Starting phenix.real_space_refine on Mon Sep 14 17:06:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u8r_20690/09_2026/6u8r_20690.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8r_20690/09_2026/6u8r_20690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u8r_20690/09_2026/6u8r_20690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8r_20690/09_2026/6u8r_20690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u8r_20690/09_2026/6u8r_20690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8r_20690/09_2026/6u8r_20690.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6u8r_20690/09_2026/6u8r_20690.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u8r_20690/09_2026/6u8r_20690.cif" } resolution = 3.91 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= 0.084 sd= 3.293 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 72 5.49 5 S 176 5.16 5 C 19656 2.51 5 N 5400 2.21 5 O 6224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31528 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: "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: "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: "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: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 7.16, per 1000 atoms: 0.23 Number of scatterers: 31528 At special positions: 0 Unit cell: (139.65, 148.05, 139.65, 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 72 15.00 O 6224 8.00 N 5400 7.00 C 19656 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 47 sheets defined 37.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.807A pdb=" N ASN A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) 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 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.697A pdb=" N ARG A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.916A pdb=" N ALA A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.695A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 4.037A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.980A 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 342 through 355 removed outlier: 3.530A pdb=" N TYR A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 removed outlier: 3.608A pdb=" N ALA A 374 " --> pdb=" O VAL A 370 " (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 475 through 486 removed outlier: 3.719A pdb=" N ARG A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid 19 through 27 removed outlier: 5.095A pdb=" N PHE B 24 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASN B 25 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 26 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 27 " --> pdb=" O PHE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.542A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.672A pdb=" N GLN B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 4.107A pdb=" N LYS B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.887A pdb=" N GLU B 177 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.588A pdb=" N LYS B 229 " --> pdb=" O THR B 225 " (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: 3.699A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 removed outlier: 3.893A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.026A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.722A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.991A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 removed outlier: 3.616A pdb=" N MET B 420 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 472 removed outlier: 3.619A pdb=" N TYR B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.827A pdb=" N GLU B 500 " --> pdb=" O SER B 496 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' 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 removed outlier: 3.615A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 86 removed outlier: 3.536A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.634A pdb=" N GLN C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.736A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.513A pdb=" N GLU C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' 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 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.636A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (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 355 removed outlier: 3.588A pdb=" N TYR C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 removed outlier: 3.602A pdb=" N ALA C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.562A pdb=" N GLY C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.708A pdb=" N LYS D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 137 Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.746A pdb=" N ASP D 162 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 163 " --> pdb=" O SER D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 163' Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.703A pdb=" N GLU D 177 " --> pdb=" O PHE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.612A pdb=" N ALA D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 removed outlier: 3.795A pdb=" N ASN D 230 " --> pdb=" O LEU D 227 " (cutoff:3.500A) 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 267 removed outlier: 4.000A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 263 " --> pdb=" O ARG D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.802A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (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 removed outlier: 4.161A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.729A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 456 through 472 removed outlier: 3.581A pdb=" N GLY D 472 " --> pdb=" O CYS D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 486 Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.557A pdb=" N ASN E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) 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 75 through 86 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.659A pdb=" N ALA E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.588A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.926A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.008A 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 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.545A pdb=" N TYR E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 removed outlier: 3.656A pdb=" N ALA E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 486 Processing helix chain 'E' and resid 494 through 502 removed outlier: 3.618A pdb=" N VAL E 499 " --> pdb=" O SER E 495 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 27 removed outlier: 4.815A pdb=" N PHE F 24 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN F 25 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY F 27 " --> pdb=" O PHE F 24 " (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 86 removed outlier: 3.583A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.688A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.934A pdb=" N LYS F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 removed outlier: 3.759A pdb=" N ALA F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU F 199 " --> pdb=" O LYS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 228 removed outlier: 3.529A pdb=" N LYS F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) 