 TYR cc_start: 0.9434 (t80) cc_final: 0.9220 (t80) REVERT: H 286 MET cc_start: 0.9661 (tpt) cc_final: 0.9265 (tpt) REVERT: H 289 TYR cc_start: 0.9410 (t80) cc_final: 0.9051 (t80) REVERT: H 290 ILE cc_start: 0.9740 (pt) cc_final: 0.9361 (pt) REVERT: H 311 LYS cc_start: 0.9179 (tttt) cc_final: 0.8678 (tmmt) REVERT: H 315 ASP cc_start: 0.9408 (m-30) cc_final: 0.9056 (m-30) REVERT: H 343 GLN cc_start: 0.8142 (pm20) cc_final: 0.7790 (pt0) REVERT: H 349 LYS cc_start: 0.9566 (mmtp) cc_final: 0.9178 (mmmm) REVERT: H 352 GLU cc_start: 0.9331 (tm-30) cc_final: 0.8992 (tm-30) REVERT: H 368 GLN cc_start: 0.8576 (mt0) cc_final: 0.8050 (mm-40) REVERT: H 375 LYS cc_start: 0.9570 (pttt) cc_final: 0.9304 (pttt) REVERT: H 385 MET cc_start: 0.8111 (tpt) cc_final: 0.6911 (tpt) REVERT: H 386 MET cc_start: 0.8316 (ptm) cc_final: 0.7856 (ptm) REVERT: H 400 TYR cc_start: 0.7757 (m-80) cc_final: 0.7367 (m-80) REVERT: H 414 MET cc_start: 0.8466 (pmm) cc_final: 0.7915 (pmm) REVERT: H 418 ASP cc_start: 0.9334 (t70) cc_final: 0.9093 (t0) REVERT: H 465 GLN cc_start: 0.8782 (pp30) cc_final: 0.7985 (pp30) REVERT: H 468 CYS cc_start: 0.9251 (t) cc_final: 0.8978 (t) REVERT: H 469 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8732 (mm-40) REVERT: H 478 GLN cc_start: 0.9425 (mt0) cc_final: 0.8838 (mt0) REVERT: H 482 MET cc_start: 0.8947 (tpt) cc_final: 0.8550 (tpt) REVERT: L 1 MET cc_start: 0.8481 (mpp) cc_final: 0.8002 (pmm) outliers start: 19 outliers final: 3 residues processed: 1530 average time/residue: 0.2045 time to fit residues: 502.3106 Evaluate side-chains 1265 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1260 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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: 8.9990 chunk 122 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 361 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 466 HIS ** A 469 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** 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 ** 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 448 GLN E 454 HIS E 466 HIS ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 265 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** 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 = 0.3639 r_free = 0.3639 target = 0.119892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.084707 restraints weight = 73700.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.088313 restraints weight = 40558.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.090887 restraints weight = 26537.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092689 restraints weight = 19237.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093865 restraints weight = 15103.548| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 32220 Z= 0.226 Angle : 0.861 11.325 43712 Z= 0.439 Chirality : 0.052 0.291 4984 Planarity : 0.005 0.066 5452 Dihedral : 17.731 177.557 5344 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 0.18 % Allowed : 7.61 % Favored : 92.21 % 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 aren not related in a simple way. whole: -3.33 (0.12), residues: 3968 helix: -1.97 (0.13), residues: 1254 sheet: -2.85 (0.23), residues: 378 loop : -2.29 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 480 TYR 0.028 0.002 TYR A 353 PHE 0.020 0.002 PHE C 131 HIS 0.009 0.002 HIS G 504 Details of bonding type rmsd covalent geometry : bond 0.00483 (32212) covalent geometry : angle 0.86118 (43712) hydrogen bonds : bond 0.04726 ( 966) hydrogen bonds : angle 6.77419 ( 2655) Misc. bond : bond 0.00317 ( 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 1467 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1461 time to evaluate : 1.222 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: A 21 GLN cc_start: 0.9355 (pm20) cc_final: 0.8922 (pm20) REVERT: A 28 ASP cc_start: 0.8930 (t70) cc_final: 0.8459 (t70) REVERT: A 32 TYR cc_start: 0.9097 (m-80) cc_final: 0.8888 (m-10) REVERT: A 36 LEU cc_start: 0.9084 (tp) cc_final: 0.8312 (tp) REVERT: A 38 LEU cc_start: 0.9641 (mm) cc_final: 0.8893 (mm) REVERT: A 48 GLN cc_start: 0.9248 (mt0) cc_final: 0.8917 (mt0) REVERT: A 105 ARG cc_start: 0.9024 (mmm160) cc_final: 0.8166 (tpm170) REVERT: A 108 LYS cc_start: 0.9497 (tptp) cc_final: 0.8998 (mmtt) REVERT: A 109 LYS cc_start: 0.9577 (ptpp) cc_final: 0.8768 (pttt) REVERT: A 158 ILE cc_start: 0.8905 (mm) cc_final: 0.8362 (tp) REVERT: A 179 MET cc_start: 0.7355 (pmm) cc_final: 0.7001 (pmm) REVERT: A 203 ARG cc_start: 0.9383 (ttp-110) cc_final: 0.9142 (mtm110) REVERT: A 269 ASP cc_start: 0.8016 (m-30) cc_final: 0.7597 (m-30) REVERT: A 332 ILE cc_start: 0.9346 (pt) cc_final: 0.8857 (pt) REVERT: A 334 GLN cc_start: 0.9484 (mp10) cc_final: 0.9266 (mp10) REVERT: A 335 GLU cc_start: 0.8747 (mp0) cc_final: 0.8006 (mp0) REVERT: A 352 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8812 (tm-30) REVERT: A 355 ARG cc_start: 0.8866 (ptm-80) cc_final: 0.8493 (ptt90) REVERT: A 364 ASP cc_start: 0.8201 (m-30) cc_final: 0.7283 (m-30) REVERT: A 375 LYS cc_start: 0.9683 (pttt) cc_final: 0.9433 (pttt) REVERT: A 385 MET cc_start: 0.8801 (ttp) cc_final: 0.8018 (ttp) REVERT: A 386 MET cc_start: 0.8726 (ppp) cc_final: 0.7972 (ppp) REVERT: A 414 MET cc_start: 0.8242 (ptt) cc_final: 0.7937 (ptt) REVERT: A 420 MET cc_start: 0.8372 (mtm) cc_final: 0.7877 (mtp) REVERT: A 456 PHE cc_start: 0.9460 (t80) cc_final: 0.9224 (t80) REVERT: A 460 LEU cc_start: 0.9686 (mp) cc_final: 0.9388 (mp) REVERT: A 480 ARG cc_start: 0.9003 (mtm110) cc_final: 0.8567 (mtm110) REVERT: A 482 MET cc_start: 0.9146 (ttt) cc_final: 0.8928 (ttt) REVERT: A 496 SER cc_start: 0.9323 (t) cc_final: 0.8951 (t) REVERT: B 16 ASP cc_start: 0.7990 (t0) cc_final: 0.6326 (t0) REVERT: B 18 LEU cc_start: 0.9577 (tp) cc_final: 0.9313 (tp) REVERT: B 34 ASP cc_start: 0.8337 (m-30) cc_final: 0.7850 (m-30) REVERT: B 37 ILE cc_start: 0.8999 (mm) cc_final: 0.8622 (mm) REVERT: B 41 TYR cc_start: 0.9297 (t80) cc_final: 0.9095 (t80) REVERT: B 82 MET cc_start: 0.9476 (ttm) cc_final: 0.9224 (ttm) REVERT: B 91 ILE cc_start: 0.9292 (mm) cc_final: 0.9044 (mm) REVERT: B 108 LYS cc_start: 0.9463 (pttm) cc_final: 0.8563 (tppt) REVERT: B 132 GLU cc_start: 0.9568 (pt0) cc_final: 0.9255 (pt0) REVERT: B 144 ILE cc_start: 0.9418 (tp) cc_final: 0.9163 (tp) REVERT: B 166 LEU cc_start: 0.9469 (mm) cc_final: 0.8914 (tp) REVERT: B 172 ASP cc_start: 0.8434 (t0) cc_final: 0.8146 (t0) REVERT: B 185 LEU cc_start: 0.8948 (mt) cc_final: 0.8450 (mt) REVERT: B 216 ASP cc_start: 0.9453 (t70) cc_final: 0.9252 (t0) REVERT: B 238 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8504 (tppt) REVERT: B 250 ILE cc_start: 0.9290 (mp) cc_final: 0.8827 (tp) REVERT: B 289 TYR cc_start: 0.9513 (t80) cc_final: 0.9129 (t80) REVERT: B 291 LYS cc_start: 0.9619 (mmmt) cc_final: 0.9033 (tppt) REVERT: B 311 LYS cc_start: 0.9156 (tmmt) cc_final: 0.8940 (tmmt) REVERT: B 322 ARG cc_start: 0.8824 (ttt90) cc_final: 0.8248 (ttt90) REVERT: B 334 GLN cc_start: 0.9310 (mt0) cc_final: 0.8942 (mm-40) REVERT: B 335 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 343 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 355 ARG cc_start: 0.8275 (ppt170) cc_final: 0.7966 (ttp-170) REVERT: B 364 ASP cc_start: 0.7034 (m-30) cc_final: 0.6699 (m-30) REVERT: B 372 HIS cc_start: 0.9094 (m170) cc_final: 0.8520 (m90) REVERT: B 404 ASP cc_start: 0.8611 (t0) cc_final: 0.8309 (t0) REVERT: B 491 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8132 (tm-30) REVERT: C 32 TYR cc_start: 0.8977 (m-10) cc_final: 0.8621 (m-10) REVERT: C 43 ASP cc_start: 0.8533 (m-30) cc_final: 0.8277 (m-30) REVERT: C 47 ASP cc_start: 0.9593 (m-30) cc_final: 0.8944 (p0) REVERT: C 78 MET cc_start: 0.9146 (mmm) cc_final: 0.8916 (mmm) REVERT: C 82 MET cc_start: 0.9622 (tpp) cc_final: 0.9279 (tpp) REVERT: C 90 PHE cc_start: 0.8930 (m-80) cc_final: 0.8587 (m-80) REVERT: C 175 LEU cc_start: 0.9148 (mt) cc_final: 0.8939 (mt) REVERT: C 199 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8687 (tp30) REVERT: C 200 ILE cc_start: 0.9260 (mm) cc_final: 0.8935 (mm) REVERT: C 203 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.7897 (mtm110) REVERT: C 229 LYS cc_start: 0.9375 (ptpp) cc_final: 0.9061 (mmmt) REVERT: C 274 ASP cc_start: 0.9150 (t0) cc_final: 0.8899 (t70) REVERT: C 289 TYR cc_start: 0.9371 (t80) cc_final: 0.9055 (t80) REVERT: C 290 ILE cc_start: 0.9435 (pt) cc_final: 0.9098 (pt) REVERT: C 291 LYS cc_start: 0.9162 (pttt) cc_final: 0.8892 (pttt) REVERT: C 331 CYS cc_start: 0.8995 (t) cc_final: 0.8639 (t) REVERT: C 333 THR cc_start: 0.9733 (p) cc_final: 0.9241 (p) REVERT: C 334 GLN cc_start: 0.9151 (mp10) cc_final: 0.8525 (mp10) REVERT: C 335 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 336 VAL cc_start: 0.9572 (m) cc_final: 0.8807 (m) REVERT: C 349 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8489 (mtmt) REVERT: C 385 MET cc_start: 0.8010 (tmm) cc_final: 0.6441 (tmm) REVERT: C 390 LEU cc_start: 0.9413 (pt) cc_final: 0.9080 (pt) REVERT: C 482 MET cc_start: 0.9343 (tpp) cc_final: 0.8789 (tpp) REVERT: C 487 GLU cc_start: 0.8674 (pm20) cc_final: 0.8345 (pm20) REVERT: C 492 LYS cc_start: 0.8584 (pptt) cc_final: 0.8285 (pptt) REVERT: C 494 THR cc_start: 0.8956 (p) cc_final: 0.8728 (p) REVERT: C 500 GLU cc_start: 0.9244 (pp20) cc_final: 0.8607 (pp20) REVERT: D 12 TYR cc_start: 0.8299 (t80) cc_final: 0.6972 (m-80) REVERT: D 16 ASP cc_start: 0.8349 (m-30) cc_final: 0.8098 (m-30) REVERT: D 21 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8306 (tm-30) REVERT: D 25 ASN cc_start: 0.8522 (m110) cc_final: 0.8037 (m110) REVERT: D 32 TYR cc_start: 0.9050 (m-80) cc_final: 0.8485 (m-80) REVERT: D 33 ASN cc_start: 0.9148 (t0) cc_final: 0.8808 (t0) REVERT: D 51 LEU cc_start: 0.9463 (pp) cc_final: 0.9245 (pp) REVERT: D 71 ASP cc_start: 0.9353 (t0) cc_final: 0.8327 (t0) REVERT: D 91 ILE cc_start: 0.9152 (tp) cc_final: 0.8945 (tp) REVERT: D 112 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8766 (tm-30) REVERT: D 179 MET cc_start: 0.6621 (ppp) cc_final: 0.5524 (pmm) REVERT: D 192 ILE cc_start: 0.8351 (tp) cc_final: 0.7657 (tt) REVERT: D 215 ASP cc_start: 0.9531 (m-30) cc_final: 0.9010 (p0) REVERT: D 257 LYS cc_start: 0.9785 (ptpp) cc_final: 0.9492 (mmtm) REVERT: D 258 TYR cc_start: 0.9457 (t80) cc_final: 0.9228 (t80) REVERT: D 286 MET cc_start: 0.9640 (tpt) cc_final: 0.9303 (tpt) REVERT: D 289 TYR cc_start: 0.9389 (t80) cc_final: 0.9010 (t80) REVERT: D 290 ILE cc_start: 0.9759 (pt) cc_final: 0.9368 (pt) REVERT: D 311 LYS cc_start: 0.9179 (ttpp) cc_final: 0.8782 (ttpp) REVERT: D 343 GLN cc_start: 0.8560 (pm20) cc_final: 0.8077 (pm20) REVERT: D 352 GLU cc_start: 0.9351 (tm-30) cc_final: 0.9029 (tm-30) REVERT: D 385 MET cc_start: 0.8721 (tpt) cc_final: 0.7877 (tpt) REVERT: D 386 MET cc_start: 0.8660 (ptm) cc_final: 0.8375 (ptm) REVERT: D 410 LYS cc_start: 0.9242 (mptt) cc_final: 0.8738 (mmtm) REVERT: D 418 ASP cc_start: 0.9333 (t70) cc_final: 0.9104 (t0) REVERT: D 465 GLN cc_start: 0.8786 (pp30) cc_final: 0.8106 (pp30) REVERT: D 468 CYS cc_start: 0.9287 (t) cc_final: 0.9022 (t) REVERT: D 469 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8877 (mm-40) REVERT: D 482 MET cc_start: 0.9095 (tpt) cc_final: 0.8809 (tpt) REVERT: D 491 GLU cc_start: 0.8994 (tp30) cc_final: 0.8775 (tp30) REVERT: P 1 MET cc_start: 0.8768 (mpp) cc_final: 0.8304 (pmm) REVERT: E 21 GLN cc_start: 0.9280 (pm20) cc_final: 0.8886 (pm20) REVERT: E 28 ASP cc_start: 0.8893 (t70) cc_final: 0.8550 (t70) REVERT: E 32 TYR cc_start: 0.9424 (m-80) cc_final: 0.8760 (m-80) REVERT: E 36 LEU cc_start: 0.9037 (tp) cc_final: 0.8339 (tp) REVERT: E 38 LEU cc_start: 0.9661 (mm) cc_final: 0.8932 (mm) REVERT: E 42 ILE cc_start: 0.9404 (mt) cc_final: 0.9157 (mm) REVERT: E 48 GLN cc_start: 0.9258 (mt0) cc_final: 0.8909 (mt0) REVERT: E 69 PRO cc_start: 0.9556 (Cg_endo) cc_final: 0.9344 (Cg_exo) REVERT: E 98 GLU cc_start: 0.9138 (mp0) cc_final: 0.8908 (mp0) REVERT: E 105 ARG cc_start: 0.8994 (mmm160) cc_final: 0.8434 (tpp-160) REVERT: E 108 LYS cc_start: 0.9382 (tppt) cc_final: 0.8696 (mmtt) REVERT: E 142 ILE cc_start: 0.8585 (tp) cc_final: 0.8205 (tp) REVERT: E 158 ILE cc_start: 0.8777 (mm) cc_final: 0.8434 (tp) REVERT: E 244 LEU cc_start: 0.9430 (pt) cc_final: 0.9221 (pt) REVERT: E 246 CYS cc_start: 0.9436 (t) cc_final: 0.9144 (t) REVERT: E 250 ILE cc_start: 0.9430 (pt) cc_final: 0.9229 (pt) REVERT: E 256 ASP cc_start: 0.9152 (p0) cc_final: 0.8708 (m-30) REVERT: E 262 LEU cc_start: 0.9616 (pt) cc_final: 0.9385 (pt) REVERT: E 288 LYS cc_start: 0.9580 (mtmm) cc_final: 0.9266 (mttt) REVERT: E 294 TYR cc_start: 0.9369 (m-80) cc_final: 0.9150 (m-80) REVERT: E 303 ASN cc_start: 0.7854 (m-40) cc_final: 0.7634 (m110) REVERT: E 319 ASP cc_start: 0.7594 (t70) cc_final: 0.7013 (t70) REVERT: E 325 MET cc_start: 0.9044 (ptm) cc_final: 0.8191 (ptm) REVERT: E 332 ILE cc_start: 0.9344 (pt) cc_final: 0.8843 (pt) REVERT: E 334 GLN cc_start: 0.9404 (mp10) cc_final: 0.9196 (mp10) REVERT: E 335 GLU cc_start: 0.8665 (mp0) cc_final: 0.7956 (mp0) REVERT: E 352 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8744 (tm-30) REVERT: E 355 ARG cc_start: 0.8717 (ptm-80) cc_final: 0.8410 (ptt90) REVERT: E 364 ASP cc_start: 0.8093 (m-30) cc_final: 0.7173 (m-30) REVERT: E 375 LYS cc_start: 0.9726 (pttt) cc_final: 0.9468 (pttt) REVERT: E 386 MET cc_start: 0.8671 (ppp) cc_final: 0.8103 (ppp) REVERT: E 420 MET cc_start: 0.8425 (mtm) cc_final: 0.7864 (mtp) REVERT: E 448 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8341 (mp10) REVERT: E 456 PHE cc_start: 0.9498 (t80) cc_final: 0.9293 (t80) REVERT: E 460 LEU cc_start: 0.9691 (mp) cc_final: 0.9420 (mp) REVERT: E 482 MET cc_start: 0.9059 (ttt) cc_final: 0.8844 (ttt) REVERT: E 507 HIS cc_start: 0.8862 (t-90) cc_final: 0.8542 (t70) REVERT: E 509 TYR cc_start: 0.9145 (p90) cc_final: 0.8918 (p90) REVERT: E 513 LEU cc_start: 0.9159 (mp) cc_final: 0.8956 (mp) REVERT: F 16 ASP cc_start: 0.7840 (t0) cc_final: 0.6669 (t0) REVERT: F 18 LEU cc_start: 0.9552 (tp) cc_final: 0.9342 (tp) REVERT: F 34 ASP cc_start: 0.8346 (m-30) cc_final: 0.8087 (m-30) REVERT: F 37 ILE cc_start: 0.9026 (mm) cc_final: 0.8653 (mm) REVERT: F 41 TYR cc_start: 0.9325 (t80) cc_final: 0.9090 (t80) REVERT: F 70 MET cc_start: 0.7991 (tpp) cc_final: 0.6709 (tpt) REVERT: F 103 GLU cc_start: 0.9650 (tp30) cc_final: 0.9296 (tp30) REVERT: F 106 LYS cc_start: 0.9427 (mtpt) cc_final: 0.9194 (mtpt) REVERT: F 132 GLU cc_start: 0.9486 (pt0) cc_final: 0.9166 (pt0) REVERT: F 136 ARG cc_start: 0.9293 (mmp-170) cc_final: 0.8786 (mmm160) REVERT: F 144 ILE cc_start: 0.9428 (tp) cc_final: 0.9193 (tp) REVERT: F 166 LEU cc_start: 0.9470 (mm) cc_final: 0.8361 (tp) REVERT: F 185 LEU cc_start: 0.8985 (mt) cc_final: 0.8465 (mt) REVERT: F 238 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8572 (tppt) REVERT: F 250 ILE cc_start: 0.9353 (mp) cc_final: 0.8759 (tp) REVERT: F 289 TYR cc_start: 0.9499 (t80) cc_final: 0.9117 (t80) REVERT: F 294 TYR cc_start: 0.9386 (m-80) cc_final: 0.9149 (m-80) REVERT: F 334 GLN cc_start: 0.9325 (mt0) cc_final: 0.8936 (mm-40) REVERT: F 335 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8290 (tm-30) REVERT: F 343 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7764 (tm-30) REVERT: F 355 ARG cc_start: 0.8331 (ppt170) cc_final: 0.7226 (ptm-80) REVERT: F 372 HIS cc_start: 0.9210 (m170) cc_final: 0.8604 (m90) REVERT: F 400 TYR cc_start: 0.7420 (m-80) cc_final: 0.7015 (m-80) REVERT: F 404 ASP cc_start: 0.8603 (t0) cc_final: 0.8391 (t0) REVERT: F 455 LYS cc_start: 0.9447 (pttp) cc_final: 0.9183 (ptmm) REVERT: F 456 PHE cc_start: 0.9580 (t80) cc_final: 0.9378 (t80) REVERT: F 468 CYS cc_start: 0.9300 (t) cc_final: 0.9066 (t) REVERT: F 491 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8417 (tm-30) REVERT: G 43 ASP cc_start: 0.8355 (m-30) cc_final: 0.8086 (m-30) REVERT: G 78 MET cc_start: 0.9523 (tpp) cc_final: 0.9231 (tpp) REVERT: G 106 LYS cc_start: 0.7858 (mttp) cc_final: 0.7657 (mtmm) REVERT: G 175 LEU cc_start: 0.9210 (mt) cc_final: 0.8983 (mt) REVERT: G 179 MET cc_start: 0.7897 (ppp) cc_final: 0.7577 (ppp) REVERT: G 199 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8541 (tp30) REVERT: G 200 ILE cc_start: 0.9281 (mm) cc_final: 0.8837 (mm) REVERT: G 203 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.8040 (mtm110) REVERT: G 229 LYS cc_start: 0.9386 (ptpp) cc_final: 0.9072 (mmmt) REVERT: G 274 ASP cc_start: 0.9220 (t0) cc_final: 0.8868 (t70) REVERT: G 287 ILE cc_start: 0.9683 (OUTLIER) cc_final: 0.9271 (tt) REVERT: G 289 TYR cc_start: 0.9353 (t80) cc_final: 0.8985 (t80) REVERT: G 290 ILE cc_start: 0.9427 (pt) cc_final: 0.9153 (pt) REVERT: G 291 LYS cc_start: 0.9090 (ptpp) cc_final: 0.8757 (pttm) REVERT: G 331 CYS cc_start: 0.9149 (t) cc_final: 0.8660 (t) REVERT: G 332 ILE cc_start: 0.9617 (pt) cc_final: 0.9368 (pt) REVERT: G 333 THR cc_start: 0.9732 (p) cc_final: 0.9274 (p) REVERT: G 334 GLN cc_start: 0.9121 (mp10) cc_final: 0.8450 (mp10) REVERT: G 335 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8085 (tm-30) REVERT: G 336 VAL cc_start: 0.9589 (m) cc_final: 0.8680 (m) REVERT: G 395 GLU cc_start: 0.8791 (mp0) cc_final: 0.8472 (mp0) REVERT: G 482 MET cc_start: 0.9326 (tpp) cc_final: 0.8637 (tpp) REVERT: G 492 LYS cc_start: 0.8590 (pptt) cc_final: 0.8264 (pptt) REVERT: G 494 THR cc_start: 0.8931 (p) cc_final: 0.8695 (p) REVERT: G 500 GLU cc_start: 0.9264 (pp20) cc_final: 0.8727 (pp20) REVERT: H 16 ASP cc_start: 0.8370 (m-30) cc_final: 0.8156 (m-30) REVERT: H 21 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8606 (tm-30) REVERT: H 33 ASN cc_start: 0.9109 (t0) cc_final: 0.8361 (t0) REVERT: H 91 ILE cc_start: 0.9273 (tp) cc_final: 0.9016 (tp) REVERT: H 93 HIS cc_start: 0.9072 (p-80) cc_final: 0.8635 (p-80) REVERT: H 108 LYS cc_start: 0.9037 (tptm) cc_final: 0.8599 (tptp) REVERT: H 112 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8894 (tm-30) REVERT: H 150 MET cc_start: 0.7059 (tmm) cc_final: 0.6709 (tmm) REVERT: H 179 MET cc_start: 0.7563 (ppp) cc_final: 0.6958 (ppp) REVERT: H 215 ASP cc_start: 0.9519 (m-30) cc_final: 0.9038 (p0) REVERT: H 257 LYS cc_start: 0.9791 (ptpp) cc_final: 0.9544 (mmtm) REVERT: H 286 MET cc_start: 0.9646 (tpt) cc_final: 0.9275 (tpt) REVERT: H 289 TYR cc_start: 0.9398 (t80) cc_final: 0.9052 (t80) REVERT: H 290 ILE cc_start: 0.9764 (pt) cc_final: 0.9356 (pt) REVERT: H 315 ASP cc_start: 0.9405 (m-30) cc_final: 0.8938 (p0) REVERT: H 335 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8597 (tm-30) REVERT: H 343 GLN cc_start: 0.8408 (pm20) cc_final: 0.8079 (pt0) REVERT: H 349 LYS cc_start: 0.9559 (mmtp) cc_final: 0.9234 (mmmm) REVERT: H 352 GLU cc_start: 0.9334 (tm-30) cc_final: 0.9006 (tm-30) REVERT: H 368 GLN cc_start: 0.8625 (mt0) cc_final: 0.8135 (mm110) REVERT: H 385 MET cc_start: 0.8678 (tpt) cc_final: 0.8004 (tpt) REVERT: H 410 LYS cc_start: 0.9322 (mptt) cc_final: 0.9014 (mmtm) REVERT: H 418 ASP cc_start: 0.9391 (t70) cc_final: 0.9132 (t0) REVERT: H 465 GLN cc_start: 0.8811 (pp30) cc_final: 0.8228 (pp30) REVERT: H 468 CYS cc_start: 0.9249 (t) cc_final: 0.8982 (t) REVERT: H 469 GLN cc_start: 0.9043 (mm110) cc_final: 0.8790 (mm110) REVERT: H 482 MET cc_start: 0.9029 (tpt) cc_final: 0.8730 (tpt) REVERT: H 491 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7609 (tm-30) REVERT: H 493 ARG cc_start: 0.9090 (mtm110) cc_final: 0.8806 (mtm110) REVERT: K 1 MET cc_start: 0.8148 (mmt) cc_final: 0.7935 (mmp) REVERT: L 1 MET cc_start: 0.8508 (mpp) cc_final: 0.8086 (pmm) outliers start: 6 outliers final: 0 residues processed: 1461 average time/residue: 0.2033 time to fit residues: 480.2275 Evaluate side-chains 1214 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1212 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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: 10.0000 chunk 132 optimal weight: 0.5980 chunk 221 optimal weight: 1.9990 chunk 330 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 299 optimal weight: 0.7980 chunk 373 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS A 507 HIS B 21 GLN B 100 GLN B 171 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN E 22 GLN E 93 HIS ** 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 202 GLN ** F 243 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 303 ASN ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.124121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.087797 restraints weight = 72475.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.091638 restraints weight = 39873.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094203 restraints weight = 26073.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096276 restraints weight = 19174.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097680 restraints weight = 14879.544| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32220 Z= 0.146 Angle : 0.833 10.112 43712 Z= 0.416 Chirality : 0.052 0.286 4984 Planarity : 0.005 0.070 5452 Dihedral : 17.028 175.720 5344 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.34 % Favored : 91.63 % Rotamer: Outliers : 0.28 % Allowed : 5.72 % Favored : 94.01 % 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 aren not related in a simple way. whole: -3.06 (0.12), residues: 3968 helix: -1.80 (0.13), residues: 1250 sheet: -2.45 (0.24), residues: 360 loop : -2.15 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 480 TYR 0.021 0.002 TYR F 233 PHE 0.036 0.002 PHE F 131 HIS 0.008 0.001 HIS C 504 Details of bonding type rmsd covalent geometry : bond 0.00319 (32212) covalent geometry : angle 0.83342 (43712) hydrogen bonds : bond 0.04252 ( 966) hydrogen bonds : angle 6.49565 ( 2655) Misc. bond : bond 0.00149 ( 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 1492 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1483 time to evaluate : 1.201 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: 0.9264 (pm20) cc_final: 0.8962 (pm20) REVERT: A 28 ASP cc_start: 0.8993 (t70) cc_final: 0.8539 (t70) REVERT: A 32 TYR cc_start: 0.8895 (m-10) cc_final: 0.8523 (m-10) REVERT: A 36 LEU cc_start: 0.9164 (tp) cc_final: 0.8476 (tp) REVERT: A 38 LEU cc_start: 0.9579 (mm) cc_final: 0.8727 (mm) REVERT: A 48 GLN cc_start: 0.9266 (mt0) cc_final: 0.8914 (mt0) REVERT: A 105 ARG cc_start: 0.8985 (mmm160) cc_final: 0.8424 (tpm170) REVERT: A 108 LYS cc_start: 0.9489 (tptp) cc_final: 0.9029 (tppt) REVERT: A 158 ILE cc_start: 0.8887 (mm) cc_final: 0.8340 (tp) REVERT: A 179 MET cc_start: 0.7295 (pmm) cc_final: 0.6875 (pmm) REVERT: A 203 ARG cc_start: 0.9379 (ttp-110) cc_final: 0.9171 (mtm110) REVERT: A 231 ARG cc_start: 0.9252 (ptm-80) cc_final: 0.9040 (ptm-80) REVERT: A 246 CYS cc_start: 0.9419 (t) cc_final: 0.8646 (p) REVERT: A 262 LEU cc_start: 0.9551 (pt) cc_final: 0.8865 (mt) REVERT: A 273 LEU cc_start: 0.9393 (tt) cc_final: 0.8230 (tt) REVERT: A 319 ASP cc_start: 0.7529 (t70) cc_final: 0.7160 (t70) REVERT: A 334 GLN cc_start: 0.9446 (mp10) cc_final: 0.8487 (mp10) REVERT: A 335 GLU cc_start: 0.8655 (mp0) cc_final: 0.8049 (mp0) REVERT: A 352 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 369 ASN cc_start: 0.9099 (p0) cc_final: 0.7498 (p0) REVERT: A 372 HIS cc_start: 0.9359 (m170) cc_final: 0.8357 (m90) REVERT: A 386 MET cc_start: 0.8624 (ppp) cc_final: 0.8184 (tmm) REVERT: A 402 PHE cc_start: 0.9304 (m-80) cc_final: 0.9099 (m-80) REVERT: A 414 MET cc_start: 0.8082 (ptt) cc_final: 0.7858 (ptt) REVERT: A 420 MET cc_start: 0.8332 (mtm) cc_final: 0.7826 (mtp) REVERT: A 444 SER cc_start: 0.8409 (p) cc_final: 0.8129 (p) REVERT: A 454 HIS cc_start: 0.8847 (m90) cc_final: 0.8526 (m90) REVERT: A 480 ARG cc_start: 0.8839 (mpp80) cc_final: 0.8548 (mtm110) REVERT: A 496 SER cc_start: 0.9237 (t) cc_final: 0.8754 (t) REVERT: A 510 GLU cc_start: 0.8469 (pp20) cc_final: 0.8247 (pp20) REVERT: B 18 LEU cc_start: 0.9474 (tp) cc_final: 0.9224 (tp) REVERT: B 34 ASP cc_start: 0.8312 (m-30) cc_final: 0.7753 (m-30) REVERT: B 36 LEU cc_start: 0.9421 (tp) cc_final: 0.9191 (tp) REVERT: B 37 ILE cc_start: 0.9001 (mm) cc_final: 0.8679 (mm) REVERT: B 41 TYR cc_start: 0.9273 (t80) cc_final: 0.8993 (t80) REVERT: B 70 MET cc_start: 0.8332 (tpt) cc_final: 0.7622 (tpp) REVERT: B 82 MET cc_start: 0.9490 (ttm) cc_final: 0.9273 (ttm) REVERT: B 108 LYS cc_start: 0.9359 (pttm) cc_final: 0.8545 (tppt) REVERT: B 132 GLU cc_start: 0.9554 (pt0) cc_final: 0.9264 (pt0) REVERT: B 166 LEU cc_start: 0.9415 (mm) cc_final: 0.9083 (tp) REVERT: B 185 LEU cc_start: 0.8939 (mt) cc_final: 0.8417 (mt) REVERT: B 238 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8450 (tppt) REVERT: B 250 ILE cc_start: 0.9355 (mp) cc_final: 0.8886 (tp) REVERT: B 287 ILE cc_start: 0.9530 (pt) cc_final: 0.9291 (pt) REVERT: B 289 TYR cc_start: 0.9468 (t80) cc_final: 0.9090 (t80) REVERT: B 291 LYS cc_start: 0.9623 (mmmt) cc_final: 0.9060 (tppt) REVERT: B 334 GLN cc_start: 0.9286 (mt0) cc_final: 0.8727 (mm-40) REVERT: B 335 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 355 ARG cc_start: 0.8281 (ppt170) cc_final: 0.7945 (ttp-170) REVERT: B 372 HIS cc_start: 0.8972 (m170) cc_final: 0.8430 (m170) REVERT: B 400 TYR cc_start: 0.7421 (m-80) cc_final: 0.6777 (m-80) REVERT: B 404 ASP cc_start: 0.8551 (t0) cc_final: 0.8226 (t0) REVERT: B 491 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 493 ARG cc_start: 0.8713 (ptt-90) cc_final: 0.8395 (ptt-90) REVERT: B 506 LEU cc_start: 0.8797 (pp) cc_final: 0.8552 (pt) REVERT: C 32 TYR cc_start: 0.8874 (m-10) cc_final: 0.8431 (m-10) REVERT: C 33 ASN cc_start: 0.8865 (m110) cc_final: 0.8545 (m110) REVERT: C 47 ASP cc_start: 0.9582 (m-30) cc_final: 0.8932 (p0) REVERT: C 58 LYS cc_start: 0.8861 (mppt) cc_final: 0.8556 (mppt) REVERT: C 78 MET cc_start: 0.9192 (mmm) cc_final: 0.8932 (mmm) REVERT: C 82 MET cc_start: 0.9637 (tpp) cc_final: 0.9346 (tpp) REVERT: C 90 PHE cc_start: 0.9029 (m-80) cc_final: 0.8568 (m-80) REVERT: C 99 PHE cc_start: 0.9552 (t80) cc_final: 0.9256 (t80) REVERT: C 150 MET cc_start: 0.8458 (tpp) cc_final: 0.8136 (tpp) REVERT: C 175 LEU cc_start: 0.9143 (mt) cc_final: 0.8778 (mt) REVERT: C 199 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8651 (tp30) REVERT: C 200 ILE cc_start: 0.9271 (mm) cc_final: 0.8908 (mm) REVERT: C 203 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8136 (mtm110) REVERT: C 229 LYS cc_start: 0.9366 (ptpp) cc_final: 0.9088 (mmmt) REVERT: C 274 ASP cc_start: 0.9055 (t0) cc_final: 0.8811 (t70) REVERT: C 287 ILE cc_start: 0.9705 (OUTLIER) cc_final: 0.9041 (tt) REVERT: C 289 TYR cc_start: 0.9390 (t80) cc_final: 0.9130 (t80) REVERT: C 290 ILE cc_start: 0.9464 (pt) cc_final: 0.9134 (pt) REVERT: C 291 LYS cc_start: 0.9143 (pttt) cc_final: 0.8690 (pttt) REVERT: C 331 CYS cc_start: 0.9031 (t) cc_final: 0.8640 (t) REVERT: C 333 THR cc_start: 0.9757 (p) cc_final: 0.9208 (p) REVERT: C 334 GLN cc_start: 0.9150 (mp10) cc_final: 0.8468 (mp10) REVERT: C 336 VAL cc_start: 0.9534 (m) cc_final: 0.9333 (m) REVERT: C 362 ILE cc_start: 0.9453 (pt) cc_final: 0.9179 (mm) REVERT: C 441 GLN cc_start: 0.8537 (mp-120) cc_final: 0.8201 (mp-120) REVERT: C 482 MET cc_start: 0.9427 (tpp) cc_final: 0.8709 (tpp) REVERT: C 493 ARG cc_start: 0.8712 (mtm180) cc_final: 0.8449 (ptp90) REVERT: C 494 THR cc_start: 0.8843 (p) cc_final: 0.8545 (p) REVERT: C 500 GLU cc_start: 0.9197 (pp20) cc_final: 0.8545 (pp20) REVERT: D 12 TYR cc_start: 0.8254 (t80) cc_final: 0.6975 (m-80) REVERT: D 21 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8509 (tp40) REVERT: D 25 ASN cc_start: 0.8605 (m110) cc_final: 0.7533 (m110) REVERT: D 32 TYR cc_start: 0.9075 (m-80) cc_final: 0.8494 (m-10) REVERT: D 33 ASN cc_start: 0.9063 (t0) cc_final: 0.8525 (t0) REVERT: D 51 LEU cc_start: 0.9498 (pp) cc_final: 0.9268 (pp) REVERT: D 71 ASP cc_start: 0.8968 (t0) cc_final: 0.8391 (t0) REVERT: D 91 ILE cc_start: 0.9120 (tp) cc_final: 0.8900 (tp) REVERT: D 100 GLN cc_start: 0.9395 (mp10) cc_final: 0.8312 (pp30) REVERT: D 112 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8797 (tm-30) REVERT: D 144 ILE cc_start: 0.9091 (mm) cc_final: 0.8771 (mp) REVERT: D 179 MET cc_start: 0.6822 (ppp) cc_final: 0.5887 (pmm) REVERT: D 215 ASP cc_start: 0.9539 (m-30) cc_final: 0.8713 (t70) REVERT: D 257 LYS cc_start: 0.9805 (ptpp) cc_final: 0.9484 (mmtm) REVERT: D 286 MET cc_start: 0.9656 (tpt) cc_final: 0.9313 (tpt) REVERT: D 289 TYR cc_start: 0.9409 (t80) cc_final: 0.9001 (t80) REVERT: D 290 ILE cc_start: 0.9734 (pt) cc_final: 0.9357 (pt) REVERT: D 352 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9002 (tm-30) REVERT: D 385 MET cc_start: 0.8585 (tpt) cc_final: 0.7397 (tpt) REVERT: D 386 MET cc_start: 0.8349 (ptm) cc_final: 0.7975 (ptm) REVERT: D 400 TYR cc_start: 0.7586 (m-80) cc_final: 0.7299 (m-80) REVERT: D 465 GLN cc_start: 0.8765 (pp30) cc_final: 0.8194 (pp30) REVERT: D 468 CYS cc_start: 0.9283 (t) cc_final: 0.8984 (t) REVERT: D 482 MET cc_start: 0.9221 (tpp) cc_final: 0.8802 (tpp) REVERT: D 489 LYS cc_start: 0.8930 (ptpt) cc_final: 0.8442 (ptpt) REVERT: P 1 MET cc_start: 0.8642 (mpp) cc_final: 0.8247 (pmm) REVERT: E 21 GLN cc_start: 0.9252 (pm20) cc_final: 0.8859 (pm20) REVERT: E 32 TYR cc_start: 0.9380 (m-80) cc_final: 0.8695 (m-80) REVERT: E 36 LEU cc_start: 0.9070 (tp) cc_final: 0.8434 (tp) REVERT: E 38 LEU cc_start: 0.9580 (mm) cc_final: 0.8811 (mm) REVERT: E 48 GLN cc_start: 0.9322 (mt0) cc_final: 0.8927 (mt0) REVERT: E 100 GLN cc_start: 0.9463 (mp-120) cc_final: 0.9174 (mp10) REVERT: E 105 ARG cc_start: 0.8960 (mmm160) cc_final: 0.8030 (tpm170) REVERT: E 108 LYS cc_start: 0.9410 (tppt) cc_final: 0.8862 (tppt) REVERT: E 165 PHE cc_start: 0.8440 (p90) cc_final: 0.8178 (p90) REVERT: E 227 LEU cc_start: 0.9106 (tt) cc_final: 0.8890 (tt) REVERT: E 246 CYS cc_start: 0.9442 (t) cc_final: 0.8736 (p) REVERT: E 273 LEU cc_start: 0.9197 (tt) cc_final: 0.8985 (tt) REVERT: E 288 LYS cc_start: 0.9601 (mtmm) cc_final: 0.9294 (mttt) REVERT: E 325 MET cc_start: 0.8560 (ptm) cc_final: 0.7960 (ptm) REVERT: E 332 ILE cc_start: 0.9349 (pt) cc_final: 0.9109 (pt) REVERT: E 334 GLN cc_start: 0.9324 (mp10) cc_final: 0.8405 (mp10) REVERT: E 335 GLU cc_start: 0.8589 (mp0) cc_final: 0.7981 (mp0) REVERT: E 352 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8752 (tm-30) REVERT: E 353 TYR cc_start: 0.8846 (t80) cc_final: 0.8528 (t80) REVERT: E 355 ARG cc_start: 0.8652 (ptm-80) cc_final: 0.8449 (ptm-80) REVERT: E 357 PHE cc_start: 0.9296 (m-80) cc_final: 0.8941 (m-10) REVERT: E 364 ASP cc_start: 0.8336 (m-30) cc_final: 0.6888 (m-30) REVERT: E 375 LYS cc_start: 0.9664 (pttt) cc_final: 0.9442 (pttt) REVERT: E 385 MET cc_start: 0.8740 (ttp) cc_final: 0.8025 (ttp) REVERT: E 386 MET cc_start: 0.8722 (ppp) cc_final: 0.8365 (ppp) REVERT: E 420 MET cc_start: 0.8388 (mtm) cc_final: 0.7803 (mtp) REVERT: E 482 MET cc_start: 0.8968 (ttt) cc_final: 0.8761 (ttt) REVERT: E 507 HIS cc_start: 0.8684 (t-90) cc_final: 0.8418 (t70) REVERT: E 513 LEU cc_start: 0.9048 (mp) cc_final: 0.8838 (mp) REVERT: F 18 LEU cc_start: 0.9523 (tp) cc_final: 0.9299 (tp) REVERT: F 37 ILE cc_start: 0.8963 (mm) cc_final: 0.8577 (mm) REVERT: F 68 SER cc_start: 0.9334 (t) cc_final: 0.9124 (t) REVERT: F 70 MET cc_start: 0.8036 (tpp) cc_final: 0.6625 (tpt) REVERT: F 92 HIS cc_start: 0.9005 (p90) cc_final: 0.8724 (p-80) REVERT: F 103 GLU cc_start: 0.9620 (tp30) cc_final: 0.9213 (tp30) REVERT: F 106 LYS cc_start: 0.9400 (mtpt) cc_final: 0.9110 (mtpt) REVERT: F 108 LYS cc_start: 0.9216 (pttm) cc_final: 0.8012 (tppt) REVERT: F 131 PHE cc_start: 0.9119 (m-80) cc_final: 0.8838 (m-80) REVERT: F 132 GLU cc_start: 0.9494 (pt0) cc_final: 0.9162 (pt0) REVERT: F 157 ILE cc_start: 0.9280 (tt) cc_final: 0.9066 (tt) REVERT: F 185 LEU cc_start: 0.9001 (mt) cc_final: 0.8363 (mt) REVERT: F 229 LYS cc_start: 0.9485 (ptpt) cc_final: 0.9204 (ptpt) REVERT: F 238 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8361 (tppt) REVERT: F 250 ILE cc_start: 0.9333 (mp) cc_final: 0.8797 (tp) REVERT: F 334 GLN cc_start: 0.9301 (mt0) cc_final: 0.8725 (mm-40) REVERT: F 343 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7799 (tm-30) REVERT: F 351 SER cc_start: 0.9347 (p) cc_final: 0.9142 (p) REVERT: F 355 ARG cc_start: 0.8396 (ppt170) cc_final: 0.7985 (ttp-170) REVERT: F 372 HIS cc_start: 0.9063 (m170) cc_final: 0.8529 (m170) REVERT: F 386 MET cc_start: 0.6897 (ptm) cc_final: 0.6434 (ppp) REVERT: F 399 GLU cc_start: 0.7625 (mp0) cc_final: 0.7403 (mp0) REVERT: F 403 SER cc_start: 0.9248 (t) cc_final: 0.9037 (t) REVERT: F 404 ASP cc_start: 0.8496 (t0) cc_final: 0.8214 (t0) REVERT: F 455 LYS cc_start: 0.9462 (pttp) cc_final: 0.9198 (ptmm) REVERT: F 482 MET cc_start: 0.8941 (ptp) cc_final: 0.8713 (ptp) REVERT: F 491 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8209 (tm-30) REVERT: F 493 ARG cc_start: 0.8644 (ptt-90) cc_final: 0.8404 (ptt-90) REVERT: G 16 ASP cc_start: 0.7669 (t0) cc_final: 0.7332 (t0) REVERT: G 43 ASP cc_start: 0.8349 (m-30) cc_final: 0.8128 (m-30) REVERT: G 47 ASP cc_start: 0.9591 (m-30) cc_final: 0.8944 (p0) REVERT: G 78 MET cc_start: 0.9558 (tpp) cc_final: 0.9248 (tpp) REVERT: G 199 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8554 (tp30) REVERT: G 200 ILE cc_start: 0.9288 (mm) cc_final: 0.8787 (mm) REVERT: G 203 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8165 (mtm110) REVERT: G 209 LEU cc_start: 0.7677 (mt) cc_final: 0.7445 (mp) REVERT: G 229 LYS cc_start: 0.9356 (ptpp) cc_final: 0.9065 (mmmt) REVERT: G 243 GLN cc_start: 0.9250 (tp-100) cc_final: 0.8755 (tp-100) REVERT: G 274 ASP cc_start: 0.9156 (t0) cc_final: 0.8734 (t70) REVERT: G 287 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9228 (tt) REVERT: G 289 TYR cc_start: 0.9387 (t80) cc_final: 0.9067 (t80) REVERT: G 290 ILE cc_start: 0.9447 (pt) cc_final: 0.9182 (pt) REVERT: G 291 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8620 (pttm) REVERT: G 331 CYS cc_start: 0.9119 (t) cc_final: 0.8852 (t) REVERT: G 333 THR cc_start: 0.9729 (p) cc_final: 0.9147 (p) REVERT: G 334 GLN cc_start: 0.9124 (mp10) cc_final: 0.8505 (mp10) REVERT: G 335 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8074 (tm-30) REVERT: G 336 VAL cc_start: 0.9535 (m) cc_final: 0.8681 (m) REVERT: G 349 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8724 (mtpt) REVERT: G 386 MET cc_start: 0.9001 (tmm) cc_final: 0.8630 (tmm) REVERT: G 395 GLU cc_start: 0.8770 (mp0) cc_final: 0.8512 (mp0) REVERT: G 410 LYS cc_start: 0.8686 (tppt) cc_final: 0.8485 (tppt) REVERT: G 414 MET cc_start: 0.9225 (pmm) cc_final: 0.8686 (ptt) REVERT: G 441 GLN cc_start: 0.8490 (mp-120) cc_final: 0.8098 (mp-120) REVERT: G 444 SER cc_start: 0.8538 (t) cc_final: 0.8133 (t) REVERT: G 482 MET cc_start: 0.9390 (tpp) cc_final: 0.8842 (tpp) REVERT: G 493 ARG cc_start: 0.8786 (mtm180) cc_final: 0.8131 (mtm-85) REVERT: G 500 GLU cc_start: 0.9245 (pp20) cc_final: 0.8681 (pp20) REVERT: H 21 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8405 (tp40) REVERT: H 25 ASN cc_start: 0.8533 (m110) cc_final: 0.7167 (m110) REVERT: H 63 THR cc_start: 0.8149 (t) cc_final: 0.7940 (t) REVERT: H 91 ILE cc_start: 0.9247 (tp) cc_final: 0.8965 (tp) REVERT: H 93 HIS cc_start: 0.9038 (p-80) cc_final: 0.8582 (p-80) REVERT: H 108 LYS cc_start: 0.8973 (tptm) cc_final: 0.8501 (tptp) REVERT: H 112 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8919 (tm-30) REVERT: H 179 MET cc_start: 0.7529 (ppp) cc_final: 0.7000 (ppp) REVERT: H 286 MET cc_start: 0.9663 (tpt) cc_final: 0.9201 (tpt) REVERT: H 290 ILE cc_start: 0.9757 (pt) cc_final: 0.9377 (pt) REVERT: H 315 ASP cc_start: 0.9319 (m-30) cc_final: 0.8878 (p0) REVERT: H 349 LYS cc_start: 0.9543 (mmtp) cc_final: 0.9287 (mmmm) REVERT: H 352 GLU cc_start: 0.9370 (tm-30) cc_final: 0.9026 (tm-30) REVERT: H 368 GLN cc_start: 0.8626 (mt0) cc_final: 0.8124 (mm-40) REVERT: H 385 MET cc_start: 0.7740 (tpt) cc_final: 0.6772 (tpt) REVERT: H 386 MET cc_start: 0.7482 (ptm) cc_final: 0.7204 (ptm) REVERT: H 399 GLU cc_start: 0.7602 (pp20) cc_final: 0.7303 (pp20) REVERT: H 410 LYS cc_start: 0.9071 (mptt) cc_final: 0.8823 (mmtm) REVERT: H 414 MET cc_start: 0.8641 (pmm) cc_final: 0.7916 (pmm) REVERT: H 465 GLN cc_start: 0.8796 (pp30) cc_final: 0.8540 (tt0) REVERT: H 468 CYS cc_start: 0.9234 (t) cc_final: 0.8936 (t) REVERT: H 478 GLN cc_start: 0.9406 (mt0) cc_final: 0.8794 (mt0) REVERT: H 491 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7502 (tm-30) REVERT: H 492 LYS cc_start: 0.9009 (pttt) cc_final: 0.8761 (pttp) REVERT: K 1 MET cc_start: 0.8030 (mmt) cc_final: 0.7806 (mmp) REVERT: L 1 MET cc_start: 0.8570 (mpp) cc_final: 0.8185 (pmm) outliers start: 9 outliers final: 1 residues processed: 1487 average time/residue: 0.2003 time to fit residues: 483.5705 Evaluate side-chains 1235 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1232 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 304 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 240 optimal weight: 0.3980 chunk 301 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 94 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN A 309 GLN A 466 HIS A 504 HIS A 507 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN ** 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 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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 368 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN H 283 GLN ** H 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.121268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.085071 restraints weight = 74489.