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 266 removed outlier: 3.765A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 removed outlier: 3.868A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 4.108A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.059A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.908A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 420 removed outlier: 3.608A pdb=" N MET F 420 " --> pdb=" O LEU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 472 removed outlier: 3.602A pdb=" N TYR F 459 " --> pdb=" O LYS F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 495 through 502 removed outlier: 4.066A pdb=" N VAL F 499 " --> pdb=" O SER F 495 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU F 500 " --> pdb=" O SER F 496 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY F 501 " --> pdb=" O ALA F 497 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 495 through 502' Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 25 through 27 No H-bonds generated for 'chain 'G' and resid 25 through 27' 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 removed outlier: 3.703A pdb=" N GLN G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.752A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 removed outlier: 3.737A pdb=" N GLN G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG G 105 " --> pdb=" O ALA G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 Processing helix chain 'G' and resid 159 through 163 removed outlier: 4.058A pdb=" N ILE G 163 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 3.549A pdb=" N GLU G 177 " --> pdb=" O PHE G 174 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE G 178 " --> pdb=" O LEU G 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 174 through 178' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 229 removed outlier: 3.618A pdb=" N LYS G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 257 Processing helix chain 'G' and resid 258 through 265 removed outlier: 3.852A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.818A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (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 355 removed outlier: 3.878A pdb=" N LYS G 349 " --> pdb=" O THR G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.988A pdb=" N ALA H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 removed outlier: 3.813A pdb=" N LYS H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.549A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 removed outlier: 3.718A pdb=" N ASP H 162 " --> pdb=" O SER H 159 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE H 163 " --> pdb=" O SER H 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 159 through 163' Processing helix chain 'H' and resid 174 through 178 removed outlier: 3.561A pdb=" N GLU H 177 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 205 removed outlier: 3.561A pdb=" N ALA H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 230 removed outlier: 3.918A pdb=" N LYS H 228 " --> pdb=" O THR H 225 " (cutoff:3.500A) 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 267 removed outlier: 4.040A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU H 263 " --> pdb=" O ARG H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.845A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.922A 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 342 through 355 removed outlier: 4.154A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.822A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 420 Processing helix chain 'H' and resid 452 through 455 Processing helix chain 'H' and resid 456 through 472 removed outlier: 3.647A pdb=" N GLY H 472 " --> pdb=" O CYS H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 497 through 502 Processing helix chain 'M' and resid 3 through 8 removed outlier: 4.460A pdb=" N SER M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'I' and resid 2 through 6 removed outlier: 3.512A pdb=" N LEU I 5 " --> pdb=" O ALA I 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE I 6 " --> pdb=" O ASP I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2 through 6' Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'K' and resid 2 through 6 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 removed outlier: 4.618A pdb=" N LYS A 489 " --> pdb=" O LEU A 38 " (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 65 through 67 removed outlier: 6.795A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 271 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.739A pdb=" N LEU A 408 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 403 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.852A pdb=" N SER A 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 403 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 37 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 67 removed outlier: 6.134A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.735A pdb=" N ILE B 142 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE B 157 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 144 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 212 Processing sheet with id=AB3, first strand: chain 'B' and resid 401 through 403 removed outlier: 3.853A pdb=" N SER B 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.839A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 248 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB8, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.877A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 401 through 403 removed outlier: 3.664A pdb=" N SER C 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER D 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.763A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY D 302 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP D 274 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 142 through 145 removed outlier: 7.664A pdb=" N ILE D 142 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE D 157 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.411A 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: 6.221A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 209 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 38 removed outlier: 4.654A pdb=" N LYS E 489 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.798A pdb=" N VAL E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AD1, first strand: chain 'E' and resid 208 through 212 removed outlier: 3.665A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.615A pdb=" N LEU E 408 " --> pdb=" O PHE E 401 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 403 " --> pdb=" O ILE E 406 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.830A pdb=" N SER E 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER H 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER H 403 " --> pdb=" O ILE H 406 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 65 through 67 removed outlier: 7.330A pdb=" N VAL F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLY F 302 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 142 through 145 removed outlier: 6.562A pdb=" N ILE F 142 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE F 157 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE F 144 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 211 