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088789 restraints weight = 41399.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091418 restraints weight = 27239.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.093305 restraints weight = 19845.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094612 restraints weight = 15599.140| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32220 Z= 0.193 Angle : 0.839 10.126 43712 Z= 0.423 Chirality : 0.052 0.327 4984 Planarity : 0.006 0.301 5452 Dihedral : 16.820 174.711 5344 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.30 % Favored : 90.68 % Rotamer: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % 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 aren not related in a simple way. whole: -2.96 (0.12), residues: 3968 helix: -1.71 (0.13), residues: 1244 sheet: -2.53 (0.23), residues: 396 loop : -2.03 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 480 TYR 0.027 0.002 TYR B 233 PHE 0.024 0.002 PHE H 131 HIS 0.010 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00425 (32212) covalent geometry : angle 0.83950 (43712) hydrogen bonds : bond 0.04301 ( 966) hydrogen bonds : angle 6.50205 ( 2655) Misc. bond : bond 0.00242 ( 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 1432 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1429 time to evaluate : 1.234 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: A 21 GLN cc_start: 0.9284 (pm20) cc_final: 0.9053 (pm20) REVERT: A 28 ASP cc_start: 0.8978 (t70) cc_final: 0.8468 (t70) REVERT: A 36 LEU cc_start: 0.9191 (tp) cc_final: 0.8488 (tp) REVERT: A 38 LEU cc_start: 0.9599 (mm) cc_final: 0.8784 (mm) REVERT: A 48 GLN cc_start: 0.9292 (mt0) cc_final: 0.8912 (mt0) REVERT: A 78 MET cc_start: 0.9242 (tpp) cc_final: 0.8856 (tpp) REVERT: A 105 ARG cc_start: 0.9005 (mmm160) cc_final: 0.8440 (tpm170) REVERT: A 108 LYS cc_start: 0.9541 (tptp) cc_final: 0.8853 (mmtt) REVERT: A 109 LYS cc_start: 0.9521 (ptpp) cc_final: 0.9243 (ptpt) REVERT: A 129 ASP cc_start: 0.8978 (m-30) cc_final: 0.8748 (m-30) REVERT: A 158 ILE cc_start: 0.8923 (mm) cc_final: 0.8390 (tp) REVERT: A 179 MET cc_start: 0.7399 (pmm) cc_final: 0.6851 (pmm) REVERT: A 246 CYS cc_start: 0.9385 (t) cc_final: 0.9116 (t) REVERT: A 262 LEU cc_start: 0.9569 (pt) cc_final: 0.9310 (pp) REVERT: A 269 ASP cc_start: 0.7956 (m-30) cc_final: 0.7677 (m-30) REVERT: A 319 ASP cc_start: 0.7524 (t70) cc_final: 0.7156 (t70) REVERT: A 334 GLN cc_start: 0.9407 (mp10) cc_final: 0.8497 (mp10) REVERT: A 335 GLU cc_start: 0.8647 (mp0) cc_final: 0.8208 (mp0) REVERT: A 352 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8750 (tm-30) REVERT: A 369 ASN cc_start: 0.9155 (p0) cc_final: 0.8838 (p0) REVERT: A 386 MET cc_start: 0.8650 (ppp) cc_final: 0.8249 (ppp) REVERT: A 420 MET cc_start: 0.8320 (mtm) cc_final: 0.7833 (mtp) REVERT: A 454 HIS cc_start: 0.8913 (m90) cc_final: 0.8597 (m90) REVERT: A 460 LEU cc_start: 0.9683 (mp) cc_final: 0.9401 (mp) REVERT: A 480 ARG cc_start: 0.8870 (mpp80) cc_final: 0.8459 (mtm110) REVERT: A 496 SER cc_start: 0.9351 (t) cc_final: 0.8921 (t) REVERT: A 507 HIS cc_start: 0.8678 (t-90) cc_final: 0.8300 (t70) REVERT: A 509 TYR cc_start: 0.9024 (p90) cc_final: 0.8816 (p90) REVERT: B 18 LEU cc_start: 0.9600 (tp) cc_final: 0.9377 (tp) REVERT: B 34 ASP cc_start: 0.8368 (m-30) cc_final: 0.7758 (m-30) REVERT: B 36 LEU cc_start: 0.9453 (tp) cc_final: 0.9177 (tp) REVERT: B 37 ILE cc_start: 0.9195 (mm) cc_final: 0.8821 (mm) REVERT: B 41 TYR cc_start: 0.9253 (t80) cc_final: 0.8964 (t80) REVERT: B 68 SER cc_start: 0.9412 (t) cc_final: 0.9199 (t) REVERT: B 82 MET cc_start: 0.9484 (ttm) cc_final: 0.9206 (ttm) REVERT: B 106 LYS cc_start: 0.9415 (mtpt) cc_final: 0.9200 (mtpt) REVERT: B 108 LYS cc_start: 0.9380 (pttm) cc_final: 0.8598 (tppt) REVERT: B 117 ASP cc_start: 0.9388 (p0) cc_final: 0.9169 (p0) REVERT: B 131 PHE cc_start: 0.9477 (m-80) cc_final: 0.8825 (m-80) REVERT: B 132 GLU cc_start: 0.9570 (pt0) cc_final: 0.9248 (pt0) REVERT: B 166 LEU cc_start: 0.9391 (mm) cc_final: 0.9053 (tp) REVERT: B 185 LEU cc_start: 0.8897 (mt) cc_final: 0.8358 (mt) REVERT: B 287 ILE cc_start: 0.9550 (pt) cc_final: 0.9292 (pt) REVERT: B 291 LYS cc_start: 0.9614 (mmmt) cc_final: 0.9090 (tppt) REVERT: B 334 GLN cc_start: 0.9288 (mt0) cc_final: 0.8726 (mm-40) REVERT: B 351 SER cc_start: 0.9348 (p) cc_final: 0.8996 (p) REVERT: B 372 HIS cc_start: 0.9095 (m170) cc_final: 0.8569 (m90) REVERT: B 399 GLU cc_start: 0.8348 (mp0) cc_final: 0.8065 (pm20) REVERT: B 403 SER cc_start: 0.9340 (t) cc_final: 0.9137 (t) REVERT: B 404 ASP cc_start: 0.8671 (t0) cc_final: 0.8368 (t0) REVERT: B 491 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8149 (tm-30) REVERT: C 47 ASP cc_start: 0.9581 (m-30) cc_final: 0.8926 (p0) REVERT: C 78 MET cc_start: 0.9231 (mmm) cc_final: 0.8886 (mmm) REVERT: C 82 MET cc_start: 0.9645 (tpp) cc_final: 0.9346 (tpp) REVERT: C 90 PHE cc_start: 0.9030 (m-80) cc_final: 0.8661 (m-80) REVERT: C 99 PHE cc_start: 0.9539 (t80) cc_final: 0.9207 (t80) REVERT: C 175 LEU cc_start: 0.9177 (mt) cc_final: 0.8931 (mt) REVERT: C 199 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8675 (tp30) REVERT: C 200 ILE cc_start: 0.9300 (mm) cc_final: 0.8922 (mm) REVERT: C 203 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.8202 (mtm110) REVERT: C 229 LYS cc_start: 0.9377 (ptpp) cc_final: 0.9073 (mmmt) REVERT: C 274 ASP cc_start: 0.9140 (t0) cc_final: 0.8744 (t70) REVERT: C 287 ILE cc_start: 0.9711 (mp) cc_final: 0.9008 (tt) REVERT: C 289 TYR cc_start: 0.9389 (t80) cc_final: 0.9154 (t80) REVERT: C 290 ILE cc_start: 0.9443 (pt) cc_final: 0.9118 (pt) REVERT: C 291 LYS cc_start: 0.9217 (pttt) cc_final: 0.8804 (pttt) REVERT: C 331 CYS cc_start: 0.9038 (t) cc_final: 0.8686 (t) REVERT: C 333 THR cc_start: 0.9721 (p) cc_final: 0.9121 (p) REVERT: C 334 GLN cc_start: 0.9143 (mp10) cc_final: 0.8393 (mp10) REVERT: C 362 ILE cc_start: 0.9448 (pt) cc_final: 0.9192 (mm) REVERT: C 385 MET cc_start: 0.7814 (tmm) cc_final: 0.6567 (tmm) REVERT: C 408 LEU cc_start: 0.8877 (pt) cc_final: 0.8562 (pp) REVERT: C 441 GLN cc_start: 0.8500 (mp-120) cc_final: 0.8158 (mp-120) REVERT: C 482 MET cc_start: 0.9376 (tpp) cc_final: 0.8749 (mmm) REVERT: C 500 GLU cc_start: 0.9168 (pp20) cc_final: 0.8628 (pp20) REVERT: D 12 TYR cc_start: 0.8357 (t80) cc_final: 0.7070 (m-80) REVERT: D 21 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 25 ASN cc_start: 0.8600 (m110) cc_final: 0.8086 (m110) REVERT: D 32 TYR cc_start: 0.9115 (m-80) cc_final: 0.8587 (m-10) REVERT: D 33 ASN cc_start: 0.9092 (t0) cc_final: 0.8545 (t0) REVERT: D 63 THR cc_start: 0.8107 (t) cc_final: 0.7895 (t) REVERT: D 91 ILE cc_start: 0.9161 (tp) cc_final: 0.8917 (tp) REVERT: D 94 ASN cc_start: 0.8940 (m110) cc_final: 0.8714 (t0) REVERT: D 144 ILE cc_start: 0.9072 (mm) cc_final: 0.8746 (mp) REVERT: D 179 MET cc_start: 0.6068 (ppp) cc_final: 0.4812 (pmm) REVERT: D 215 ASP cc_start: 0.9525 (m-30) cc_final: 0.9027 (p0) REVERT: D 229 LYS cc_start: 0.8933 (tmtt) cc_final: 0.8473 (mmtt) REVERT: D 242 LYS cc_start: 0.9299 (mmpt) cc_final: 0.9063 (mmmt) REVERT: D 257 LYS cc_start: 0.9806 (ptpp) cc_final: 0.9514 (mmtm) REVERT: D 281 ILE cc_start: 0.9727 (mm) cc_final: 0.9489 (mm) REVERT: D 285 ASN cc_start: 0.9762 (m-40) cc_final: 0.9318 (p0) REVERT: D 286 MET cc_start: 0.9638 (tpt) cc_final: 0.9405 (tpt) REVERT: D 289 TYR cc_start: 0.9382 (t80) cc_final: 0.9025 (t80) REVERT: D 290 ILE cc_start: 0.9754 (pt) cc_final: 0.9375 (pt) REVERT: D 349 LYS cc_start: 0.9656 (mmtp) cc_final: 0.9326 (mmmm) REVERT: D 352 GLU cc_start: 0.9363 (tm-30) cc_final: 0.8994 (tm-30) REVERT: D 385 MET cc_start: 0.8751 (tpt) cc_final: 0.7664 (tpt) REVERT: D 386 MET cc_start: 0.8532 (ptm) cc_final: 0.8153 (ptm) REVERT: D 465 GLN cc_start: 0.8603 (pp30) cc_final: 0.8278 (tt0) REVERT: D 468 CYS cc_start: 0.9254 (t) cc_final: 0.8894 (t) REVERT: D 478 GLN cc_start: 0.9409 (mt0) cc_final: 0.9007 (mt0) REVERT: D 482 MET cc_start: 0.9230 (tpp) cc_final: 0.8711 (tpt) REVERT: D 487 GLU cc_start: 0.8861 (pm20) cc_final: 0.8524 (pm20) REVERT: P 1 MET cc_start: 0.8566 (mpp) cc_final: 0.8196 (pmm) REVERT: E 21 GLN cc_start: 0.9274 (pm20) cc_final: 0.8933 (pm20) REVERT: E 32 TYR cc_start: 0.9385 (m-80) cc_final: 0.8667 (m-80) REVERT: E 36 LEU cc_start: 0.9180 (tp) cc_final: 0.8623 (tp) REVERT: E 38 LEU cc_start: 0.9594 (mm) cc_final: 0.8867 (mm) REVERT: E 48 GLN cc_start: 0.9314 (mt0) cc_final: 0.8890 (mt0) REVERT: E 82 MET cc_start: 0.9387 (ttp) cc_final: 0.9154 (tmm) REVERT: E 100 GLN cc_start: 0.9447 (mp-120) cc_final: 0.9198 (mp10) REVERT: E 105 ARG cc_start: 0.9005 (mmm160) cc_final: 0.8303 (tpp-160) REVERT: E 108 LYS cc_start: 0.9450 (tppt) cc_final: 0.9049 (tppt) REVERT: E 109 LYS cc_start: 0.9397 (ptpp) cc_final: 0.9084 (mtmt) REVERT: E 165 PHE cc_start: 0.8498 (p90) cc_final: 0.8260 (p90) REVERT: E 179 MET cc_start: 0.7349 (pmm) cc_final: 0.6948 (pmm) REVERT: E 228 LYS cc_start: 0.9526 (ptpp) cc_final: 0.9301 (ptpp) REVERT: E 246 CYS cc_start: 0.9459 (t) cc_final: 0.8649 (p) REVERT: E 262 LEU cc_start: 0.9631 (pt) cc_final: 0.9419 (pt) REVERT: E 325 MET cc_start: 0.8868 (ptm) cc_final: 0.8411 (ptm) REVERT: E 334 GLN cc_start: 0.9290 (mp10) cc_final: 0.8403 (mp10) REVERT: E 335 GLU cc_start: 0.8662 (mp0) cc_final: 0.8068 (mp0) REVERT: E 352 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8735 (tm-30) REVERT: E 355 ARG cc_start: 0.8733 (ptm-80) cc_final: 0.8357 (ptm-80) REVERT: E 364 ASP cc_start: 0.8442 (m-30) cc_final: 0.6981 (m-30) REVERT: E 385 MET cc_start: 0.8353 (ttp) cc_final: 0.7857 (ttp) REVERT: E 420 MET cc_start: 0.8391 (mtm) cc_final: 0.7820 (mtp) REVERT: E 454 HIS cc_start: 0.8914 (m90) cc_final: 0.8662 (m90) REVERT: E 460 LEU cc_start: 0.9687 (mp) cc_final: 0.9413 (mp) REVERT: E 507 HIS cc_start: 0.8641 (t-90) cc_final: 0.8382 (t70) REVERT: F 18 LEU cc_start: 0.9536 (tp) cc_final: 0.9290 (tp) REVERT: F 37 ILE cc_start: 0.9206 (mm) cc_final: 0.8788 (mm) REVERT: F 41 TYR cc_start: 0.9302 (t80) cc_final: 0.9020 (t80) REVERT: F 70 MET cc_start: 0.8113 (tpp) cc_final: 0.7364 (mmm) REVERT: F 82 MET cc_start: 0.9402 (ttt) cc_final: 0.8650 (tmm) REVERT: F 108 LYS cc_start: 0.9247 (pttm) cc_final: 0.7982 (tppt) REVERT: F 132 GLU cc_start: 0.9485 (pt0) cc_final: 0.9226 (pt0) REVERT: F 185 LEU cc_start: 0.8848 (mt) cc_final: 0.8284 (mt) REVERT: F 229 LYS cc_start: 0.9479 (ptpt) cc_final: 0.9165 (ptpt) REVERT: F 238 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8554 (tppt) REVERT: F 250 ILE cc_start: 0.9385 (mp) cc_final: 0.8833 (tp) REVERT: F 287 ILE cc_start: 0.9533 (pt) cc_final: 0.9305 (pt) REVERT: F 291 LYS cc_start: 0.9526 (mmtt) cc_final: 0.9272 (tppt) REVERT: F 294 TYR cc_start: 0.9431 (m-80) cc_final: 0.9201 (m-80) REVERT: F 334 GLN cc_start: 0.9321 (mt0) cc_final: 0.8907 (mm-40) REVERT: F 337 LEU cc_start: 0.9363 (mm) cc_final: 0.9154 (mm) REVERT: F 343 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7990 (tm-30) REVERT: F 355 ARG cc_start: 0.8505 (ppt170) cc_final: 0.7934 (ttp-170) REVERT: F 372 HIS cc_start: 0.9139 (m170) cc_final: 0.8744 (m-70) REVERT: F 386 MET cc_start: 0.6797 (ptm) cc_final: 0.6527 (ppp) REVERT: F 400 TYR cc_start: 0.7350 (m-80) cc_final: 0.6518 (m-80) REVERT: F 404 ASP cc_start: 0.8564 (t0) cc_final: 0.8341 (t0) REVERT: F 449 ASP cc_start: 0.8538 (t0) cc_final: 0.8217 (t0) REVERT: F 455 LYS cc_start: 0.9453 (pttp) cc_final: 0.9200 (ptmm) REVERT: F 482 MET cc_start: 0.8891 (ptp) cc_final: 0.8573 (ptp) REVERT: F 491 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8511 (tm-30) REVERT: G 43 ASP cc_start: 0.8379 (m-30) cc_final: 0.8172 (m-30) REVERT: G 47 ASP cc_start: 0.9612 (m-30) cc_final: 0.8993 (p0) REVERT: G 78 MET cc_start: 0.9580 (tpp) cc_final: 0.9179 (tpp) REVERT: G 199 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8793 (tp30) REVERT: G 229 LYS cc_start: 0.9364 (ptpp) cc_final: 0.9063 (mmmt) REVERT: G 274 ASP cc_start: 0.9078 (t0) cc_final: 0.8660 (t70) REVERT: G 277 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8141 (tm-30) REVERT: G 287 ILE cc_start: 0.9694 (mp) cc_final: 0.9261 (tt) REVERT: G 289 TYR cc_start: 0.9373 (t80) cc_final: 0.9074 (t80) REVERT: G 290 ILE cc_start: 0.9448 (pt) cc_final: 0.9171 (pt) REVERT: G 291 LYS cc_start: 0.9066 (ptpp) cc_final: 0.8690 (pttm) REVERT: G 331 CYS cc_start: 0.9119 (t) cc_final: 0.8660 (t) REVERT: G 332 ILE cc_start: 0.9607 (pt) cc_final: 0.9390 (pt) REVERT: G 333 THR cc_start: 0.9723 (p) cc_final: 0.9135 (p) REVERT: G 334 GLN cc_start: 0.9142 (mp10) cc_final: 0.8394 (mp10) REVERT: G 335 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8129 (tm-30) REVERT: G 336 VAL cc_start: 0.9530 (m) cc_final: 0.8682 (m) REVERT: G 349 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8747 (mtpt) REVERT: G 362 ILE cc_start: 0.9459 (pt) cc_final: 0.9182 (mm) REVERT: G 386 MET cc_start: 0.9008 (tmm) cc_final: 0.8642 (tmm) REVERT: G 390 LEU cc_start: 0.9256 (pt) cc_final: 0.8862 (pt) REVERT: G 395 GLU cc_start: 0.8816 (mp0) cc_final: 0.8422 (mp0) REVERT: G 410 LYS cc_start: 0.8687 (tppt) cc_final: 0.8469 (tppt) REVERT: G 441 GLN cc_start: 0.8543 (mp-120) cc_final: 0.8136 (mp-120) REVERT: G 444 SER cc_start: 0.8637 (t) cc_final: 0.8316 (t) REVERT: G 482 MET cc_start: 0.9394 (tpp) cc_final: 0.8968 (tmm) REVERT: G 493 ARG cc_start: 0.8953 (mtm180) cc_final: 0.8146 (mtm-85) REVERT: G 500 GLU cc_start: 0.9228 (pp20) cc_final: 0.8628 (pp20) REVERT: H 21 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8609 (tm-30) REVERT: H 32 TYR cc_start: 0.9117 (m-80) cc_final: 0.8569 (m-10) REVERT: H 33 ASN cc_start: 0.9160 (t0) cc_final: 0.8650 (t0) REVERT: H 36 LEU cc_start: 0.9103 (pt) cc_final: 0.8873 (pt) REVERT: H 63 THR cc_start: 0.8210 (t) cc_final: 0.7983 (t) REVERT: H 91 ILE cc_start: 0.9235 (tp) cc_final: 0.8960 (tp) REVERT: H 93 HIS cc_start: 0.9068 (p-80) cc_final: 0.8627 (p-80) REVERT: H 108 LYS cc_start: 0.9055 (tptm) cc_final: 0.8581 (tptp) REVERT: H 112 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8927 (tm-30) REVERT: H 179 MET cc_start: 0.7340 (ppp) cc_final: 0.6772 (ppp) REVERT: H 215 ASP cc_start: 0.9550 (m-30) cc_final: 0.9086 (p0) REVERT: H 229 LYS cc_start: 0.8879 (pttt) cc_final: 0.8633 (mmtt) REVERT: H 286 MET cc_start: 0.9655 (tpt) cc_final: 0.9186 (tpt) REVERT: H 290 ILE cc_start: 0.9757 (pt) cc_final: 0.9353 (pt) REVERT: H 311 LYS cc_start: 0.9156 (tttt) cc_final: 0.8948 (tttt) REVERT: H 315 ASP cc_start: 0.9307 (m-30) cc_final: 0.8887 (p0) REVERT: H 343 GLN cc_start: 0.8728 (pm20) cc_final: 0.8457 (pm20) REVERT: H 349 LYS cc_start: 0.9626 (mmtp) cc_final: 0.9257 (mmmm) REVERT: H 352 GLU cc_start: 0.9356 (tm-30) cc_final: 0.9012 (tm-30) REVERT: H 368 GLN cc_start: 0.8680 (mt0) cc_final: 0.8210 (mm-40) REVERT: H 385 MET cc_start: 0.8473 (tpt) cc_final: 0.7744 (tpt) REVERT: H 410 LYS cc_start: 0.9092 (mptt) cc_final: 0.8859 (mmtm) REVERT: H 465 GLN cc_start: 0.8657 (pp30) cc_final: 0.8260 (tt0) REVERT: H 468 CYS cc_start: 0.9210 (t) cc_final: 0.8927 (t) REVERT: H 478 GLN cc_start: 0.9381 (mt0) cc_final: 0.8984 (mt0) REVERT: H 491 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7563 (tm-30) REVERT: H 492 LYS cc_start: 0.9086 (pttt) cc_final: 0.8798 (pttp) REVERT: J 4 TYR cc_start: 0.9580 (t80) cc_final: 0.9380 (t80) REVERT: K 1 MET cc_start: 0.7999 (mmt) cc_final: 0.7797 (mmp) REVERT: L 1 MET cc_start: 0.8563 (mpp) cc_final: 0.8250 (pmm) outliers start: 3 outliers final: 2 residues processed: 1432 average time/residue: 0.2027 time to fit residues: 472.8975 Evaluate side-chains 1218 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1216 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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: 0.5980 chunk 391 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 308 optimal weight: 0.0060 chunk 111 optimal weight: 10.0000 chunk 334 optimal weight: 0.0970 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 466 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** 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** E 22 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 466 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.125637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089141 restraints weight = 73448.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092990 restraints weight = 41123.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095697 restraints weight = 27080.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097642 restraints weight = 19732.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099069 restraints weight = 15535.775| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32220 Z= 0.148 Angle : 0.847 10.662 43712 Z= 0.420 Chirality : 0.052 0.433 4984 Planarity : 0.005 0.085 5452 Dihedral : 16.232 172.925 5344 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.92 % Favored : 91.05 % Rotamer: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.87 % 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 aren not related in a simple way. whole: -2.82 (0.12), residues: 3968 helix: -1.68 (0.13), residues: 1236 sheet: -2.56 (0.22), residues: 414 loop : -1.86 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 322 TYR 0.039 0.002 TYR F 233 PHE 0.025 0.002 PHE G 131 HIS 0.008 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00329 (32212) covalent geometry : angle 0.84696 (43712) hydrogen bonds : bond 0.04114 ( 966) hydrogen bonds : angle 6.45208 ( 2655) Misc. bond : bond 0.00124 ( 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 1452 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1449 time to evaluate : 1.512 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: A 21 GLN cc_start: 0.9210 (pm20) cc_final: 0.8956 (pm20) REVERT: A 28 ASP cc_start: 0.8879 (t70) cc_final: 0.8452 (t70) REVERT: A 32 TYR cc_start: 0.8865 (m-10) cc_final: 0.8527 (m-10) REVERT: A 36 LEU cc_start: 0.9058 (tp) cc_final: 0.8253 (tp) REVERT: A 38 LEU cc_start: 0.9570 (mm) cc_final: 0.8775 (mm) REVERT: A 48 GLN cc_start: 0.9293 (mt0) cc_final: 0.8880 (mt0) REVERT: A 78 MET cc_start: 0.9130 (tpp) cc_final: 0.8858 (tpp) REVERT: A 105 ARG cc_start: 0.8978 (mmm160) cc_final: 0.8242 (tpm170) REVERT: A 108 LYS cc_start: 0.9506 (tptp) cc_final: 0.8849 (mmtt) REVERT: A 109 LYS cc_start: 0.9449 (ptpp) cc_final: 0.9127 (ptpt) REVERT: A 150 MET cc_start: 0.7653 (tpt) cc_final: 0.7101 (tpt) REVERT: A 158 ILE cc_start: 0.8909 (mm) cc_final: 0.8430 (tp) REVERT: A 179 MET cc_start: 0.7431 (pmm) cc_final: 0.6917 (pmm) REVERT: A 246 CYS cc_start: 0.9363 (t) cc_final: 0.9117 (t) REVERT: A 254 GLU cc_start: 0.9200 (tp30) cc_final: 0.8908 (pm20) REVERT: A 262 LEU cc_start: 0.9554 (pt) cc_final: 0.9310 (pp) REVERT: A 269 ASP cc_start: 0.8042 (m-30) cc_final: 0.7802 (m-30) REVERT: A 273 LEU cc_start: 0.9602 (tp) cc_final: 0.9178 (tp) REVERT: A 319 ASP cc_start: 0.7729 (t70) cc_final: 0.7436 (t70) REVERT: A 322 ARG cc_start: 0.8191 (tmm-80) cc_final: 0.7121 (tmm-80) REVERT: A 325 MET cc_start: 0.8533 (ptm) cc_final: 0.7974 (ptm) REVERT: A 332 ILE cc_start: 0.9379 (pt) cc_final: 0.9011 (pt) REVERT: A 334 GLN cc_start: 0.9428 (mp10) cc_final: 0.8517 (mp10) REVERT: A 335 GLU cc_start: 0.8679 (mp0) cc_final: 0.7821 (mp0) REVERT: A 343 GLN cc_start: 0.8048 (pp30) cc_final: 0.7476 (pp30) REVERT: A 352 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8731 (tm-30) REVERT: A 355 ARG cc_start: 0.8516 (ptt90) cc_final: 0.8108 (ptt90) REVERT: A 368 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8208 (mm-40) REVERT: A 375 LYS cc_start: 0.9605 (pttt) cc_final: 0.9286 (pttt) REVERT: A 385 MET cc_start: 0.8533 (ttp) cc_final: 0.8112 (ttp) REVERT: A 386 MET cc_start: 0.8546 (ppp) cc_final: 0.8335 (ppp) REVERT: A 420 MET cc_start: 0.8327 (mtm) cc_final: 0.7798 (mtp) REVERT: A 454 HIS cc_start: 0.8899 (m90) cc_final: 0.8633 (m90) REVERT: A 480 ARG cc_start: 0.8788 (mpp80) cc_final: 0.8098 (mpp80) REVERT: A 496 SER cc_start: 0.9242 (t) cc_final: 0.8733 (t) REVERT: A 507 HIS cc_start: 0.8533 (t-90) cc_final: 0.8175 (t70) REVERT: B 18 LEU cc_start: 0.9483 (tp) cc_final: 0.9278 (tp) REVERT: B 31 THR cc_start: 0.8031 (m) cc_final: 0.7127 (m) REVERT: B 34 ASP cc_start: 0.8229 (m-30) cc_final: 0.7594 (m-30) REVERT: B 36 LEU cc_start: 0.9460 (tp) cc_final: 0.9098 (tp) REVERT: B 37 ILE cc_start: 0.9209 (mm) cc_final: 0.8856 (mm) REVERT: B 41 TYR cc_start: 0.9199 (t80) cc_final: 0.8843 (t80) REVERT: B 82 MET cc_start: 0.9467 (ttm) cc_final: 0.9219 (ttm) REVERT: B 106 LYS cc_start: 0.9391 (mtpt) cc_final: 0.9147 (mtpt) REVERT: B 131 PHE cc_start: 0.9490 (m-80) cc_final: 0.8390 (m-80) REVERT: B 132 GLU cc_start: 0.9558 (pt0) cc_final: 0.9240 (pt0) REVERT: B 134 LYS cc_start: 0.9465 (pttp) cc_final: 0.9130 (tttt) REVERT: B 166 LEU cc_start: 0.9331 (mm) cc_final: 0.9069 (tp) REVERT: B 179 MET cc_start: 0.6930 (ppp) cc_final: 0.6704 (ppp) REVERT: B 185 LEU cc_start: 0.8852 (mt) cc_final: 0.8309 (mt) REVERT: B 200 ILE cc_start: 0.9755 (mt) cc_final: 0.9361 (mm) REVERT: B 250 ILE cc_start: 0.9290 (mp) cc_final: 0.8911 (tp) REVERT: B 287 ILE cc_start: 0.9538 (pt) cc_final: 0.9338 (pt) REVERT: B 289 TYR cc_start: 0.9464 (t80) cc_final: 0.9191 (t80) REVERT: B 291 LYS cc_start: 0.9592 (mmmt) cc_final: 0.9029 (tppt) REVERT: B 334 GLN cc_start: 0.9282 (mt0) cc_final: 0.8733 (mm-40) REVERT: B 343 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: B 352 GLU cc_start: 0.8792 (pm20) cc_final: 0.8544 (pm20) REVERT: B 372 HIS cc_start: 0.8997 (m170) cc_final: 0.8423 (m170) REVERT: B 399 GLU cc_start: 0.8295 (mp0) cc_final: 0.8035 (pm20) REVERT: B 400 TYR cc_start: 0.7440 (m-80) cc_final: 0.7222 (m-80) REVERT: B 403 SER cc_start: 0.9328 (t) cc_final: 0.9115 (t) REVERT: B 404 ASP cc_start: 0.8521 (t0) cc_final: 0.8208 (t0) REVERT: B 414 MET cc_start: 0.8873 (mpp) cc_final: 0.8574 (mpp) REVERT: B 455 LYS cc_start: 0.9321 (ptmm) cc_final: 0.9060 (ptmm) REVERT: B 491 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 493 ARG cc_start: 0.8580 (ptt-90) cc_final: 0.8261 (ptt-90) REVERT: C 47 ASP cc_start: 0.9576 (m-30) cc_final: 0.8938 (p0) REVERT: C 78 MET cc_start: 0.9219 (mmm) cc_final: 0.8857 (mmm) REVERT: C 82 MET cc_start: 0.9625 (tpp) cc_final: 0.9325 (tpp) REVERT: C 90 PHE cc_start: 0.9123 (m-80) cc_final: 0.8692 (m-80) REVERT: C 199 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8651 (tp30) REVERT: C 200 ILE cc_start: 0.9315 (mm) cc_final: 0.8874 (mm) REVERT: C 203 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8179 (mtm110) REVERT: C 229 LYS cc_start: 0.9389 (ptpp) cc_final: 0.9120 (mmmt) REVERT: C 274 ASP cc_start: 0.9181 (t0) cc_final: 0.8755 (t70) REVERT: C 289 TYR cc_start: 0.9364 (t80) cc_final: 0.9159 (t80) REVERT: C 290 ILE cc_start: 0.9466 (pt) cc_final: 0.9162 (pt) REVERT: C 291 LYS cc_start: 0.9200 (pttt) cc_final: 0.8970 (pttt) REVERT: C 311 LYS cc_start: 0.8892 (tttt) cc_final: 0.8685 (ttmt) REVERT: C 331 CYS cc_start: 0.9004 (t) cc_final: 0.8682 (t) REVERT: C 333 THR cc_start: 0.9725 (p) cc_final: 0.9128 (p) REVERT: C 334 GLN cc_start: 0.9129 (mp10) cc_final: 0.8375 (mp10) REVERT: C 349 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8117 (mtmt) REVERT: C 362 ILE cc_start: 0.9393 (pt) cc_final: 0.9133 (mm) REVERT: C 386 MET cc_start: 0.8934 (tmm) cc_final: 0.8706 (tmm) REVERT: C 390 LEU cc_start: 0.9329 (pt) cc_final: 0.9046 (pt) REVERT: C 441 GLN cc_start: 0.8596 (mp-120) cc_final: 0.8161 (mp-120) REVERT: C 482 MET cc_start: 0.9353 (tpp) cc_final: 0.8689 (mmm) REVERT: C 493 ARG cc_start: 0.8831 (mtm180) cc_final: 0.8081 (mtm-85) REVERT: C 500 GLU cc_start: 0.9200 (pp20) cc_final: 0.8672 (pp20) REVERT: D 12 TYR cc_start: 0.8147 (t80) cc_final: 0.7017 (m-80) REVERT: D 21 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8463 (tp40) REVERT: D 25 ASN cc_start: 0.8635 (m110) cc_final: 0.7476 (m110) REVERT: D 91 ILE cc_start: 0.9152 (tp) cc_final: 0.8876 (tp) REVERT: D 93 HIS cc_start: 0.9431 (p-80) cc_final: 0.9012 (p-80) REVERT: D 144 ILE cc_start: 0.9140 (mm) cc_final: 0.8834 (mp) REVERT: D 150 MET cc_start: 0.7322 (tmm) cc_final: 0.6934 (tmm) REVERT: D 179 MET cc_start: 0.6081 (ppp) cc_final: 0.4812 (pmm) REVERT: D 215 ASP cc_start: 0.9551 (m-30) cc_final: 0.9038 (p0) REVERT: D 229 LYS cc_start: 0.8929 (tmtt) cc_final: 0.8438 (mmtt) REVERT: D 242 LYS cc_start: 0.9309 (mmpt) cc_final: 0.9065 (mmmt) REVERT: D 257 LYS cc_start: 0.9806 (ptpp) cc_final: 0.9483 (mmtm) REVERT: D 281 ILE cc_start: 0.9730 (mm) cc_final: 0.9475 (mm) REVERT: D 285 ASN cc_start: 0.9734 (m-40) cc_final: 0.9304 (p0) REVERT: D 286 MET cc_start: 0.9639 (tpt) cc_final: 0.9389 (tpt) REVERT: D 289 TYR cc_start: 0.9387 (t80) cc_final: 0.8988 (t80) REVERT: D 290 ILE cc_start: 0.9721 (pt) cc_final: 0.9384 (pt) REVERT: D 349 LYS cc_start: 0.9652 (mmtp) cc_final: 0.9414 (mmtp) REVERT: D 352 GLU cc_start: 0.9389 (tm-30) cc_final: 0.9035 (tm-30) REVERT: D 379 LEU cc_start: 0.9518 (mm) cc_final: 0.9277 (mm) REVERT: D 385 MET cc_start: 0.8655 (tpt) cc_final: 0.7247 (tpt) REVERT: D 386 MET cc_start: 0.8275 (ptm) cc_final: 0.7814 (ptm) REVERT: D 400 TYR cc_start: 0.7324 (m-80) cc_final: 0.7009 (m-80) REVERT: D 465 GLN cc_start: 0.8615 (pp30) cc_final: 0.8266 (tt0) REVERT: D 468 CYS cc_start: 0.9230 (t) cc_final: 0.8898 (t) REVERT: D 478 GLN cc_start: 0.9417 (mt0) cc_final: 0.8995 (mt0) REVERT: D 482 MET cc_start: 0.9159 (tpp) cc_final: 0.8775 (tpt) REVERT: N 5 LEU cc_start: 0.9460 (mt) cc_final: 0.9108 (mt) REVERT: N 11 SER cc_start: 0.8208 (p) cc_final: 0.7877 (p) REVERT: N 12 TYR cc_start: 0.8900 (t80) cc_final: 0.8017 (t80) REVERT: P 1 MET cc_start: 0.8477 (mpp) cc_final: 0.8246 (pmm) REVERT: E 21 GLN cc_start: 0.9133 (pm20) cc_final: 0.8821 (pm20) REVERT: E 28 ASP cc_start: 0.9016 (t70) cc_final: 0.8528 (t70) REVERT: E 32 TYR cc_start: 0.9284 (m-80) cc_final: 0.8711 (m-80) REVERT: E 36 LEU cc_start: 0.9028 (tp) cc_final: 0.8336 (tp) REVERT: E 38 LEU cc_start: 0.9580 (mm) cc_final: 0.8865 (mm) REVERT: E 48 GLN cc_start: 0.9339 (mt0) cc_final: 0.8889 (mt0) REVERT: E 100 GLN cc_start: 0.9437 (mp-120) cc_final: 0.9173 (mp10) REVERT: E 105 ARG cc_start: 0.8976 (mmm160) cc_final: 0.8324 (tpp-160) REVERT: E 108 LYS cc_start: 0.9393 (tppt) cc_final: 0.8570 (mmtt) REVERT: E 109 LYS cc_start: 0.9319 (ptpp) cc_final: 0.9028 (mtmt) REVERT: E 150 MET cc_start: 0.7871 (tpt) cc_final: 0.7084 (tpt) REVERT: E 165 PHE cc_start: 0.8417 (p90) cc_final: 0.8201 (p90) REVERT: E 179 MET cc_start: 0.7402 (pmm) cc_final: 0.7110 (pmm) REVERT: E 228 LYS cc_start: 0.9518 (ptpp) cc_final: 0.9294 (ptpp) REVERT: E 246 CYS cc_start: 0.9423 (t) cc_final: 0.9120 (t) REVERT: E 273 LEU cc_start: 0.9084 (tt) cc_final: 0.8594 (tt) REVERT: E 322 ARG cc_start: 0.8255 (tmm-80) cc_final: 0.7519 (tmm-80) REVERT: E 325 MET cc_start: 0.8801 (ptm) cc_final: 0.8288 (ptm) REVERT: E 332 ILE cc_start: 0.9409 (pt) cc_final: 0.9017 (pt) REVERT: E 334 GLN cc_start: 0.9291 (mp10) cc_final: 0.8429 (mp10) REVERT: E 335 GLU cc_start: 0.8649 (mp0) cc_final: 0.7822 (mp0) REVERT: E 341 ARG cc_start: 0.9486 (ptm160) cc_final: 0.8968 (ptm160) REVERT: E 352 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8708 (tm-30) REVERT: E 353 TYR cc_start: 0.8871 (t80) cc_final: 0.8669 (t80) REVERT: E 355 ARG cc_start: 0.8651 (ptm-80) cc_final: 0.8397 (ptm-80) REVERT: E 364 ASP cc_start: 0.8562 (m-30) cc_final: 0.6925 (m-30) REVERT: E 372 HIS cc_start: 0.9065 (m170) cc_final: 0.8246 (m90) REVERT: E 375 LYS cc_start: 0.9699 (pttt) cc_final: 0.9412 (pttt) REVERT: E 385 MET cc_start: 0.8407 (ttp) cc_final: 0.7593 (ttp) REVERT: E 420 MET cc_start: 0.8321 (mtm) cc_final: 0.7699 (mtp) REVERT: E 454 HIS cc_start: 0.8877 (m90) cc_final: 0.8628 (m90) REVERT: E 483 MET cc_start: 0.9678 (tmm) cc_final: 0.9413 (tmm) REVERT: E 507 HIS cc_start: 0.8533 (t-90) cc_final: 0.8266 (t70) REVERT: F 18 LEU cc_start: 0.9409 (tp) cc_final: 0.9178 (tp) REVERT: F 37 ILE cc_start: 0.9224 (mm) cc_final: 0.8833 (mm) REVERT: F 41 TYR cc_start: 0.9253 (t80) cc_final: 0.8935 (t80) REVERT: F 70 MET cc_start: 0.7917 (tpp) cc_final: 0.7125 (mmm) REVERT: F 82 MET cc_start: 0.9366 (ttt) cc_final: 0.8924 (tmm) REVERT: F 92 HIS cc_start: 0.8946 (p90) cc_final: 0.8621 (p-80) REVERT: F 108 LYS cc_start: 0.9033 (pttm) cc_final: 0.7932 (tppt) REVERT: F 131 PHE cc_start: 0.9277 (m-10) cc_final: 0.8791 (m-80) REVERT: F 132 GLU cc_start: 0.9484 (pt0) cc_final: 0.9175 (pt0) REVERT: F 134 LYS cc_start: 0.9316 (ptpp) cc_final: 0.9024 (pttt) REVERT: F 185 LEU cc_start: 0.8864 (mt) cc_final: 0.8369 (mt) REVERT: F 242 LYS cc_start: 0.8375 (tttt) cc_final: 0.8174 (tptt) REVERT: F 250 ILE cc_start: 0.9317 (mp) cc_final: 0.8852 (tp) REVERT: F 287 ILE cc_start: 0.9498 (pt) cc_final: 0.9290 (pt) REVERT: F 291 LYS cc_start: 0.9518 (mmtt) cc_final: 0.9216 (tppt) REVERT: F 334 GLN cc_start: 0.9293 (mt0) cc_final: 0.8900 (mm-40) REVERT: F 337 LEU cc_start: 0.9238 (mm) cc_final: 0.9000 (mm) REVERT: F 343 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: F 352 GLU cc_start: 0.9045 (pm20) cc_final: 0.8742 (pm20) REVERT: F 355 ARG cc_start: 0.8457 (ppt170) cc_final: 0.7767 (ttp-170) REVERT: F 372 HIS cc_start: 0.9113 (m170) cc_final: 0.8593 (m90) REVERT: F 400 TYR cc_start: 0.7299 (m-80) cc_final: 0.6427 (m-80) REVERT: F 404 ASP cc_start: 0.8437 (t0) cc_final: 0.8205 (t0) REVERT: F 449 ASP cc_start: 0.8550 (t0) cc_final: 0.8279 (t0) REVERT: F 455 LYS cc_start: 0.9424 (pttp) cc_final: 0.9146 (ptmm) REVERT: F 491 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8276 (tm-30) REVERT: F 493 ARG cc_start: 0.8715 (ptt-90) cc_final: 0.8454 (ptt-90) REVERT: G 32 TYR cc_start: 0.8774 (m-10) cc_final: 0.8301 (m-10) REVERT: G 47 ASP cc_start: 0.9581 (m-30) cc_final: 0.8905 (p0) REVERT: G 78 MET cc_start: 0.9545 (tpp) cc_final: 0.9131 (tpp) REVERT: G 199 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8972 (mt-10) REVERT: G 222 ILE cc_start: 0.7387 (mm) cc_final: 0.7162 (mm) REVERT: G 229 LYS cc_start: 0.9368 (ptpp) cc_final: 0.9070 (mmmt) REVERT: G 274 ASP cc_start: 0.9114 (t0) cc_final: 0.8751 (t70) REVERT: G 289 TYR cc_start: 0.9378 (t80) cc_final: 0.9118 (t80) REVERT: G 321 LEU cc_start: 0.9340 (tp) cc_final: 0.9135 (tp) REVERT: G 331 CYS cc_start: 0.9088 (t) cc_final: 0.8702 (t) REVERT: G 333 THR cc_start: 0.9707 (p) cc_final: 0.9109 (p) REVERT: G 334 GLN cc_start: 0.9105 (mp10) cc_final: 0.8327 (mp10) REVERT: G 335 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8057 (tm-30) REVERT: G 336 VAL cc_start: 0.9474 (m) cc_final: 0.8620 (m) REVERT: G 349 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8719 (mtpt) REVERT: G 362 ILE cc_start: 0.9438 (pt) cc_final: 0.9203 (mm) REVERT: G 395 GLU cc_start: 0.8755 (mp0) cc_final: 0.8516 (mp0) REVERT: G 414 MET cc_start: 0.9248 (pmm) cc_final: 0.8670 (ptt) REVERT: G 493 ARG cc_start: 0.8877 (mtm180) cc_final: 0.8131 (mtm-85) REVERT: G 500 GLU cc_start: 0.9166 (pp20) cc_final: 0.8430 (pp20) REVERT: G 504 HIS cc_start: 0.8555 (p90) cc_final: 0.7728 (p90) REVERT: H 21 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8115 (tm-30) REVERT: H 25 ASN cc_start: 0.8583 (m110) cc_final: 0.8126 (m110) REVERT: H 32 TYR cc_start: 0.9137 (m-80) cc_final: 0.8300 (m-10) REVERT: H 33 ASN cc_start: 0.9082 (t0) cc_final: 0.8166 (t0) REVERT: H 91 ILE cc_start: 0.9282 (tp) cc_final: 0.9043 (tp) REVERT: H 93 HIS cc_start: 0.9033 (p90) cc_final: 0.8600 (p-80) REVERT: H 108 LYS cc_start: 0.9014 (tptm) cc_final: 0.8580 (tptp) REVERT: H 112 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8919 (tm-30) REVERT: H 150 MET cc_start: 0.7298 (tmm) cc_final: 0.6877 (tmm) REVERT: H 179 MET cc_start: 0.7459 (ppp) cc_final: 0.6840 (ppp) REVERT: H 215 ASP cc_start: 0.9523 (m-30) cc_final: 0.9031 (p0) REVERT: H 229 LYS cc_start: 0.8858 (pttt) cc_final: 0.8626 (mmtt) REVERT: H 242 LYS cc_start: 0.9384 (mmpt) cc_final: 0.9180 (mmmt) REVERT: H 286 MET cc_start: 0.9638 (tpt) cc_final: 0.9153 (tpt) REVERT: H 290 ILE cc_start: 0.9738 (pt) cc_final: 0.9355 (pt) REVERT: H 311 LYS cc_start: 0.9097 (tttt) cc_final: 0.8891 (tttt) REVERT: H 315 ASP cc_start: 0.9238 (m-30) cc_final: 0.8828 (p0) REVERT: H 343 GLN cc_start: 0.8577 (pm20) cc_final: 0.8245 (pm20) REVERT: H 349 LYS cc_start: 0.9606 (mmtp) cc_final: 0.8988 (mtmt) REVERT: H 352 GLU cc_start: 0.9372 (tm-30) cc_final: 0.9031 (tm-30) REVERT: H 368 GLN cc_start: 0.8670 (mt0) cc_final: 0.8157 (mm-40) REVERT: H 385 MET cc_start: 0.8192 (tpt) cc_final: 0.7630 (tpt) REVERT: H 410 LYS cc_start: 0.8934 (mptt) cc_final: 0.8715 (mmtm) REVERT: H 414 MET cc_start: 0.8639 (pmm) cc_final: 0.8322 (pmm) REVERT: H 465 GLN cc_start: 0.8623 (pp30) cc_final: 0.8322 (tt0) REVERT: H 468 CYS cc_start: 0.9115 (t) cc_final: 0.8807 (t) REVERT: H 491 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7725 (tm-30) REVERT: K 1 MET cc_start: 0.7945 (mmt) cc_final: 0.7691 (mmp) outliers start: 3 outliers final: 0 residues processed: 1450 average time/residue: 0.2006 time to fit residues: 471.1177 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 : 1.415 ------------------------------------------------------------------------------- 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: 5.9990 chunk 181 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 282 optimal weight: 0.0970 chunk 72 optimal weight: 0.0070 chunk 56 optimal weight: 0.6980 chunk 368 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 377 optimal weight: 0.6980 chunk 336 optimal weight: 4.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 ASN ** A 283 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 466 HIS B 100 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 277 GLN E 309 GLN E 454 HIS ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.128404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091632 restraints weight = 72878.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095609 restraints weight = 40811.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098389 restraints weight = 26794.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.100388 restraints weight = 19517.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101540 restraints weight = 15301.060| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32220 Z= 0.144 Angle : 0.856 11.542 43712 Z= 0.421 Chirality : 0.052 0.397 4984 Planarity : 0.006 0.298 5452 Dihedral : 15.851 170.273 5344 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.52 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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 aren not related in a simple way. whole: -2.75 (0.12), residues: 3968 helix: -1.67 (0.13), residues: 1228 sheet: -2.42 (0.22), residues: 438 loop : -1.79 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG H 322 TYR 0.036 0.002 TYR E 110 PHE 0.031 0.002 PHE A 456 HIS 0.004 0.001 HIS G 504 Details of bonding type rmsd covalent geometry : bond 0.00318 (32212) covalent geometry : angle 0.85581 (43712) hydrogen bonds : bond 0.04089 ( 966) hydrogen bonds : angle 6.42828 ( 2655) Misc. bond : bond 0.00205 ( 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 1467 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1467 time to evaluate : 1.206 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: A 12 TYR cc_start: 0.7468 (t80) cc_final: 0.6776 (m-80) REVERT: A 21 GLN cc_start: 0.9150 (pm20) cc_final: 0.8879 (pm20) REVERT: A 28 ASP cc_start: 0.8955 (t70) cc_final: 0.8543 (t70) REVERT: A 32 TYR cc_start: 0.8871 (m-10) cc_final: 0.8473 (m-10) REVERT: A 36 LEU cc_start: 0.9007 (tp) cc_final: 0.8134 (tp) REVERT: A 38 LEU cc_start: 0.9553 (mm) cc_final: 0.8768 (mm) REVERT: A 48 GLN cc_start: 0.9236 (mt0) cc_final: 0.8847 (mt0) REVERT: A 108 LYS cc_start: 0.9482 (tptp) cc_final: 0.9259 (pttp) REVERT: A 129 ASP cc_start: 0.8986 (m-30) cc_final: 0.8731 (m-30) REVERT: A 150 MET cc_start: 0.7830 (tpt) cc_final: 0.7233 (tpt) REVERT: A 158 ILE cc_start: 0.9059 (mm) cc_final: 0.8636 (tp) REVERT: A 179 MET cc_start: 0.7219 (pmm) cc_final: 0.6935 (pmm) REVERT: A 246 CYS cc_start: 0.9403 (t) cc_final: 0.8744 (p) REVERT: A 250 ILE cc_start: 0.9513 (pt) cc_final: 0.9218 (pt) REVERT: A 254 GLU cc_start: 0.9194 (tp30) cc_final: 0.8679 (pm20) REVERT: A 262 LEU cc_start: 0.9584 (pt) cc_final: 0.9278 (pp) REVERT: A 273 LEU cc_start: 0.9603 (tp) cc_final: 0.9221 (tp) REVERT: A 319 ASP cc_start: 0.7690 (t70) cc_final: 0.7438 (t70) REVERT: A 322 ARG cc_start: 0.8298 (tmm-80) cc_final: 0.7281 (tmm-80) REVERT: A 325 MET cc_start: 0.8989 (ptm) cc_final: 0.8575 (ptm) REVERT: A 332 ILE cc_start: 0.9295 (pt) cc_final: 0.8863 (pt) REVERT: A 334 GLN cc_start: 0.9392 (mp10) cc_final: 0.8427 (mp10) REVERT: A 335 GLU cc_start: 0.8768 (mp0) cc_final: 0.7849 (mp0) REVERT: A 341 ARG cc_start: 0.9397 (ptm160) cc_final: 0.8868 (ptm160) REVERT: A 343 GLN cc_start: 0.8041 (pp30) cc_final: 0.7298 (pp30) REVERT: A 353 TYR cc_start: 0.8926 (t80) cc_final: 0.8642 (t80) REVERT: A 357 PHE cc_start: 0.9178 (m-80) cc_final: 0.8912 (m-10) REVERT: A 375 LYS cc_start: 0.9610 (pttt) cc_final: 0.9356 (pttt) REVERT: A 385 MET cc_start: 0.8572 (ttp) cc_final: 0.8133 (ttp) REVERT: A 386 MET cc_start: 0.8609 (ppp) cc_final: 0.8009 (tmm) REVERT: A 420 MET cc_start: 0.8291 (mtm) cc_final: 0.7767 (mtp) REVERT: A 454 HIS cc_start: 0.8898 (m90) cc_final: 0.8642 (m90) REVERT: A 480 ARG cc_start: 0.8811 (mpp80) cc_final: 0.8395 (mtm110) REVERT: A 496 SER cc_start: 0.9211 (t) cc_final: 0.8672 (t) REVERT: A 507 HIS cc_start: 0.8433 (t-90) cc_final: 0.8071 (t70) REVERT: B 18 LEU cc_start: 0.9416 (tp) cc_final: 0.9110 (tp) REVERT: B 34 ASP cc_start: 0.8191 (m-30) cc_final: 0.7532 (m-30) REVERT: B 36 LEU cc_start: 0.9443 (tp) cc_final: 0.9224 (tp) REVERT: B 37 ILE cc_start: 0.9141 (mm) cc_final: 0.8843 (mm) REVERT: B 42 ILE cc_start: 0.9289 (pt) cc_final: 0.9085 (pt) REVERT: B 82 MET cc_start: 0.9457 (ttm) cc_final: 0.9182 (ttm) REVERT: B 92 HIS cc_start: 0.9078 (p90) cc_final: 0.8718 (p-80) REVERT: B 106 LYS cc_start: 0.9373 (mtpt) cc_final: 0.9141 (mtpt) REVERT: B 108 LYS cc_start: 0.9294 (pttm) cc_final: 0.8451 (tppt) REVERT: B 131 PHE cc_start: 0.9503 (m-80) cc_final: 0.8473 (m-80) REVERT: B 132 GLU cc_start: 0.9573 (pt0) cc_final: 0.9263 (pt0) REVERT: B 134 LYS cc_start: 0.9433 (pttp) cc_final: 0.9073 (tttt) REVERT: B 185 LEU cc_start: 0.8801 (mt) cc_final: 0.8218 (mt) REVERT: B 192 ILE cc_start: 0.9251 (mt) cc_final: 0.9008 (mt) REVERT: B 200 ILE cc_start: 0.9750 (mt) cc_final: 0.9534 (mt) REVERT: B 242 LYS cc_start: 0.8501 (tttm) cc_final: 0.8231 (mmmm) REVERT: B 250 ILE cc_start: 0.9405 (mp) cc_final: 0.9021 (tp) REVERT: B 291 LYS cc_start: 0.9607 (mmmt) cc_final: 0.9064 (tppt) REVERT: B 297 LEU cc_start: 0.9188 (tt) cc_final: 0.8899 (mm) REVERT: B 334 GLN cc_start: 0.9317 (mt0) cc_final: 0.8757 (mm-40) REVERT: B 351 SER cc_start: 0.9367 (p) cc_final: 0.9081 (p) REVERT: B 372 HIS cc_start: 0.8958 (m170) cc_final: 0.8459 (m170) REVERT: B 400 TYR cc_start: 0.7420 (m-80) cc_final: 0.7119 (m-80) REVERT: B 403 SER cc_start: 0.9320 (t) cc_final: 0.9102 (t) REVERT: B 404 ASP cc_start: 0.8507 (t0) cc_final: 0.8204 (t0) REVERT: B 449 ASP cc_start: 0.8714 (t0) cc_final: 0.8410 (t0) REVERT: B 491 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8228 (tm-30) REVERT: B 506 LEU cc_start: 0.8713 (pt) cc_final: 0.8423 (pt) REVERT: C 33 ASN cc_start: 0.8887 (m110) cc_final: 0.8530 (m-40) REVERT: C 47 ASP cc_start: 0.9585 (m-30) cc_final: 0.8913 (p0) REVERT: C 78 MET cc_start: 0.9189 (mmm) cc_final: 0.8806 (mmm) REVERT: C 82 MET cc_start: 0.9635 (tpp) cc_final: 0.9359 (tpp) REVERT: C 90 PHE cc_start: 0.9110 (m-80) cc_final: 0.8621 (m-80) REVERT: C 199 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8567 (tp30) REVERT: C 200 ILE cc_start: 0.9324 (mm) cc_final: 0.8862 (mm) REVERT: C 203 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8284 (mtm110) REVERT: C 229 LYS cc_start: 0.9393 (ptpp) cc_final: 0.9098 (mmmt) REVERT: C 274 ASP cc_start: 0.9122 (t0) cc_final: 0.8705 (t70) REVERT: C 331 CYS cc_start: 0.9034 (t) cc_final: 0.8646 (t) REVERT: C 333 THR cc_start: 0.9721 (p) cc_final: 0.9126 (p) REVERT: C 334 GLN cc_start: 0.9102 (mp10) cc_final: 0.8388 (mp10) REVERT: C 349 LYS cc_start: 0.8402 (mtpt) cc_final: 0.7868 (mtmm) REVERT: C 357 PHE cc_start: 0.9221 (m-80) cc_final: 0.9008 (m-80) REVERT: C 386 MET cc_start: 0.8919 (tmm) cc_final: 0.8567 (tmm) REVERT: C 390 LEU cc_start: 0.9240 (pt) cc_final: 0.8924 (pt) REVERT: C 414 MET cc_start: 0.9242 (pmm) cc_final: 0.8772 (ptt) REVERT: C 456 PHE cc_start: 0.9749 (t80) cc_final: 0.9436 (t80) REVERT: C 482 MET cc_start: 0.9360 (tpp) cc_final: 0.8737 (mmm) REVERT: C 493 ARG cc_start: 0.8803 (mtm180) cc_final: 0.8437 (ptp90) REVERT: C 500 GLU cc_start: 0.9150 (pp20) cc_final: 0.8465 (pp20) REVERT: D 12 TYR cc_start: 0.8042 (t80) cc_final: 0.6932 (m-80) REVERT: D 21 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8478 (tp40) REVERT: D 25 ASN cc_start: 0.8644 (m110) cc_final: 0.7474 (m110) REVERT: D 50 ASP cc_start: 0.8709 (t0) cc_final: 0.8308 (p0) REVERT: D 91 ILE cc_start: 0.9164 (tp) cc_final: 0.8859 (tp) REVERT: D 93 HIS cc_start: 0.9393 (p-80) cc_final: 0.8677 (p-80) REVERT: D 94 ASN cc_start: 0.8942 (m110) cc_final: 0.8708 (t0) REVERT: D 144 ILE cc_start: 0.9117 (mm) cc_final: 0.8716 (mp) REVERT: D 179 MET cc_start: 0.6117 (ppp) cc_final: 0.4854 (pmm) REVERT: D 215 ASP cc_start: 0.9552 (m-30) cc_final: 0.8838 (t70) REVERT: D 242 LYS cc_start: 0.9269 (mmpt) cc_final: 0.9008 (mmmt) REVERT: D 243 GLN cc_start: 0.9580 (mt0) cc_final: 0.9152 (mt0) REVERT: D 257 LYS cc_start: 0.9800 (ptpp) cc_final: 0.9492 (mmtm) REVERT: D 281 ILE cc_start: 0.9728 (mm) cc_final: 0.9483 (mm) REVERT: D 286 MET cc_start: 0.9633 (tpt) cc_final: 0.9302 (tpt) REVERT: D 289 TYR cc_start: 0.9387 (t80) cc_final: 0.9003 (t80) REVERT: D 290 ILE cc_start: 0.9734 (pt) cc_final: 0.9348 (pt) REVERT: D 335 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8400 (tm-30) REVERT: D 349 LYS cc_start: 0.9648 (mmtp) cc_final: 0.9432 (mmtp) REVERT: D 352 GLU cc_start: 0.9377 (tm-30) cc_final: 0.8983 (tm-30) REVERT: D 375 LYS cc_start: 0.9484 (pttt) cc_final: 0.9255 (pttt) REVERT: D 379 LEU cc_start: 0.9525 (mm) cc_final: 0.9295 (mm) REVERT: D 385 MET cc_start: 0.8429 (tpt) cc_final: 0.7206 (tpt) REVERT: D 386 MET cc_start: 0.8123 (ptp) cc_final: 0.7427 (ptp) REVERT: D 453 ILE cc_start: 0.9632 (pt) cc_final: 0.9213 (pt) REVERT: D 465 GLN cc_start: 0.8585 (pp30) cc_final: 0.7711 (tt0) REVERT: D 468 CYS cc_start: 0.9222 (t) cc_final: 0.8904 (t) REVERT: D 469 GLN cc_start: 0.8614 (mm110) cc_final: 0.8301 (mm-40) REVERT: D 482 MET cc_start: 0.9093 (tpp) cc_final: 0.8783 (tpt) REVERT: N 11 SER cc_start: 0.8523 (p) cc_final: 0.7845 (p) REVERT: O 1 MET cc_start: 0.7964 (mmm) cc_final: 0.7355 (mmp) REVERT: E 12 TYR cc_start: 0.7398 (t80) cc_final: 0.6723 (m-80) REVERT: E 21 GLN cc_start: 0.9128 (pm20) cc_final: 0.8833 (pm20) REVERT: E 32 TYR cc_start: 0.9262 (m-80) cc_final: 0.8687 (m-80) REVERT: E 36 LEU cc_start: 0.8732 (tp) cc_final: 0.8192 (tp) REVERT: E 38 LEU cc_start: 0.9554 (mm) cc_final: 0.8899 (mm) REVERT: E 48 GLN cc_start: 0.9302 (mt0) cc_final: 0.8832 (mt0) REVERT: E 105 ARG cc_start: 0.8966 (mmm160) cc_final: 0.8072 (tpm170) REVERT: E 108 LYS cc_start: 0.9377 (tppt) cc_final: 0.8738 (tppt) REVERT: E 109 LYS cc_start: 0.9300 (ptpp) cc_final: 0.8659 (ptpp) REVERT: E 150 MET cc_start: 0.7880 (tpt) cc_final: 0.7044 (tpt) REVERT: E 165 PHE cc_start: 0.8343 (p90) cc_final: 0.8121 (p90) REVERT: E 203 ARG cc_start: 0.9380 (ttp-110) cc_final: 0.9004 (mtm110) REVERT: E 228 LYS cc_start: 0.9518 (ptpp) cc_final: 0.9281 (ptpp) REVERT: E 246 CYS cc_start: 0.9397 (t) cc_final: 0.8666 (p) REVERT: E 254 GLU cc_start: 0.9268 (tp30) cc_final: 0.8959 (pm20) REVERT: E 262 LEU cc_start: 0.9649 (pt) cc_final: 0.9398 (pt) REVERT: E 273 LEU cc_start: 0.9044 (tt) cc_final: 0.8388 (tt) REVERT: E 288 LYS cc_start: 0.9599 (mtmm) cc_final: 0.9304 (mttt) REVERT: E 322 ARG cc_start: 0.8208 (tmm-80) cc_final: 0.7527 (tmm-80) REVERT: E 334 GLN cc_start: 0.9353 (mp10) cc_final: 0.8405 (mp10) REVERT: E 335 GLU cc_start: 0.8696 (mp0) cc_final: 0.8123 (mp0) REVERT: E 352 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8779 (tm-30) REVERT: E 353 TYR cc_start: 0.8770 (t80) cc_final: 0.8561 (t80) REVERT: E 364 ASP cc_start: 0.8477 (m-30) cc_final: 0.6763 (m-30) REVERT: E 372 HIS cc_start: 0.9069 (m170) cc_final: 0.8256 (m90) REVERT: E 375 LYS cc_start: 0.9716 (pttt) cc_final: 0.9446 (pttt) REVERT: E 385 MET cc_start: 0.8350 (ttp) cc_final: 0.7482 (ttp) REVERT: E 386 MET cc_start: 0.8373 (ppp) cc_final: 0.8106 (tmm) REVERT: E 420 MET cc_start: 0.8241 (mtm) cc_final: 0.7620 (mtp) REVERT: E 450 LYS cc_start: 0.9367 (mttp) cc_final: 0.8851 (mttp) REVERT: E 483 MET cc_start: 0.9683 (tmm) cc_final: 0.9427 (tmm) REVERT: E 507 HIS cc_start: 0.8484 (t-90) cc_final: 0.8202 (t70) REVERT: F 16 ASP cc_start: 0.7869 (t0) cc_final: 0.6352 (t0) REVERT: F 18 LEU cc_start: 0.9357 (tp) cc_final: 0.9153 (tp) REVERT: F 36 LEU cc_start: 0.9313 (tp) cc_final: 0.9112 (tp) REVERT: F 37 ILE cc_start: 0.9226 (mm) cc_final: 0.8853 (mm) REVERT: F 66 VAL cc_start: 0.9172 (p) cc_final: 0.8943 (p) REVERT: F 70 MET cc_start: 0.8026 (tpp) cc_final: 0.7373 (mmm) REVERT: F 82 MET cc_start: 0.9426 (ttt) cc_final: 0.9073 (tmm) REVERT: F 88 ILE cc_start: 0.9328 (tp) cc_final: 0.8750 (tp) REVERT: F 92 HIS cc_start: 0.8853 (p90) cc_final: 0.8486 (p-80) REVERT: F 108 LYS cc_start: 0.9066 (pttm) cc_final: 0.7751 (tppt) REVERT: F 131 PHE cc_start: 0.9251 (m-10) cc_final: 0.8910 (m-80) REVERT: F 132 GLU cc_start: 0.9489 (pt0) cc_final: 0.9189 (pt0) REVERT: F 136 ARG cc_start: 0.9313 (mmp-170) cc_final: 0.8876 (mmm160) REVERT: F 157 ILE cc_start: 0.9227 (tt) cc_final: 0.9017 (tt) REVERT: F 166 LEU cc_start: 0.9412 (mm) cc_final: 0.8554 (tp) REVERT: F 176 GLU cc_start: 0.8124 (mp0) cc_final: 0.7886 (mp0) REVERT: F 185 LEU cc_start: 0.8882 (mt) cc_final: 0.8341 (mt) REVERT: F 199 GLU cc_start: 0.9547 (mt-10) cc_final: 0.9306 (mt-10) REVERT: F 242 LYS cc_start: 0.8421 (tttt) cc_final: 0.8078 (tptt) REVERT: F 250 ILE cc_start: 0.9323 (mp) cc_final: 0.8854 (tp) REVERT: F 291 LYS cc_start: 0.9521 (mmtt) cc_final: 0.9201 (tppt) REVERT: F 322 ARG cc_start: 0.8533 (ttt90) cc_final: 0.7926 (tpt-90) REVERT: F 334 GLN cc_start: 0.9356 (mt0) cc_final: 0.8946 (mm-40) REVERT: F 337 LEU cc_start: 0.9225 (mm) cc_final: 0.8914 (mm) REVERT: F 343 GLN cc_start: 0.8030 (tm130) cc_final: 0.7479 (tm-30) REVERT: F 348 TYR cc_start: 0.9411 (t80) cc_final: 0.8906 (t80) REVERT: F 352 GLU cc_start: 0.9066 (pm20) cc_final: 0.8771 (pm20) REVERT: F 355 ARG cc_start: 0.8421 (ppt170) cc_final: 0.7863 (ttp-170) REVERT: F 372 HIS cc_start: 0.9010 (m170) cc_final: 0.8656 (m90) REVERT: F 400 TYR cc_start: 0.7356 (m-80) cc_final: 0.6593 (m-80) REVERT: F 404 ASP cc_start: 0.8442 (t0) cc_final: 0.8178 (t0) REVERT: F 449 ASP cc_start: 0.8527 (t0) cc_final: 0.8302 (t0) REVERT: F 455 LYS cc_start: 0.9447 (pttp) cc_final: 0.9110 (ptmm) REVERT: F 482 MET cc_start: 0.8779 (ptp) cc_final: 0.8511 (ptp) REVERT: F 491 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8419 (tm-30) REVERT: F 493 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.8411 (ptt-90) REVERT: F 506 LEU cc_start: 0.8676 (pt) cc_final: 0.8383 (pt) REVERT: G 32 TYR cc_start: 0.8638 (m-10) cc_final: 0.8288 (m-10) REVERT: G 47 ASP cc_start: 0.9581 (m-30) cc_final: 0.8964 (p0) REVERT: G 78 MET cc_start: 0.9557 (tpp) cc_final: 0.9086 (tpp) REVERT: G 175 LEU cc_start: 0.9222 (mt) cc_final: 0.8969 (mp) REVERT: G 222 ILE cc_start: 0.7460 (mm) cc_final: 0.7199 (mm) REVERT: G 229 LYS cc_start: 0.9360 (ptpp) cc_final: 0.9038 (mmmt) REVERT: G 274 ASP cc_start: 0.8920 (t0) cc_final: 0.8516 (t70) REVERT: G 289 TYR cc_start: 0.9365 (t80) cc_final: 0.9157 (t80) REVERT: G 331 CYS cc_start: 0.8979 (t) cc_final: 0.8504 (t) REVERT: G 333 THR cc_start: 0.9716 (p) cc_final: 0.9106 (p) REVERT: G 334 GLN cc_start: 0.9061 (mp10) cc_final: 0.8263 (mp10) REVERT: G 335 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7930 (tm-30) REVERT: G 336 VAL cc_start: 0.9403 (m) cc_final: 0.8639 (m) REVERT: G 349 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8691 (mtmt) REVERT: G 362 ILE cc_start: 0.9377 (pt) cc_final: 0.9156 (mm) REVERT: G 386 MET cc_start: 0.8937 (tmm) cc_final: 0.8566 (tmm) REVERT: G 395 GLU cc_start: 0.8781 (mp0) cc_final: 0.8514 (mp0) REVERT: G 408 LEU cc_start: 0.8670 (pt) cc_final: 0.8454 (pp) REVERT: G 482 MET cc_start: 0.9273 (tpp) cc_final: 0.8950 (tpt) REVERT: G 493 ARG cc_start: 0.8841 (mtm180) cc_final: 0.8060 (mtm-85) REVERT: G 500 GLU cc_start: 0.9153 (pp20) cc_final: 0.8312 (pp20) REVERT: G 504 HIS cc_start: 0.8480 (p90) cc_final: 0.7514 (p90) REVERT: H 21 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8446 (tp40) REVERT: H 25 ASN cc_start: 0.8579 (m110) cc_final: 0.7433 (m110) REVERT: H 32 TYR cc_start: 0.9145 (m-80) cc_final: 0.8382 (m-10) REVERT: H 33 ASN cc_start: 0.9245 (t0) cc_final: 0.8634 (t0) REVERT: H 62 LYS cc_start: 0.9349 (mmtt) cc_final: 0.8928 (mtpp) REVERT: H 91 ILE cc_start: 0.9211 (tp) cc_final: 0.8956 (tp) REVERT: H 93 HIS cc_start: 0.8957 (p90) cc_final: 0.8442 (p-80) REVERT: H 108 LYS cc_start: 0.9003 (tptm) cc_final: 0.8580 (tptp) REVERT: H 112 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8804 (tm-30) REVERT: H 158 ILE cc_start: 0.8189 (tp) cc_final: 0.7930 (tp) REVERT: H 179 MET cc_start: 0.7055 (ppp) cc_final: 0.6242 (ppp) REVERT: H 215 ASP cc_start: 0.9489 (m-30) cc_final: 0.8972 (p0) REVERT: H 221 ILE cc_start: 0.9344 (tp) cc_final: 0.9118 (mp) REVERT: H 229 LYS cc_start: 0.8892 (pttt) cc_final: 0.8679 (mmtt) REVERT: H 242 LYS cc_start: 0.9374 (mmpt) cc_final: 0.9157 (mmmt) REVERT: H 286 MET cc_start: 0.9650 (tpt) cc_final: 0.9171 (tpt) REVERT: H 290 ILE cc_start: 0.9723 (pt) cc_final: 0.9407 (pt) REVERT: H 315 ASP cc_start: 0.9174 (m-30) cc_final: 0.8714 (p0) REVERT: H 335 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8456 (tm-30) REVERT: H 349 LYS cc_start: 0.9619 (mmtp) cc_final: 0.9363 (mmtp) REVERT: H 352 GLU cc_start: 0.9390 (tm-30) cc_final: 0.8981 (tm-30) REVERT: H 368 GLN cc_start: 0.8710 (mt0) cc_final: 0.8237 (mm-40) REVERT: H 375 LYS cc_start: 0.9458 (pttt) cc_final: 0.9207 (pttt) REVERT: H 385 MET cc_start: 0.8025 (tpt) cc_final: 0.6830 (tpt) REVERT: H 410 LYS cc_start: 0.8869 (mptt) cc_final: 0.8647 (mmtm) REVERT: H 414 MET cc_start: 0.8486 (pmm) cc_final: 0.8218 (pmm) REVERT: H 465 GLN cc_start: 0.8603 (pp30) cc_final: 0.8325 (tt0) REVERT: H 468 CYS cc_start: 0.9116 (t) cc_final: 0.8849 (t) REVERT: H 478 GLN cc_start: 0.9588 (tt0) cc_final: 0.9181 (tt0) REVERT: H 491 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7633 (tm-30) REVERT: H 492 LYS cc_start: 0.9065 (pttt) cc_final: 0.8772 (pttp) REVERT: J 12 TYR cc_start: 0.8327 (t80) cc_final: 0.7725 (t80) outliers start: 0 outliers final: 0 residues processed: 1467 average time/residue: 0.2003 time to fit residues: 477.7140 Evaluate side-chains 1223 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1223 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 7.9990 chunk 291 optimal weight: 0.0670 chunk 308 optimal weight: 7.9990 chunk 266 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 367 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 384 optimal weight: 0.6980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 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 454 HIS A 466 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 93 HIS ** 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 454 HIS E 22 GLN E 454 HIS E 466 HIS ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 504 HIS ** 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 = 0.3782 r_free = 0.3782 target = 0.128745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091848 restraints weight = 73184.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095877 restraints weight = 41216.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098626 restraints weight = 27091.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.100692 restraints weight = 19832.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102051 restraints weight = 15522.714| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32220 Z= 0.149 Angle : 0.862 12.852 43712 Z= 0.426 Chirality : 0.053 0.490 4984 Planarity : 0.005 0.094 5452 Dihedral : 15.455 175.161 5344 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.42 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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 aren not related in a simple way. whole: -2.74 (0.12), residues: 3968 helix: -1.66 (0.13), residues: 1236 sheet: -2.45 (0.21), residues: 458 loop : -1.76 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 322 TYR 0.039 0.002 TYR A 110 PHE 0.038 0.002 PHE F 456 HIS 0.012 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00335 (32212) covalent geometry : angle 0.86161 (43712) hydrogen bonds : bond 0.04113 ( 966) hydrogen bonds : angle 6.43291 ( 2655) Misc. bond : bond 0.00251 ( 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 1433 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1433 time to evaluate : 1.228 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: A 21 GLN cc_start: 0.9188 (pm20) cc_final: 0.8969 (pm20) REVERT: A 28 ASP cc_start: 0.9055 (t70) cc_final: 0.8592 (t70) REVERT: A 32 TYR cc_start: 0.8784 (m-10) cc_final: 0.8347 (m-10) REVERT: A 36 LEU cc_start: 0.8505 (tp) cc_final: 0.7959 (tp) REVERT: A 38 LEU cc_start: 0.9540 (mm) cc_final: 0.8841 (mm) REVERT: A 48 GLN cc_start: 0.9224 (mt0) cc_final: 0.8814 (mt0) REVERT: A 108 LYS cc_start: 0.9552 (tptp) cc_final: 0.9244 (pttm) REVERT: A 150 MET cc_start: 0.7814 (tpt) cc_final: 0.7286 (tpt) REVERT: A 158 ILE cc_start: 0.9113 (mm) cc_final: 0.8708 (tp) REVERT: A 165 PHE cc_start: 0.8497 (p90) cc_final: 0.8166 (p90) REVERT: A 179 MET cc_start: 0.7437 (pmm) cc_final: 0.6812 (pmm) REVERT: A 246 CYS cc_start: 0.9420 (t) cc_final: 0.8765 (p) REVERT: A 262 LEU cc_start: 0.9588 (pt) cc_final: 0.9273 (pp) REVERT: A 273 LEU cc_start: 0.9597 (tp) cc_final: 0.9249 (tp) REVERT: A 319 ASP cc_start: 0.7782 (t70) cc_final: 0.7567 (t70) REVERT: A 322 ARG cc_start: 0.8344 (tmm-80) cc_final: 0.7364 (tmm-80) REVERT: A 325 MET cc_start: 0.8813 (ptm) cc_final: 0.8360 (ptm) REVERT: A 332 ILE cc_start: 0.9273 (pt) cc_final: 0.8802 (pt) REVERT: A 334 GLN cc_start: 0.9386 (mp10) cc_final: 0.8396 (mp10) REVERT: A 335 GLU cc_start: 0.8577 (mp0) cc_final: 0.7693 (mp0) REVERT: A 341 ARG cc_start: 0.9416 (ptm160) cc_final: 0.9093 (ptm-80) REVERT: A 343 GLN cc_start: 0.8012 (pp30) cc_final: 0.7523 (pp30) REVERT: A 352 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8656 (tm-30) REVERT: A 353 TYR cc_start: 0.8926 (t80) cc_final: 0.8703 (t80) REVERT: A 368 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8325 (mm-40) REVERT: A 369 ASN cc_start: 0.8900 (p0) cc_final: 0.7818 (p0) REVERT: A 372 HIS cc_start: 0.9143 (m170) cc_final: 0.8546 (m-70) REVERT: A 375 LYS cc_start: 0.9595 (pttt) cc_final: 0.9374 (pttt) REVERT: A 385 MET cc_start: 0.8572 (ttp) cc_final: 0.8111 (ttp) REVERT: A 386 MET cc_start: 0.8708 (ppp) cc_final: 0.8340 (ppp) REVERT: A 420 MET cc_start: 0.8253 (mtm) cc_final: 0.7738 (mtp) REVERT: A 480 ARG cc_start: 0.8829 (mpp80) cc_final: 0.8183 (mtm110) REVERT: A 507 HIS cc_start: 0.8436 (t-90) cc_final: 0.8068 (t70) REVERT: B 18 LEU cc_start: 0.9422 (tp) cc_final: 0.9139 (tp) REVERT: B 34 ASP cc_start: 0.8244 (m-30) cc_final: 0.7776 (m-30) REVERT: B 36 LEU cc_start: 0.9473 (tp) cc_final: 0.9095 (tp) REVERT: B 37 ILE cc_start: 0.9178 (mm) cc_final: 0.8851 (mm) REVERT: B 82 MET cc_start: 0.9457 (ttm) cc_final: 0.9165 (ttm) REVERT: B 92 HIS cc_start: 0.9005 (p90) cc_final: 0.8398 (p-80) REVERT: B 100 GLN cc_start: 0.9155 (mt0) cc_final: 0.8678 (mm-40) REVERT: B 103 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9101 (tp30) REVERT: B 108 LYS cc_start: 0.9249 (pttm) cc_final: 0.8305 (tppt) REVERT: B 131 PHE cc_start: 0.9515 (m-80) cc_final: 0.8564 (m-80) REVERT: B 132 GLU cc_start: 0.9578 (pt0) cc_final: 0.9264 (pt0) REVERT: B 134 LYS cc_start: 0.9456 (pttp) cc_final: 0.9128 (tttp) REVERT: B 185 LEU cc_start: 0.8765 (mt) cc_final: 0.8267 (mp) REVERT: B 192 ILE cc_start: 0.9259 (mt) cc_final: 0.9048 (mt) REVERT: B 242 LYS cc_start: 0.8729 (tttt) cc_final: 0.8375 (tptt) REVERT: B 291 LYS cc_start: 0.9603 (mmmt) cc_final: 0.9070 (tppt) REVERT: B 297 LEU cc_start: 0.9199 (tt) cc_final: 0.8891 (mm) REVERT: B 334 GLN cc_start: 0.9342 (mt0) cc_final: 0.8802 (mm-40) REVERT: B 335 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 355 ARG cc_start: 0.8067 (ppt170) cc_final: 0.7582 (ptm-80) REVERT: B 372 HIS cc_start: 0.8977 (m170) cc_final: 0.8492 (m170) REVERT: B 400 TYR cc_start: 0.7432 (m-80) cc_final: 0.7148 (m-80) REVERT: B 403 SER cc_start: 0.9311 (t) cc_final: 0.9097 (t) REVERT: B 404 ASP cc_start: 0.8518 (t0) cc_final: 0.8282 (t0) REVERT: B 491 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8302 (tm-30) REVERT: C 33 ASN cc_start: 0.8854 (m110) cc_final: 0.8588 (m110) REVERT: C 47 ASP cc_start: 0.9586 (m-30) cc_final: 0.8910 (p0) REVERT: C 78 MET cc_start: 0.9160 (mmm) cc_final: 0.8752 (mmm) REVERT: C 82 MET cc_start: 0.9628 (tpp) cc_final: 0.9368 (tpp) REVERT: C 90 PHE cc_start: 0.9134 (m-80) cc_final: 0.8585 (m-80) REVERT: C 103 GLU cc_start: 0.9641 (mp0) cc_final: 0.9425 (mp0) REVERT: C 229 LYS cc_start: 0.9398 (ptpp) cc_final: 0.9080 (mmmt) REVERT: C 274 ASP cc_start: 0.9071 (t0) cc_final: 0.8614 (t70) REVERT: C 291 LYS cc_start: 0.8862 (ptpp) cc_final: 0.8574 (pttt) REVERT: C 331 CYS cc_start: 0.8985 (t) cc_final: 0.8623 (t) REVERT: C 333 THR cc_start: 0.9727 (p) cc_final: 0.9130 (p) REVERT: C 334 GLN cc_start: 0.9104 (mp10) cc_final: 0.8254 (mp10) REVERT: C 349 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8171 (mtpt) REVERT: C 386 MET cc_start: 0.8867 (tmm) cc_final: 0.8587 (tmm) REVERT: C 399 GLU cc_start: 0.8770 (pp20) cc_final: 0.8526 (pp20) REVERT: C 482 MET cc_start: 0.9351 (tpp) cc_final: 0.8788 (mmm) REVERT: C 493 ARG cc_start: 0.8823 (mtm180) cc_final: 0.8126 (ptp90) REVERT: C 500 GLU cc_start: 0.9156 (pp20) cc_final: 0.8439 (pp20) REVERT: D 12 TYR cc_start: 0.8059 (t80) cc_final: 0.6944 (m-80) REVERT: D 21 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8293 (tm-30) REVERT: D 25 ASN cc_start: 0.8670 (m110) cc_final: 0.8119 (m110) REVERT: D 38 LEU cc_start: 0.9453 (mt) cc_final: 0.9241 (mt) REVERT: D 50 ASP cc_start: 0.8701 (t0) cc_final: 0.8242 (p0) REVERT: D 91 ILE cc_start: 0.9198 (tp) cc_final: 0.8893 (tp) REVERT: D 93 HIS cc_start: 0.9300 (p90) cc_final: 0.8596 (p-80) REVERT: D 144 ILE cc_start: 0.9091 (mm) cc_final: 0.8767 (mp) REVERT: D 179 MET cc_start: 0.5358 (ppp) cc_final: 0.3902 (pmm) REVERT: D 215 ASP cc_start: 0.9548 (m-30) cc_final: 0.8835 (t70) REVERT: D 242 LYS cc_start: 0.9262 (mmpt) cc_final: 0.9006 (mmmt) REVERT: D 243 GLN cc_start: 0.9503 (mt0) cc_final: 0.9011 (mt0) REVERT: D 257 LYS cc_start: 0.9796 (ptpp) cc_final: 0.9497 (mmtm) REVERT: D 281 ILE cc_start: 0.9727 (mm) cc_final: 0.9490 (mm) REVERT: D 286 MET cc_start: 0.9652 (tpt) cc_final: 0.9322 (tpt) REVERT: D 289 TYR cc_start: 0.9410 (t80) cc_final: 0.9033 (t80) REVERT: D 290 ILE cc_start: 0.9739 (pt) cc_final: 0.9399 (pt) REVERT: D 352 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9033 (tm-30) REVERT: D 385 MET cc_start: 0.8411 (tpt) cc_final: 0.7294 (tpt) REVERT: D 386 MET cc_start: 0.8392 (ptp) cc_final: 0.7801 (ptp) REVERT: D 465 GLN cc_start: 0.8595 (pp30) cc_final: 0.8259 (tt0) REVERT: D 468 CYS cc_start: 0.9232 (t) cc_final: 0.8972 (t) REVERT: D 482 MET cc_start: 0.9123 (tpp) cc_final: 0.8835 (tpt) REVERT: O 1 MET cc_start: 0.7916 (mmm) cc_final: 0.7408 (mmp) REVERT: E 21 GLN cc_start: 0.9130 (pm20) cc_final: 0.8913 (pm20) REVERT: E 32 TYR cc_start: 0.9203 (m-80) cc_final: 0.8646 (m-80) REVERT: E 36 LEU cc_start: 0.8633 (tp) cc_final: 0.8154 (tp) REVERT: E 38 LEU cc_start: 0.9548 (mm) cc_final: 0.8948 (mm) REVERT: E 48 GLN cc_start: 0.9276 (mt0) cc_final: 0.8835 (mt0) REVERT: E 105 ARG cc_start: 0.8970 (mmm160) cc_final: 0.8422 (tpm170) REVERT: E 108 LYS cc_start: 0.9443 (tppt) cc_final: 0.8839 (tppt) REVERT: E 150 MET cc_start: 0.7854 (tpt) cc_final: 0.7067 (tpt) REVERT: E 165 PHE cc_start: 0.8266 (p90) cc_final: 0.8001 (p90) REVERT: E 228 LYS cc_start: 0.9517 (ptpp) cc_final: 0.9286 (ptpp) REVERT: E 246 CYS cc_start: 0.9383 (t) cc_final: 0.8638 (p) REVERT: E 250 ILE cc_start: 0.9331 (pt) cc_final: 0.9118 (pt) REVERT: E 254 GLU cc_start: 0.9242 (tp30) cc_final: 0.8965 (pm20) REVERT: E 262 LEU cc_start: 0.9655 (pt) cc_final: 0.9436 (pt) REVERT: E 273 LEU cc_start: 0.9014 (tt) cc_final: 0.8333 (tt) REVERT: E 288 LYS cc_start: 0.9579 (mtmm) cc_final: 0.9280 (mttt) REVERT: E 322 ARG cc_start: 0.8285 (tmm-80) cc_final: 0.7486 (tmm-80) REVERT: E 334 GLN cc_start: 0.9347 (mp10) cc_final: 0.8424 (mp10) REVERT: E 335 GLU cc_start: 0.8735 (mp0) cc_final: 0.8173 (mp0) REVERT: E 341 ARG cc_start: 0.9428 (ptm-80) cc_final: 0.9121 (ptm-80) REVERT: E 352 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8777 (tm-30) REVERT: E 368 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8063 (mm-40) REVERT: E 375 LYS cc_start: 0.9695 (pttt) cc_final: 0.9469 (pttt) REVERT: E 385 MET cc_start: 0.8377 (ttp) cc_final: 0.7505 (ttp) REVERT: E 386 MET cc_start: 0.8444 (ppp) cc_final: 0.8150 (ppp) REVERT: E 390 LEU cc_start: 0.9121 (pt) cc_final: 0.8913 (pt) REVERT: E 420 MET cc_start: 0.8201 (mtm) cc_final: 0.7584 (mtp) REVERT: E 441 GLN cc_start: 0.6891 (pp30) cc_final: 0.6618 (pp30) REVERT: E 450 LYS cc_start: 0.9434 (mttp) cc_final: 0.8931 (mttp) REVERT: E 483 MET cc_start: 0.9684 (tmm) cc_final: 0.9394 (tmm) REVERT: E 496 SER cc_start: 0.9305 (t) cc_final: 0.9066 (p) REVERT: E 507 HIS cc_start: 0.8475 (t-90) cc_final: 0.8167 (t70) REVERT: F 16 ASP cc_start: 0.7289 (t0) cc_final: 0.6420 (t0) REVERT: F 18 LEU cc_start: 0.9364 (tp) cc_final: 0.9058 (tp) REVERT: F 34 ASP cc_start: 0.8241 (m-30) cc_final: 0.7626 (m-30) REVERT: F 37 ILE cc_start: 0.9254 (mm) cc_final: 0.8852 (mm) REVERT: F 70 MET cc_start: 0.7968 (tpp) cc_final: 0.7403 (mmm) REVERT: F 92 HIS cc_start: 0.8761 (p90) cc_final: 0.8402 (p-80) REVERT: F 106 LYS cc_start: 0.9407 (mtpt) cc_final: 0.9203 (mtpt) REVERT: F 108 LYS cc_start: 0.9153 (pttm) cc_final: 0.7894 (tppt) REVERT: F 132 GLU cc_start: 0.9442 (pt0) cc_final: 0.9174 (pt0) REVERT: F 136 ARG cc_start: 0.9289 (mmp-170) cc_final: 0.8974 (ptp-110) REVERT: F 185 LEU cc_start: 0.8902 (mt) cc_final: 0.8420 (mt) REVERT: F 199 GLU cc_start: 0.9544 (mt-10) cc_final: 0.9254 (mt-10) REVERT: F 242 LYS cc_start: 0.8464 (tttt) cc_final: 0.8074 (tptt) REVERT: F 250 ILE cc_start: 0.9280 (mp) cc_final: 0.8955 (tp) REVERT: F 255 ASP cc_start: 0.9367 (p0) cc_final: 0.9127 (p0) REVERT: F 291 LYS cc_start: 0.9530 (mmtt) cc_final: 0.9226 (tppt) REVERT: F 294 TYR cc_start: 0.9412 (m-80) cc_final: 0.9090 (m-80) REVERT: F 322 ARG cc_start: 0.8814 (ttt-90) cc_final: 0.8408 (tpt-90) REVERT: F 334 GLN cc_start: 0.9323 (mt0) cc_final: 0.8982 (mm-40) REVERT: F 337 LEU cc_start: 0.9160 (mm) cc_final: 0.8918 (mm) REVERT: F 349 LYS cc_start: 0.9496 (mmtt) cc_final: 0.9289 (mmmm) REVERT: F 352 GLU cc_start: 0.8790 (pm20) cc_final: 0.8338 (pm20) REVERT: F 372 HIS cc_start: 0.8995 (m170) cc_final: 0.8630 (m90) REVERT: F 400 TYR cc_start: 0.7538 (m-80) cc_final: 0.6760 (m-80) REVERT: F 404 ASP cc_start: 0.8477 (t0) cc_final: 0.8273 (t0) REVERT: F 449 ASP cc_start: 0.8550 (t0) cc_final: 0.8318 (t0) REVERT: F 455 LYS cc_start: 0.9447 (pttp) cc_final: 0.9087 (ptmm) REVERT: F 482 MET cc_start: 0.8746 (ptp) cc_final: 0.8540 (ptp) REVERT: F 491 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8354 (tm-30) REVERT: G 32 TYR cc_start: 0.8622 (m-10) cc_final: 0.8288 (m-10) REVERT: G 47 ASP cc_start: 0.9553 (m-30) cc_final: 0.8928 (p0) REVERT: G 78 MET cc_start: 0.9556 (tpp) cc_final: 0.9072 (tpp) REVERT: G 143 PRO cc_start: 0.7907 (Cg_exo) cc_final: 0.7616 (Cg_endo) REVERT: G 229 LYS cc_start: 0.9376 (ptpp) cc_final: 0.9036 (mmmt) REVERT: G 274 ASP cc_start: 0.8911 (t0) cc_final: 0.8643 (t70) REVERT: G 291 LYS cc_start: 0.8893 (ptpp) cc_final: 0.8607 (pttt) REVERT: G 306 THR cc_start: 0.8997 (t) cc_final: 0.8656 (t) REVERT: G 331 CYS cc_start: 0.9045 (t) cc_final: 0.8570 (t) REVERT: G 333 THR cc_start: 0.9710 (p) cc_final: 0.9117 (p) REVERT: G 334 GLN cc_start: 0.9067 (mp10) cc_final: 0.8292 (mp10) REVERT: G 335 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7949 (tm-30) REVERT: G 336 VAL cc_start: 0.9410 (m) cc_final: 0.8654 (m) REVERT: G 349 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8709 (mtmt) REVERT: G 386 MET cc_start: 0.8773 (tmm) cc_final: 0.8531 (tmm) REVERT: G 395 GLU cc_start: 0.8824 (mp0) cc_final: 0.8539 (mp0) REVERT: G 414 MET cc_start: 0.9204 (pmm) cc_final: 0.8820 (ptp) REVERT: G 482 MET cc_start: 0.9239 (tpp) cc_final: 0.8899 (tpt) REVERT: G 493 ARG cc_start: 0.8895 (mtm180) cc_final: 0.8147 (mtm-85) REVERT: G 500 GLU cc_start: 0.9080 (pp20) cc_final: 0.8529 (pp20) REVERT: H 21 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8427 (tp40) REVERT: H 25 ASN cc_start: 0.8514 (m110) cc_final: 0.7413 (m110) REVERT: H 32 TYR cc_start: 0.9127 (m-80) cc_final: 0.8403 (m-10) REVERT: H 33 ASN cc_start: 0.9236 (t0) cc_final: 0.8812 (t0) REVERT: H 36 LEU cc_start: 0.9242 (pt) cc_final: 0.9038 (pt) REVERT: H 62 LYS cc_start: 0.9300 (mmtt) cc_final: 0.8852 (mtpp) REVERT: H 91 ILE cc_start: 0.9284 (tp) cc_final: 0.9031 (tp) REVERT: H 93 HIS cc_start: 0.8872 (p90) cc_final: 0.8371 (p-80) REVERT: H 108 LYS cc_start: 0.9070 (tptm) cc_final: 0.8641 (tptp) REVERT: H 112 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8799 (tm-30) REVERT: H 158 ILE cc_start: 0.8100 (tp) cc_final: 0.7799 (tp) REVERT: H 179 MET cc_start: 0.6712 (ppp) cc_final: 0.6115 (ppp) REVERT: H 209 LEU cc_start: 0.9001 (tp) cc_final: 0.8713 (pp) REVERT: H 215 ASP cc_start: 0.9437 (m-30) cc_final: 0.9039 (p0) REVERT: H 229 LYS cc_start: 0.8902 (pttt) cc_final: 0.8661 (mmtt) REVERT: H 242 LYS cc_start: 0.9376 (mmpt) cc_final: 0.9162 (mmmt) REVERT: H 286 MET cc_start: 0.9656 (tpt) cc_final: 0.9167 (tpt) REVERT: H 290 ILE cc_start: 0.9724 (pt) cc_final: 0.9391 (pt) REVERT: H 311 LYS cc_start: 0.9170 (ttpt) cc_final: 0.8894 (tmmt) REVERT: H 315 ASP cc_start: 0.9185 (m-30) cc_final: 0.8660 (p0) REVERT: H 349 LYS cc_start: 0.9640 (mmtp) cc_final: 0.9385 (mmtp) REVERT: H 352 GLU cc_start: 0.9381 (tm-30) cc_final: 0.8993 (tm-30) REVERT: H 368 GLN cc_start: 0.8706 (mt0) cc_final: 0.8202 (mm-40) REVERT: H 385 MET cc_start: 0.8155 (tpt) cc_final: 0.7578 (tpt) REVERT: H 410 LYS cc_start: 0.8852 (mptt) cc_final: 0.8641 (mmtm) REVERT: H 414 MET cc_start: 0.8475 (pmm) cc_final: 0.8273 (pmm) REVERT: H 453 ILE cc_start: 0.9543 (pt) cc_final: 0.9108 (pt) REVERT: H 465 GLN cc_start: 0.8589 (pp30) cc_final: 0.8355 (tt0) REVERT: H 468 CYS cc_start: 0.9094 (t) cc_final: 0.8791 (t) REVERT: H 478 GLN cc_start: 0.9599 (tt0) cc_final: 0.9175 (tt0) REVERT: H 487 GLU cc_start: 0.8939 (pm20) cc_final: 0.8735 (pm20) REVERT: H 491 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7791 (tm-30) REVERT: H 492 LYS cc_start: 0.9035 (pttt) cc_final: 0.8803 (pttp) outliers start: 0 outliers final: 0 residues processed: 1433 average time/residue: 0.1980 time to fit residues: 462.1274 Evaluate side-chains 1216 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1216 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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: 3.9990 chunk 342 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 380 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 174 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 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 454 HIS A 466 HIS B 100 GLN ** 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 368 GLN D 33 ASN ** 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 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 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** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.091637 restraints weight = 73479.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095567 restraints weight = 41464.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098461 restraints weight = 27374.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100416 restraints weight = 19872.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101603 restraints weight = 15649.146| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32220 Z= 0.154 Angle : 0.871 12.850 43712 Z= 0.432 Chirality : 0.053 0.440 4984 Planarity : 0.005 0.106 5452 Dihedral : 14.905 167.757 5344 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.39 % Favored : 91.58 % Rotamer: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % 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 aren not related in a simple way. whole: -2.68 (0.13), residues: 3968 helix: -1.59 (0.13), residues: 1226 sheet: -2.57 (0.21), residues: 456 loop : -1.70 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 322 TYR 0.039 0.002 TYR E 110 PHE 0.031 0.002 PHE A 456 HIS 0.009 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00349 (32212) covalent geometry : angle 0.87064 (43712) hydrogen bonds : bond 0.04215 ( 966) hydrogen bonds : angle 6.42735 ( 2655) Misc. bond : bond 0.00156 ( 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 1407 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1406 time to evaluate : 1.225 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: A 28 ASP cc_start: 0.9041 (t70) cc_final: 0.8561 (t70) REVERT: A 32 TYR cc_start: 0.8804 (m-10) cc_final: 0.8457 (m-10) REVERT: A 36 LEU cc_start: 0.8549 (tp) cc_final: 0.8057 (tp) REVERT: A 38 LEU cc_start: 0.9571 (mm) cc_final: 0.8885 (mm) REVERT: A 48 GLN cc_start: 0.9205 (mt0) cc_final: 0.8792 (mt0) REVERT: A 108 LYS cc_start: 0.9572 (tptp) cc_final: 0.9344 (tppt) REVERT: A 150 MET cc_start: 0.7865 (tpt) cc_final: 0.7314 (tpt) REVERT: A 158 ILE cc_start: 0.9102 (mm) cc_final: 0.8685 (tp) REVERT: A 165 PHE cc_start: 0.8426 (p90) cc_final: 0.8177 (p90) REVERT: A 246 CYS cc_start: 0.9383 (t) cc_final: 0.8805 (p) REVERT: A 262 LEU cc_start: 0.9575 (pt) cc_final: 0.9273 (pp) REVERT: A 273 LEU cc_start: 0.9585 (tp) cc_final: 0.9206 (tp) REVERT: A 319 ASP cc_start: 0.7835 (t70) cc_final: 0.7610 (t70) REVERT: A 322 ARG cc_start: 0.8385 (tmm-80) cc_final: 0.7417 (tmm-80) REVERT: A 325 MET cc_start: 0.8801 (ptm) cc_final: 0.8353 (ptm) REVERT: A 332 ILE cc_start: 0.9301 (pt) cc_final: 0.8895 (pt) REVERT: A 334 GLN cc_start: 0.9291 (mp10) cc_final: 0.8372 (mp10) REVERT: A 335 GLU cc_start: 0.8556 (mp0) cc_final: 0.7707 (mp0) REVERT: A 343 GLN cc_start: 0.8045 (pp30) cc_final: 0.7412 (pp30) REVERT: A 352 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 353 TYR cc_start: 0.8954 (t80) cc_final: 0.8718 (t80) REVERT: A 386 MET cc_start: 0.8711 (ppp) cc_final: 0.8406 (ppp) REVERT: A 420 MET cc_start: 0.8231 (mtm) cc_final: 0.7704 (mtp) REVERT: A 480 ARG cc_start: 0.8860 (mpp80) cc_final: 0.8300 (mtm110) REVERT: A 483 MET cc_start: 0.9699 (tmm) cc_final: 0.9483 (tmm) REVERT: A 496 SER cc_start: 0.9222 (t) cc_final: 0.8721 (t) REVERT: A 507 HIS cc_start: 0.8429 (t-90) cc_final: 0.8063 (t70) REVERT: B 18 LEU cc_start: 0.9453 (tp) cc_final: 0.9158 (tp) REVERT: B 31 THR cc_start: 0.8336 (m) cc_final: 0.7889 (m) REVERT: B 34 ASP cc_start: 0.8264 (m-30) cc_final: 0.7969 (m-30) REVERT: B 37 ILE cc_start: 0.9221 (mm) cc_final: 0.8883 (mm) REVERT: B 42 ILE cc_start: 0.9246 (pt) cc_final: 0.9035 (pt) REVERT: B 82 MET cc_start: 0.9427 (ttm) cc_final: 0.9128 (ttm) REVERT: B 92 HIS cc_start: 0.9140 (p90) cc_final: 0.8668 (p-80) REVERT: B 106 LYS cc_start: 0.9377 (mtpt) cc_final: 0.9175 (mtpt) REVERT: B 108 LYS cc_start: 0.9157 (pttm) cc_final: 0.8286 (tppt) REVERT: B 131 PHE cc_start: 0.9543 (m-80) cc_final: 0.8543 (m-80) REVERT: B 132 GLU cc_start: 0.9578 (pt0) cc_final: 0.9265 (pt0) REVERT: B 134 LYS cc_start: 0.9461 (pttp) cc_final: 0.9142 (tttt) REVERT: B 185 LEU cc_start: 0.8767 (mt) cc_final: 0.8268 (mt) REVERT: B 242 LYS cc_start: 0.8699 (tttt) cc_final: 0.8393 (tptt) REVERT: B 250 ILE cc_start: 0.9377 (mp) cc_final: 0.9107 (tp) REVERT: B 291 LYS cc_start: 0.9586 (mmmt) cc_final: 0.9048 (tppt) REVERT: B 297 LEU cc_start: 0.9163 (tt) cc_final: 0.8802 (mm) REVERT: B 334 GLN cc_start: 0.9289 (mt0) cc_final: 0.8686 (mm-40) REVERT: B 348 TYR cc_start: 0.9215 (t80) cc_final: 0.8454 (t80) REVERT: B 372 HIS cc_start: 0.8993 (m170) cc_final: 0.8540 (m90) REVERT: B 400 TYR cc_start: 0.7469 (m-80) cc_final: 0.7218 (m-80) REVERT: B 403 SER cc_start: 0.9268 (t) cc_final: 0.9050 (t) REVERT: B 404 ASP cc_start: 0.8521 (t0) cc_final: 0.8315 (t0) REVERT: B 414 MET cc_start: 0.8769 (mpp) cc_final: 0.8568 (mpp) REVERT: B 487 GLU cc_start: 0.8578 (pp20) cc_final: 0.8255 (pp20) REVERT: B 491 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 493 ARG cc_start: 0.8874 (ptt-90) cc_final: 0.8345 (ptt-90) REVERT: B 513 LEU cc_start: 0.9581 (mm) cc_final: 0.9223 (mm) REVERT: C 47 ASP cc_start: 0.9582 (m-30) cc_final: 0.8918 (p0) REVERT: C 74 THR cc_start: 0.7080 (t) cc_final: 0.6792 (t) REVERT: C 78 MET cc_start: 0.9166 (mmm) cc_final: 0.8786 (mmm) REVERT: C 82 MET cc_start: 0.9627 (tpp) cc_final: 0.9350 (tpp) REVERT: C 90 PHE cc_start: 0.9173 (m-80) cc_final: 0.8522 (m-80) REVERT: C 160 SER cc_start: 0.8672 (t) cc_final: 0.8264 (p) REVERT: C 229 LYS cc_start: 0.9394 (ptpp) cc_final: 0.9055 (mmmt) REVERT: C 274 ASP cc_start: 0.9058 (t0) cc_final: 0.8605 (t70) REVERT: C 289 TYR cc_start: 0.9185 (t80) cc_final: 0.8763 (t80) REVERT: C 331 CYS cc_start: 0.9068 (t) cc_final: 0.8717 (t) REVERT: C 333 THR cc_start: 0.9720 (p) cc_final: 0.9107 (p) REVERT: C 334 GLN cc_start: 0.9109 (mp10) cc_final: 0.8243 (mp10) REVERT: C 335 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7961 (tm-30) REVERT: C 482 MET cc_start: 0.9333 (tpp) cc_final: 0.8775 (tpp) REVERT: C 493 ARG cc_start: 0.8858 (mtm180) cc_final: 0.8031 (mtm-85) REVERT: C 500 GLU cc_start: 0.9180 (pp20) cc_final: 0.8463 (pp20) REVERT: D 12 TYR cc_start: 0.8072 (t80) cc_final: 0.6942 (m-80) REVERT: D 21 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8306 (tm-30) REVERT: D 25 ASN cc_start: 0.8690 (m110) cc_final: 0.8147 (m110) REVERT: D 33 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.7899 (t0) REVERT: D 38 LEU cc_start: 0.9441 (mt) cc_final: 0.9225 (mt) REVERT: D 50 ASP cc_start: 0.8597 (t0) cc_final: 0.8231 (p0) REVERT: D 91 ILE cc_start: 0.9162 (tp) cc_final: 0.8854 (tp) REVERT: D 93 HIS cc_start: 0.9059 (p90) cc_final: 0.8502 (p-80) REVERT: D 144 ILE cc_start: 0.9053 (mm) cc_final: 0.8745 (mp) REVERT: D 179 MET cc_start: 0.5328 (ppp) cc_final: 0.3723 (pmm) REVERT: D 215 ASP cc_start: 0.9561 (m-30) cc_final: 0.8857 (t70) REVERT: D 242 LYS cc_start: 0.9249 (mmpt) cc_final: 0.8981 (mmmt) REVERT: D 243 GLN cc_start: 0.9532 (mt0) cc_final: 0.9081 (mt0) REVERT: D 257 LYS cc_start: 0.9795 (ptpp) cc_final: 0.9502 (mmtm) REVERT: D 286 MET cc_start: 0.9640 (tpt) cc_final: 0.9313 (tpt) REVERT: D 289 TYR cc_start: 0.9367 (t80) cc_final: 0.9006 (t80) REVERT: D 290 ILE cc_start: 0.9743 (pt) cc_final: 0.9410 (pt) REVERT: D 352 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9018 (tm-30) REVERT: D 379 LEU cc_start: 0.9504 (mm) cc_final: 0.9294 (mm) REVERT: D 385 MET cc_start: 0.8514 (tpt) cc_final: 0.7304 (tpt) REVERT: D 386 MET cc_start: 0.8501 (ptp) cc_final: 0.7787 (ptp) REVERT: D 400 TYR cc_start: 0.6585 (m-80) cc_final: 0.6346 (m-80) REVERT: D 465 GLN cc_start: 0.8598 (pp30) cc_final: 0.8316 (tt0) REVERT: D 468 CYS cc_start: 0.9184 (t) cc_final: 0.8857 (t) REVERT: D 478 GLN cc_start: 0.9615 (tt0) cc_final: 0.9303 (tt0) REVERT: D 482 MET cc_start: 0.9065 (tpp) cc_final: 0.8839 (tpt) REVERT: D 498 GLN cc_start: 0.9023 (mt0) cc_final: 0.8435 (mm-40) REVERT: O 1 MET cc_start: 0.7941 (mmm) cc_final: 0.7456 (mmp) REVERT: P 1 MET cc_start: 0.8403 (pmm) cc_final: 0.8098 (pmm) REVERT: E 21 GLN cc_start: 0.9162 (pm20) cc_final: 0.8923 (pm20) REVERT: E 32 TYR cc_start: 0.9199 (m-80) cc_final: 0.8669 (m-80) REVERT: E 36 LEU cc_start: 0.8689 (tp) cc_final: 0.8408 (tp) REVERT: E 38 LEU cc_start: 0.9571 (mm) cc_final: 0.8864 (mm) REVERT: E 48 GLN cc_start: 0.9262 (mt0) cc_final: 0.8835 (mt0) REVERT: E 100 GLN cc_start: 0.9432 (mp10) cc_final: 0.9154 (mp10) REVERT: E 105 ARG cc_start: 0.8968 (mmm160) cc_final: 0.8401 (tpm170) REVERT: E 108 LYS cc_start: 0.9437 (tppt) cc_final: 0.9149 (tppt) REVERT: E 137 HIS cc_start: 0.9477 (m90) cc_final: 0.8641 (m90) REVERT: E 150 MET cc_start: 0.7847 (tpt) cc_final: 0.7065 (tpt) REVERT: E 165 PHE cc_start: 0.8324 (p90) cc_final: 0.8088 (p90) REVERT: E 228 LYS cc_start: 0.9512 (ptpp) cc_final: 0.9288 (ptpp) REVERT: E 246 CYS cc_start: 0.9366 (t) cc_final: 0.8561 (p) REVERT: E 250 ILE cc_start: 0.9351 (pt) cc_final: 0.9139 (pt) REVERT: E 254 GLU cc_start: 0.9232 (tp30) cc_final: 0.8972 (pm20) REVERT: E 262 LEU cc_start: 0.9666 (pt) cc_final: 0.9435 (pt) REVERT: E 288 LYS cc_start: 0.9584 (mtmm) cc_final: 0.9282 (mttt) REVERT: E 322 ARG cc_start: 0.8347 (tmm-80) cc_final: 0.7506 (tmm-80) REVERT: E 332 ILE cc_start: 0.9350 (pt) cc_final: 0.9001 (pt) REVERT: E 334 GLN cc_start: 0.9363 (mp10) cc_final: 0.8390 (mp10) REVERT: E 335 GLU cc_start: 0.8738 (mp0) cc_final: 0.7906 (mp0) REVERT: E 341 ARG cc_start: 0.9423 (ptm-80) cc_final: 0.8991 (ptm-80) REVERT: E 352 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8833 (tm-30) REVERT: E 368 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8004 (mm-40) REVERT: E 375 LYS cc_start: 0.9696 (pttt) cc_final: 0.9488 (pttt) REVERT: E 385 MET cc_start: 0.8434 (ttp) cc_final: 0.7670 (ttp) REVERT: E 420 MET cc_start: 0.8209 (mtm) cc_final: 0.7571 (mtp) REVERT: E 441 GLN cc_start: 0.6855 (pp30) cc_final: 0.6583 (pp30) REVERT: E 450 LYS cc_start: 0.9432 (mttp) cc_final: 0.8934 (mttp) REVERT: E 483 MET cc_start: 0.9696 (tmm) cc_final: 0.9459 (tmm) REVERT: E 496 SER cc_start: 0.9296 (t) cc_final: 0.9043 (p) REVERT: E 507 HIS cc_start: 0.8486 (t-90) cc_final: 0.8182 (t70) REVERT: F 16 ASP cc_start: 0.7281 (t0) cc_final: 0.6389 (t0) REVERT: F 18 LEU cc_start: 0.9373 (tp) cc_final: 0.9088 (tp) REVERT: F 31 THR cc_start: 0.8235 (m) cc_final: 0.7754 (m) REVERT: F 34 ASP cc_start: 0.8294 (m-30) cc_final: 0.8061 (m-30) REVERT: F 37 ILE cc_start: 0.9208 (mm) cc_final: 0.8847 (mm) REVERT: F 70 MET cc_start: 0.8102 (tpp) cc_final: 0.7410 (tpp) REVERT: F 82 MET cc_start: 0.9356 (ttp) cc_final: 0.8951 (tmm) REVERT: F 92 HIS cc_start: 0.8857 (p90) cc_final: 0.8424 (p-80) REVERT: F 106 LYS cc_start: 0.9404 (mtpt) cc_final: 0.9133 (mtpt) REVERT: F 108 LYS cc_start: 0.9036 (pttm) cc_final: 0.7870 (tppt) REVERT: F 132 GLU cc_start: 0.9452 (pt0) cc_final: 0.9229 (pt0) REVERT: F 136 ARG cc_start: 0.9241 (mmp-170) cc_final: 0.8932 (ptp-110) REVERT: F 179 MET cc_start: 0.6982 (tmm) cc_final: 0.6728 (tmm) REVERT: F 185 LEU cc_start: 0.8877 (mt) cc_final: 0.8361 (mt) REVERT: F 200 ILE cc_start: 0.9731 (mm) cc_final: 0.9419 (mm) REVERT: F 238 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8362 (tppt) REVERT: F 242 LYS cc_start: 0.8456 (tttt) cc_final: 0.8140 (tptt) REVERT: F 250 ILE cc_start: 0.9408 (mp) cc_final: 0.9078 (tp) REVERT: F 291 LYS cc_start: 0.9532 (mmtt) cc_final: 0.9224 (tppt) REVERT: F 322 ARG cc_start: 0.8795 (ttt-90) cc_final: 0.8214 (tpt-90) REVERT: F 334 GLN cc_start: 0.9251 (mt0) cc_final: 0.8862 (mm-40) REVERT: F 343 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7717 (tm-30) REVERT: F 348 TYR cc_start: 0.9228 (t80) cc_final: 0.8850 (t80) REVERT: F 352 GLU cc_start: 0.8696 (pm20) cc_final: 0.8373 (pm20) REVERT: F 364 ASP cc_start: 0.6881 (m-30) cc_final: 0.5835 (m-30) REVERT: F 372 HIS cc_start: 0.8938 (m170) cc_final: 0.8589 (m170) REVERT: F 385 MET cc_start: 0.7853 (ttp) cc_final: 0.7101 (ptm) REVERT: F 400 TYR cc_start: 0.7542 (m-80) cc_final: 0.6889 (m-80) REVERT: F 455 LYS cc_start: 0.9419 (pttp) cc_final: 0.9024 (ptmm) REVERT: F 482 MET cc_start: 0.8734 (ptp) cc_final: 0.8482 (ptp) REVERT: F 491 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8433 (tm-30) REVERT: F 493 ARG cc_start: 0.8878 (ptt-90) cc_final: 0.8284 (ptt-90) REVERT: F 494 THR cc_start: 0.9033 (p) cc_final: 0.8583 (p) REVERT: G 47 ASP cc_start: 0.9561 (m-30) cc_final: 0.8911 (p0) REVERT: G 78 MET cc_start: 0.9547 (tpp) cc_final: 0.9059 (tpp) REVERT: G 140 CYS cc_start: 0.4237 (m) cc_final: 0.4001 (m) REVERT: G 143 PRO cc_start: 0.8020 (Cg_exo) cc_final: 0.7730 (Cg_endo) REVERT: G 199 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8976 (mt-10) REVERT: G 209 LEU cc_start: 0.7925 (mm) cc_final: 0.7716 (mm) REVERT: G 222 ILE cc_start: 0.7404 (mm) cc_final: 0.7097 (mm) REVERT: G 229 LYS cc_start: 0.9379 (ptpp) cc_final: 0.9038 (mmmt) REVERT: G 262 LEU cc_start: 0.9425 (pp) cc_final: 0.9054 (pp) REVERT: G 274 ASP cc_start: 0.8878 (t0) cc_final: 0.8565 (t70) REVERT: G 291 LYS cc_start: 0.8900 (ptpp) cc_final: 0.8545 (pttt) REVERT: G 306 THR cc_start: 0.8986 (t) cc_final: 0.8560 (t) REVERT: G 331 CYS cc_start: 0.8932 (t) cc_final: 0.8412 (t) REVERT: G 333 THR cc_start: 0.9711 (p) cc_final: 0.9074 (p) REVERT: G 334 GLN cc_start: 0.9093 (mp10) cc_final: 0.8253 (mp10) REVERT: G 335 GLU cc_start: 0.8545 (tm-30) cc_final: 0.7964 (tm-30) REVERT: G 336 VAL cc_start: 0.9387 (m) cc_final: 0.8644 (m) REVERT: G 349 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8729 (mtmt) REVERT: G 386 MET cc_start: 0.8777 (tmm) cc_final: 0.8507 (tmm) REVERT: G 395 GLU cc_start: 0.8839 (mp0) cc_final: 0.8564 (mp0) REVERT: G 414 MET cc_start: 0.9227 (pmm) cc_final: 0.8713 (ptt) REVERT: G 482 MET cc_start: 0.9247 (tpp) cc_final: 0.8854 (mmm) REVERT: G 493 ARG cc_start: 0.8912 (mtm180) cc_final: 0.8584 (ptp90) REVERT: G 500 GLU cc_start: 0.9023 (pp20) cc_final: 0.8192 (pp20) REVERT: G 504 HIS cc_start: 0.8381 (p90) cc_final: 0.7597 (p90) REVERT: H 16 ASP cc_start: 0.8054 (m-30) cc_final: 0.7852 (m-30) REVERT: H 21 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8155 (tm-30) REVERT: H 25 ASN cc_start: 0.8548 (m110) cc_final: 0.8037 (m110) REVERT: H 32 TYR cc_start: 0.9042 (m-80) cc_final: 0.8301 (m-10) REVERT: H 33 ASN cc_start: 0.9222 (t0) cc_final: 0.8645 (t0) REVERT: H 62 LYS cc_start: 0.9264 (mmtt) cc_final: 0.8820 (mtpp) REVERT: H 91 ILE cc_start: 0.9313 (tp) cc_final: 0.9088 (tp) REVERT: H 93 HIS cc_start: 0.8887 (p90) cc_final: 0.8387 (p90) REVERT: H 108 LYS cc_start: 0.9079 (tptm) cc_final: 0.8743 (tptp) REVERT: H 158 ILE cc_start: 0.8229 (tp) cc_final: 0.7930 (tp) REVERT: H 179 MET cc_start: 0.6357 (ppp) cc_final: 0.5733 (ppp) REVERT: H 209 LEU cc_start: 0.8997 (tp) cc_final: 0.8714 (pp) REVERT: H 215 ASP cc_start: 0.9420 (m-30) cc_final: 0.8780 (t70) REVERT: H 229 LYS cc_start: 0.8895 (pttt) cc_final: 0.8629 (mmtt) REVERT: H 242 LYS cc_start: 0.9375 (mmpt) cc_final: 0.9162 (mmmt) REVERT: H 286 MET cc_start: 0.9645 (tpt) cc_final: 0.9162 (tpt) REVERT: H 290 ILE cc_start: 0.9720 (pt) cc_final: 0.9385 (pt) REVERT: H 311 LYS cc_start: 0.9143 (ttpt) cc_final: 0.8901 (tmmt) REVERT: H 315 ASP cc_start: 0.9200 (m-30) cc_final: 0.8657 (p0) REVERT: H 349 LYS cc_start: 0.9655 (mmtp) cc_final: 0.9396 (mmtp) REVERT: H 352 GLU cc_start: 0.9392 (tm-30) cc_final: 0.8998 (tm-30) REVERT: H 368 GLN cc_start: 0.8719 (mt0) cc_final: 0.8262 (mm-40) REVERT: H 375 LYS cc_start: 0.9368 (ptmt) cc_final: 0.9037 (ptmt) REVERT: H 385 MET cc_start: 0.8451 (tpt) cc_final: 0.8170 (tpt) REVERT: H 386 MET cc_start: 0.7406 (ptm) cc_final: 0.6815 (ppp) REVERT: H 410 LYS cc_start: 0.8711 (mptt) cc_final: 0.8503 (mmtm) REVERT: H 465 GLN cc_start: 0.8603 (pp30) cc_final: 0.8368 (tt0) REVERT: H 468 CYS cc_start: 0.9079 (t) cc_final: 0.8773 (t) REVERT: H 478 GLN cc_start: 0.9601 (tt0) cc_final: 0.9200 (tt0) REVERT: H 491 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7768 (tm-30) REVERT: H 492 LYS cc_start: 0.9067 (pttt) cc_final: 0.8765 (pttm) REVERT: J 11 SER cc_start: 0.8077 (p) cc_final: 0.7743 (p) REVERT: J 12 TYR cc_start: 0.8765 (t80) cc_final: 0.8435 (t80) REVERT: L 1 MET cc_start: 0.8240 (pmm) cc_final: 0.7992 (pmm) outliers start: 1 outliers final: 0 residues processed: 1406 average time/residue: 0.1974 time to fit residues: 451.8318 Evaluate side-chains 1203 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1202 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 0.2980 chunk 114 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 372 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 187 optimal weight: 0.2980 chunk 249 optimal weight: 0.0970 chunk 390 optimal weight: 6.9990 chunk 326 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 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 448 GLN A 454 HIS 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 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** 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 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS E 466 HIS ** E 504 HIS ** 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 213 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS H 112 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** 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 = 0.3789 r_free = 0.3789 target = 0.129643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092596 restraints weight = 73184.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.096619 restraints weight = 41361.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099455 restraints weight = 27359.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101440 restraints weight = 19992.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102790 restraints weight = 15710.010| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32220 Z= 0.151 Angle : 0.878 13.702 43712 Z= 0.436 Chirality : 0.053 0.412 4984 Planarity : 0.005 0.108 5452 Dihedral : 14.511 166.027 5344 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.59 % Favored : 91.38 % Rotamer: Outliers : 0.06 % Allowed : 0.46 % Favored : 99.48 % 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 aren not related in a simple way. whole: -2.68 (0.13), residues: 3968 helix: -1.66 (0.13), residues: 1248 sheet: -2.59 (0.21), residues: 458 loop : -1.64 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 203 TYR 0.038 0.002 TYR A 110 PHE 0.030 0.002 PHE E 456 HIS 0.009 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00341 (32212) covalent geometry : angle 0.87802 (43712) hydrogen bonds : bond 0.04338 ( 966) hydrogen bonds : angle 6.45875 ( 2655) Misc. bond : bond 0.00194 ( 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 1416 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1414 time to evaluate : 1.036 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: A 12 TYR cc_start: 0.7784 (t80) cc_final: 0.6620 (m-80) REVERT: A 28 ASP cc_start: 0.9031 (t70) cc_final: 0.8592 (t70) REVERT: A 32 TYR cc_start: 0.8756 (m-10) cc_final: 0.8310 (m-10) REVERT: A 36 LEU cc_start: 0.8620 (tp) cc_final: 0.8315 (tp) REVERT: A 38 LEU cc_start: 0.9560 (mm) cc_final: 0.8895 (mm) REVERT: A 48 GLN cc_start: 0.9189 (mt0) cc_final: 0.8769 (mt0) REVERT: A 150 MET cc_start: 0.7857 (tpt) cc_final: 0.7308 (tpt) REVERT: A 158 ILE cc_start: 0.9057 (mm) cc_final: 0.8641 (tp) REVERT: A 179 MET cc_start: 0.7447 (pmm) cc_final: 0.7199 (pmm) REVERT: A 246 CYS cc_start: 0.9342 (t) cc_final: 0.8841 (p) REVERT: A 273 LEU cc_start: 0.9550 (tp) cc_final: 0.9146 (tp) REVERT: A 291 LYS cc_start: 0.9484 (tppt) cc_final: 0.9272 (tptp) REVERT: A 322 ARG cc_start: 0.8341 (tmm-80) cc_final: 0.7385 (tmm-80) REVERT: A 325 MET cc_start: 0.8354 (ptm) cc_final: 0.7951 (ptm) REVERT: A 335 GLU cc_start: 0.8657 (mp0) cc_final: 0.8258 (mp0) REVERT: A 343 GLN cc_start: 0.7916 (pp30) cc_final: 0.7207 (pp30) REVERT: A 352 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8671 (tm-30) REVERT: A 353 TYR cc_start: 0.8963 (t80) cc_final: 0.8757 (t80) REVERT: A 385 MET cc_start: 0.8582 (ttp) cc_final: 0.8122 (ttp) REVERT: A 386 MET cc_start: 0.8539 (ppp) cc_final: 0.8196 (tmm) REVERT: A 420 MET cc_start: 0.8203 (mtm) cc_final: 0.7682 (mtp) REVERT: A 480 ARG cc_start: 0.8881 (mpp80) cc_final: 0.8335 (mtm110) REVERT: A 483 MET cc_start: 0.9698 (tmm) cc_final: 0.9430 (tmm) REVERT: A 496 SER cc_start: 0.9175 (t) cc_final: 0.8717 (t) REVERT: A 507 HIS cc_start: 0.8380 (t-90) cc_final: 0.8022 (t70) REVERT: B 16 ASP cc_start: 0.7567 (t0) cc_final: 0.6335 (t0) REVERT: B 18 LEU cc_start: 0.9391 (tp) cc_final: 0.9076 (tp) REVERT: B 31 THR cc_start: 0.8284 (m) cc_final: 0.7747 (m) REVERT: B 32 TYR cc_start: 0.8099 (m-10) cc_final: 0.7843 (m-10) REVERT: B 34 ASP cc_start: 0.8235 (m-30) cc_final: 0.7903 (m-30) REVERT: B 37 ILE cc_start: 0.9006 (mm) cc_final: 0.8661 (mm) REVERT: B 70 MET cc_start: 0.8521 (tpt) cc_final: 0.8115 (mmm) REVERT: B 82 MET cc_start: 0.9412 (ttm) cc_final: 0.9114 (ttm) REVERT: B 91 ILE cc_start: 0.9272 (mm) cc_final: 0.8952 (mm) REVERT: B 92 HIS cc_start: 0.9027 (p90) cc_final: 0.8245 (p-80) REVERT: B 100 GLN cc_start: 0.9159 (mt0) cc_final: 0.8766 (mm-40) REVERT: B 108 LYS cc_start: 0.9125 (pttm) cc_final: 0.8248 (tppt) REVERT: B 131 PHE cc_start: 0.9544 (m-80) cc_final: 0.8942 (m-80) REVERT: B 132 GLU cc_start: 0.9568 (pt0) cc_final: 0.9296 (pt0) REVERT: B 134 LYS cc_start: 0.9472 (pttp) cc_final: 0.9198 (pttp) REVERT: B 185 LEU cc_start: 0.8795 (mt) cc_final: 0.8289 (mt) REVERT: B 242 LYS cc_start: 0.8674 (tttt) cc_final: 0.8345 (tptt) REVERT: B 250 ILE cc_start: 0.9334 (mp) cc_final: 0.9071 (tp) REVERT: B 291 LYS cc_start: 0.9585 (mmmt) cc_final: 0.9036 (tppt) REVERT: B 322 ARG cc_start: 0.8768 (ttt90) cc_final: 0.8003 (tpt-90) REVERT: B 334 GLN cc_start: 0.9256 (mt0) cc_final: 0.8876 (mm-40) REVERT: B 348 TYR cc_start: 0.9271 (t80) cc_final: 0.8420 (t80) REVERT: B 372 HIS cc_start: 0.8984 (m170) cc_final: 0.8579 (m90) REVERT: B 400 TYR cc_start: 0.7488 (m-80) cc_final: 0.7179 (m-80) REVERT: B 403 SER cc_start: 0.9231 (t) cc_final: 0.9012 (t) REVERT: B 404 ASP cc_start: 0.8519 (t0) cc_final: 0.8312 (t0) REVERT: B 487 GLU cc_start: 0.8594 (pp20) cc_final: 0.8304 (pp20) REVERT: B 491 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8212 (tm-30) REVERT: B 493 ARG cc_start: 0.8845 (ptt-90) cc_final: 0.8243 (ptt-90) REVERT: B 494 THR cc_start: 0.9131 (p) cc_final: 0.8905 (p) REVERT: C 47 ASP cc_start: 0.9576 (m-30) cc_final: 0.8911 (p0) REVERT: C 74 THR cc_start: 0.6984 (t) cc_final: 0.6783 (t) REVERT: C 78 MET cc_start: 0.9134 (mmm) cc_final: 0.8761 (mmm) REVERT: C 82 MET cc_start: 0.9609 (tpp) cc_final: 0.9363 (tpp) REVERT: C 90 PHE cc_start: 0.9159 (m-80) cc_final: 0.8475 (m-80) REVERT: C 229 LYS cc_start: 0.9398 (ptpp) cc_final: 0.9095 (mmmt) REVERT: C 274 ASP cc_start: 0.9126 (t0) cc_final: 0.8505 (t70) REVERT: C 289 TYR cc_start: 0.9109 (t80) cc_final: 0.8813 (t80) REVERT: C 306 THR cc_start: 0.9136 (t) cc_final: 0.8877 (t) REVERT: C 331 CYS cc_start: 0.9052 (t) cc_final: 0.8620 (t) REVERT: C 333 THR cc_start: 0.9734 (p) cc_final: 0.9101 (p) REVERT: C 334 GLN cc_start: 0.9076 (mp10) cc_final: 0.8238 (mp10) REVERT: C 335 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8007 (tm-30) REVERT: C 349 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8007 (mtmm) REVERT: C 353 TYR cc_start: 0.8821 (t80) cc_final: 0.8262 (t80) REVERT: C 386 MET cc_start: 0.8859 (tmm) cc_final: 0.8450 (tmm) REVERT: C 482 MET cc_start: 0.9339 (tpp) cc_final: 0.8802 (tpt) REVERT: C 493 ARG cc_start: 0.8818 (mtm180) cc_final: 0.8584 (ptp90) REVERT: C 500 GLU cc_start: 0.9101 (pp20) cc_final: 0.8388 (pp20) REVERT: D 12 TYR cc_start: 0.7957 (t80) cc_final: 0.6896 (m-80) REVERT: D 21 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8094 (tm-30) REVERT: D 25 ASN cc_start: 0.8707 (m110) cc_final: 0.8119 (m110) REVERT: D 33 ASN cc_start: 0.8889 (t0) cc_final: 0.8537 (t0) REVERT: D 38 LEU cc_start: 0.9322 (mt) cc_final: 0.9119 (mt) REVERT: D 91 ILE cc_start: 0.9149 (tp) cc_final: 0.8837 (tp) REVERT: D 93 HIS cc_start: 0.8958 (p90) cc_final: 0.8583 (p-80) REVERT: D 144 ILE cc_start: 0.9039 (mm) cc_final: 0.8718 (mp) REVERT: D 179 MET cc_start: 0.5395 (ppp) cc_final: 0.3513 (pmm) REVERT: D 215 ASP cc_start: 0.9491 (m-30) cc_final: 0.8754 (t70) REVERT: D 242 LYS cc_start: 0.9236 (mmpt) cc_final: 0.8962 (mmmt) REVERT: D 243 GLN cc_start: 0.9515 (mt0) cc_final: 0.9192 (mt0) REVERT: D 257 LYS cc_start: 0.9793 (ptpp) cc_final: 0.9503 (mmtm) REVERT: D 281 ILE cc_start: 0.9663 (mm) cc_final: 0.9428 (mm) REVERT: D 286 MET cc_start: 0.9649 (tpt) cc_final: 0.9329 (tpt) REVERT: D 289 TYR cc_start: 0.9396 (t80) cc_final: 0.9042 (t80) REVERT: D 290 ILE cc_start: 0.9746 (pt) cc_final: 0.9423 (pt) REVERT: D 352 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9049 (tm-30) REVERT: D 375 LYS cc_start: 0.9468 (pttt) cc_final: 0.9231 (pttt) REVERT: D 379 LEU cc_start: 0.9527 (mm) cc_final: 0.9310 (mm) REVERT: D 385 MET cc_start: 0.8350 (tpt) cc_final: 0.7178 (tpt) REVERT: D 386 MET cc_start: 0.8509 (ptp) cc_final: 0.7834 (ptp) REVERT: D 465 GLN cc_start: 0.8584 (pp30) cc_final: 0.8317 (tt0) REVERT: D 468 CYS cc_start: 0.9187 (t) cc_final: 0.8864 (t) REVERT: D 478 GLN cc_start: 0.9607 (tt0) cc_final: 0.9265 (tt0) REVERT: D 482 MET cc_start: 0.9023 (tpp) cc_final: 0.8813 (tpt) REVERT: O 1 MET cc_start: 0.7878 (mmm) cc_final: 0.7269 (mmp) REVERT: P 1 MET cc_start: 0.8259 (pmm) cc_final: 0.7914 (pmm) REVERT: E 28 ASP cc_start: 0.8968 (t70) cc_final: 0.8768 (t70) REVERT: E 32 TYR cc_start: 0.9096 (m-80) cc_final: 0.8604 (m-80) REVERT: E 36 LEU cc_start: 0.8683 (tp) cc_final: 0.8450 (tp) REVERT: E 38 LEU cc_start: 0.9573 (mm) cc_final: 0.8839 (mm) REVERT: E 48 GLN cc_start: 0.9208 (mt0) cc_final: 0.8812 (mt0) REVERT: E 105 ARG cc_start: 0.8971 (mmm160) cc_final: 0.8377 (tpm170) REVERT: E 108 LYS cc_start: 0.9440 (tppt) cc_final: 0.9130 (tppt) REVERT: E 137 HIS cc_start: 0.9473 (m90) cc_final: 0.8629 (m90) REVERT: E 150 MET cc_start: 0.7815 (tpt) cc_final: 0.7035 (tpt) REVERT: E 165 PHE cc_start: 0.8288 (p90) cc_final: 0.8064 (p90) REVERT: E 203 ARG cc_start: 0.9018 (mtm110) cc_final: 0.8740 (mtm110) REVERT: E 228 LYS cc_start: 0.9489 (ptpp) cc_final: 0.9263 (ptpp) REVERT: E 246 CYS cc_start: 0.9165 (t) cc_final: 0.8575 (p) REVERT: E 250 ILE cc_start: 0.9351 (pt) cc_final: 0.9142 (pt) REVERT: E 254 GLU cc_start: 0.9191 (tp30) cc_final: 0.8968 (pm20) REVERT: E 288 LYS cc_start: 0.9589 (mtmm) cc_final: 0.9247 (mttt) REVERT: E 322 ARG cc_start: 0.8262 (tmm-80) cc_final: 0.7522 (tmm-80) REVERT: E 332 ILE cc_start: 0.9314 (pt) cc_final: 0.8869 (pt) REVERT: E 334 GLN cc_start: 0.9335 (mp10) cc_final: 0.8344 (mp10) REVERT: E 335 GLU cc_start: 0.8597 (mp0) cc_final: 0.7741 (mp0) REVERT: E 341 ARG cc_start: 0.9377 (ptm-80) cc_final: 0.9162 (ptm-80) REVERT: E 352 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8822 (tm-30) REVERT: E 368 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8413 (mm-40) REVERT: E 369 ASN cc_start: 0.8797 (p0) cc_final: 0.8360 (p0) REVERT: E 385 MET cc_start: 0.8342 (ttp) cc_final: 0.7547 (ttp) REVERT: E 386 MET cc_start: 0.8400 (ppp) cc_final: 0.8143 (ppp) REVERT: E 420 MET cc_start: 0.8073 (mtm) cc_final: 0.7489 (mtp) REVERT: E 441 GLN cc_start: 0.6925 (pp30) cc_final: 0.6634 (pp30) REVERT: E 450 LYS cc_start: 0.9439 (mttp) cc_final: 0.9009 (mttp) REVERT: E 483 MET cc_start: 0.9695 (tmm) cc_final: 0.9448 (tmm) REVERT: E 507 HIS cc_start: 0.8405 (t-90) cc_final: 0.8103 (t70) REVERT: F 16 ASP cc_start: 0.7240 (t0) cc_final: 0.6343 (t0) REVERT: F 18 LEU cc_start: 0.9375 (tp) cc_final: 0.9085 (tp) REVERT: F 31 THR cc_start: 0.8087 (m) cc_final: 0.7629 (m) REVERT: F 70 MET cc_start: 0.8109 (tpp) cc_final: 0.7432 (tpp) REVERT: F 82 MET cc_start: 0.9147 (ttp) cc_final: 0.8872 (tmm) REVERT: F 92 HIS cc_start: 0.8826 (p90) cc_final: 0.8372 (p-80) REVERT: F 106 LYS cc_start: 0.9385 (mtpt) cc_final: 0.9172 (mtpt) REVERT: F 108 LYS cc_start: 0.9003 (pttm) cc_final: 0.7367 (tppt) REVERT: F 112 GLN cc_start: 0.8686 (mp10) cc_final: 0.8391 (mp10) REVERT: F 132 GLU cc_start: 0.9425 (pt0) cc_final: 0.9170 (pt0) REVERT: F 136 ARG cc_start: 0.9252 (mmp-170) cc_final: 0.8913 (ptp-110) REVERT: F 185 LEU cc_start: 0.8890 (mt) cc_final: 0.8231 (mt) REVERT: F 243 GLN cc_start: 0.9031 (mm110) cc_final: 0.8703 (mm110) REVERT: F 250 ILE cc_start: 0.9318 (mp) cc_final: 0.9025 (tp) REVERT: F 291 LYS cc_start: 0.9546 (mmtt) cc_final: 0.9227 (tppt) REVERT: F 294 TYR cc_start: 0.9439 (m-80) cc_final: 0.9094 (m-80) REVERT: F 322 ARG cc_start: 0.8749 (ttt-90) cc_final: 0.8202 (tpt-90) REVERT: F 334 GLN cc_start: 0.9230 (mt0) cc_final: 0.8856 (mm-40) REVERT: F 335 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7973 (tm-30) REVERT: F 352 GLU cc_start: 0.8727 (pm20) cc_final: 0.8461 (pm20) REVERT: F 364 ASP cc_start: 0.6980 (m-30) cc_final: 0.5879 (m-30) REVERT: F 372 HIS cc_start: 0.8955 (m170) cc_final: 0.8618 (m90) REVERT: F 385 MET cc_start: 0.7820 (ttp) cc_final: 0.6930 (ptm) REVERT: F 400 TYR cc_start: 0.7984 (m-80) cc_final: 0.7351 (m-80) REVERT: F 448 GLN cc_start: 0.9529 (pm20) cc_final: 0.9323 (pm20) REVERT: F 449 ASP cc_start: 0.8649 (t0) cc_final: 0.8446 (t0) REVERT: F 455 LYS cc_start: 0.9415 (pttp) cc_final: 0.9003 (ptmm) REVERT: F 482 MET cc_start: 0.8762 (ptp) cc_final: 0.8507 (ptp) REVERT: F 491 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8289 (tm-30) REVERT: F 493 ARG cc_start: 0.8824 (ptt-90) cc_final: 0.8156 (ptt-90) REVERT: F 494 THR cc_start: 0.9116 (p) cc_final: 0.8886 (p) REVERT: G 47 ASP cc_start: 0.9549 (m-30) cc_final: 0.8878 (p0) REVERT: G 78 MET cc_start: 0.9558 (tpp) cc_final: 0.9060 (tpp) REVERT: G 111 GLU cc_start: 0.9364 (tp30) cc_final: 0.9043 (mp0) REVERT: G 115 ILE cc_start: 0.8662 (pt) cc_final: 0.8414 (pt) REVERT: G 140 CYS cc_start: 0.4231 (m) cc_final: 0.4019 (m) REVERT: G 143 PRO cc_start: 0.8076 (Cg_exo) cc_final: 0.7797 (Cg_endo) REVERT: G 222 ILE cc_start: 0.7414 (mm) cc_final: 0.7172 (mm) REVERT: G 229 LYS cc_start: 0.9362 (ptpp) cc_final: 0.9037 (mmmt) REVERT: G 291 LYS cc_start: 0.8861 (ptpp) cc_final: 0.8538 (pttt) REVERT: G 306 THR cc_start: 0.8989 (t) cc_final: 0.8421 (t) REVERT: G 331 CYS cc_start: 0.8988 (t) cc_final: 0.8611 (t) REVERT: G 333 THR cc_start: 0.9704 (p) cc_final: 0.9048 (p) REVERT: G 334 GLN cc_start: 0.9060 (mp10) cc_final: 0.8233 (mp10) REVERT: G 335 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7938 (tm-30) REVERT: G 336 VAL cc_start: 0.9357 (m) cc_final: 0.8613 (m) REVERT: G 349 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8725 (mtmt) REVERT: G 386 MET cc_start: 0.8851 (tmm) cc_final: 0.8624 (tmm) REVERT: G 482 MET cc_start: 0.9230 (tpp) cc_final: 0.8860 (mmm) REVERT: G 493 ARG cc_start: 0.8869 (mtm180) cc_final: 0.8575 (ptp90) REVERT: G 500 GLU cc_start: 0.8994 (pp20) cc_final: 0.8406 (pp20) REVERT: G 504 HIS cc_start: 0.8320 (p90) cc_final: 0.7906 (p90) REVERT: H 16 ASP cc_start: 0.8039 (m-30) cc_final: 0.7825 (m-30) REVERT: H 21 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8411 (tp40) REVERT: H 25 ASN cc_start: 0.8575 (m110) cc_final: 0.7614 (m110) REVERT: H 33 ASN cc_start: 0.9212 (t0) cc_final: 0.8672 (t0) REVERT: H 62 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8797 (mtpp) REVERT: H 91 ILE cc_start: 0.9251 (tp) cc_final: 0.9030 (tp) REVERT: H 93 HIS cc_start: 0.8833 (p90) cc_final: 0.8473 (p90) REVERT: H 108 LYS cc_start: 0.9085 (tptm) cc_final: 0.8759 (tptp) REVERT: H 150 MET cc_start: 0.7098 (tmm) cc_final: 0.6701 (tmm) REVERT: H 158 ILE cc_start: 0.8226 (tp) cc_final: 0.7928 (tp) REVERT: H 179 MET cc_start: 0.6169 (ppp) cc_final: 0.5464 (ppp) REVERT: H 209 LEU cc_start: 0.9028 (tp) cc_final: 0.8784 (pp) REVERT: H 215 ASP cc_start: 0.9428 (m-30) cc_final: 0.8783 (t70) REVERT: H 229 LYS cc_start: 0.8889 (pttt) cc_final: 0.8624 (mmtt) REVERT: H 242 LYS cc_start: 0.9378 (mmpt) cc_final: 0.9018 (tppt) REVERT: H 258 TYR cc_start: 0.9408 (t80) cc_final: 0.9196 (t80) REVERT: H 286 MET cc_start: 0.9654 (tpt) cc_final: 0.9164 (tpt) REVERT: H 290 ILE cc_start: 0.9719 (pt) cc_final: 0.9386 (pt) REVERT: H 311 LYS cc_start: 0.9134 (ttpt) cc_final: 0.8888 (tmmt) REVERT: H 315 ASP cc_start: 0.9185 (m-30) cc_final: 0.8579 (p0) REVERT: H 349 LYS cc_start: 0.9658 (mmtp) cc_final: 0.9401 (mmtp) REVERT: H 352 GLU cc_start: 0.9391 (tm-30) cc_final: 0.9009 (tm-30) REVERT: H 368 GLN cc_start: 0.8661 (mt0) cc_final: 0.8130 (mm-40) REVERT: H 375 LYS cc_start: 0.9341 (ptmt) cc_final: 0.9002 (ptmt) REVERT: H 385 MET cc_start: 0.8450 (tpt) cc_final: 0.8051 (tpt) REVERT: H 386 MET cc_start: 0.7336 (ptm) cc_final: 0.6624 (ppp) REVERT: H 465 GLN cc_start: 0.8589 (pp30) cc_final: 0.8277 (tt0) REVERT: H 468 CYS cc_start: 0.9070 (t) cc_final: 0.8766 (t) REVERT: H 478 GLN cc_start: 0.9599 (tt0) cc_final: 0.9220 (tt0) REVERT: H 491 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7760 (tm-30) REVERT: H 492 LYS cc_start: 0.9063 (pttt) cc_final: 0.8792 (pttp) REVERT: J 12 TYR cc_start: 0.8713 (t80) cc_final: 0.8465 (t80) REVERT: K 1 MET cc_start: 0.7877 (mmm) cc_final: 0.7294 (mmp) REVERT: K 4 TYR cc_start: 0.7233 (p90) cc_final: 0.6934 (p90) REVERT: L 1 MET cc_start: 0.8288 (pmm) cc_final: 0.7934 (pmm) outliers start: 2 outliers final: 0 residues processed: 1414 average time/residue: 0.1963 time to fit residues: 452.8152 Evaluate side-chains 1208 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1208 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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: 2.9990 chunk 385 optimal weight: 0.6980 chunk 265 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 264 optimal weight: 0.0670 chunk 83 optimal weight: 0.0050 chunk 236 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 overall best weight: 0.5332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 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 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 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** 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** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.131038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093925 restraints weight = 72890.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098000 restraints weight = 41360.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.100851 restraints weight = 27369.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102871 restraints weight = 20017.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104278 restraints weight = 15745.813| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32220 Z= 0.147 Angle : 0.877 14.113 43712 Z= 0.434 Chirality : 0.052 0.464 4984 Planarity : 0.005 0.106 5452 Dihedral : 14.225 163.207 5344 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.63 % 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 aren not related in a simple way. whole: -2.69 (0.12), residues: 3968 helix: -1.72 (0.13), residues: 1256 sheet: -2.40 (0.22), residues: 430 loop : -1.69 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 322 TYR 0.040 0.002 TYR E 110 PHE 0.038 0.002 PHE B 456 HIS 0.008 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00328 (32212) covalent geometry : angle 0.87724 (43712) hydrogen bonds : bond 0.04236 ( 966) hydrogen bonds : angle 6.42811 ( 2655) Misc. bond : bond 0.00145 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8642.52 seconds wall clock time: 149 minutes 59.91 seconds (8999.91 seconds total)