through 212 Processing sheet with id=AD9, first strand: chain 'F' and resid 401 through 403 removed outlier: 3.783A pdb=" N SER F 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER G 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.974A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 143 through 144 Processing sheet with id=AE5, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.011A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU G 209 " --> pdb=" O ILE G 221 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE G 221 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 401 through 403 removed outlier: 3.642A pdb=" N LYS G 409 " --> pdb=" O VAL G 447 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER G 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER H 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 88 through 89 removed outlier: 3.938A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY H 302 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 143 through 145 removed outlier: 3.891A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 208 through 213 removed outlier: 6.875A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5311 1.30 - 1.43: 7761 1.43 - 1.56: 18536 1.56 - 1.69: 160 1.69 - 1.82: 304 Bond restraints: 32072 Sorted by residual: bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.244 0.287 1.20e-02 6.94e+03 5.71e+02 bond pdb=" C2' ATP H 602 " pdb=" C3' ATP H 602 " ideal model delta sigma weight residual 1.531 1.245 0.286 1.20e-02 6.94e+03 5.70e+02 bond pdb=" C2' ATP E 603 " pdb=" C3' ATP E 603 " 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 604 " pdb=" C3' ATP A 604 " 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 E 604 " pdb=" C3' ATP E 604 " ideal model delta sigma weight residual 1.531 1.246 0.285 1.20e-02 6.94e+03 5.64e+02 ... (remaining 32067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.62: 42368 4.62 - 9.23: 913 9.23 - 13.85: 100 13.85 - 18.47: 72 18.47 - 23.08: 35 Bond angle restraints: 43488 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 116.79 23.08 1.00e+00 1.00e+00 5.33e+02 angle pdb=" PB ATP H 602 " pdb=" O3B ATP H 602 " pdb=" PG ATP H 602 " ideal model delta sigma weight residual 139.87 117.45 22.42 1.00e+00 1.00e+00 5.02e+02 angle pdb=" PB ATP G 602 " pdb=" O3B ATP G 602 " pdb=" PG ATP G 602 " ideal model delta sigma weight residual 139.87 119.16 20.71 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 119.17 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 119.45 20.42 1.00e+00 1.00e+00 4.17e+02 ... (remaining 43483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.57: 17578 20.57 - 41.15: 1186 41.15 - 61.72: 159 61.72 - 82.30: 27 82.30 - 102.87: 10 Dihedral angle restraints: 18960 sinusoidal: 7552 harmonic: 11408 Sorted by residual: dihedral pdb=" CA ASP D 164 " pdb=" C ASP D 164 " pdb=" N PHE D 165 " pdb=" CA PHE D 165 " ideal model delta harmonic sigma weight residual -180.00 -143.66 -36.34 0 5.00e+00 4.00e-02 5.28e+01 dihedral pdb=" CA THR E 74 " pdb=" C THR E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta harmonic sigma weight residual 180.00 143.81 36.19 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA LYS D 62 " pdb=" C LYS D 62 " pdb=" N THR D 63 " pdb=" CA THR D 63 " ideal model delta harmonic sigma weight residual 180.00 148.44 31.56 0 5.00e+00 4.00e-02 3.98e+01 ... (remaining 18957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4345 0.122 - 0.244: 564 0.244 - 0.366: 53 0.366 - 0.488: 4 0.488 - 0.610: 2 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CB ILE G 362 " pdb=" CA ILE G 362 " pdb=" CG1 ILE G 362 " pdb=" CG2 ILE G 362 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB ILE H 300 " pdb=" CA ILE H 300 " pdb=" CG1 ILE H 300 " pdb=" CG2 ILE H 300 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.88e+00 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 2.16 0.48 2.00e-01 2.50e+01 5.85e+00 ... (remaining 4965 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 411 " -0.021 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR C 411 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 411 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 411 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 411 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 411 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR C 411 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 411 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 63 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO H 64 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO H 64 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 64 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 111 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C GLU F 111 " 0.051 2.00e-02 2.50e+03 pdb=" O GLU F 111 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN F 112 " -0.017 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4602 2.73 - 3.27: 30827 3.27 - 3.82: 55756 3.82 - 4.36: 63232 4.36 - 4.90: 104238 Nonbonded interactions: 258655 Sorted by model distance: nonbonded pdb=" OG SER A 329 " pdb=" O HIS B 504 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR H 147 " pdb=" OG SER H 152 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP G 50 " pdb=" OG SER G 475 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP D 364 " pdb=" O2' IMP D 603 " model vdw 2.238 3.040 nonbonded pdb=" OG SER E 159 " pdb=" O1B ATP E 603 " model vdw 2.242 3.040 ... (remaining 258650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 514) selection = (chain 'B' and resid 11 through 514) selection = (chain 'C' and resid 11 through 514) selection = (chain 'D' and resid 11 through 514) selection = (chain 'E' and resid 11 through 514) selection = (chain 'F' and resid 11 through 514) selection = (chain 'G' and resid 11 through 514) selection = (chain 'H' and resid 11 through 514) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.170 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.019 0.287 32073 Z= 1.098 Angle : 1.853 23.084 43488 Z= 1.145 Chirality : 0.085 0.610 4968 Planarity : 0.008 0.081 5448 Dihedral : 14.055 102.870 11680 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.74 % Favored : 90.98 % Rotamer: Outliers : 3.21 % Allowed : 12.32 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.11), residues: 3968 helix: -3.72 (0.09), residues: 1247 sheet: -2.56 (0.22), residues: 432 loop : -2.57 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG B 355 TYR 0.058 0.004 TYR C 411 PHE 0.044 0.005 PHE F 174 HIS 0.017 0.003 HIS H 504 Details of bonding type rmsd/Z covalent geometry : bond 0.01882 / 1.10 (32072) covalent geometry : angle 1.85333 / 1.14 (43488) hydrogen bonds : bond 0.22090 / 14.33 ( 961) hydrogen bonds : angle 8.67212 / 5.97 ( 2700) Misc. bond : bond 0.00309 / 0.16 ( 1) *********************** 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 1284 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1179 time to evaluate : 1.274 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: A 34 ASP cc_start: 0.8392 (t70) cc_final: 0.8191 (t70) REVERT: A 173 CYS cc_start: 0.5872 (m) cc_final: 0.5473 (m) REVERT: A 195 LYS cc_start: 0.8384 (mmmm) cc_final: 0.8115 (tptt) REVERT: A 224 ARG cc_start: 0.8592 (ttt-90) cc_final: 0.8262 (tpp80) REVERT: A 230 ASN cc_start: 0.9417 (t160) cc_final: 0.9168 (t0) REVERT: A 246 CYS cc_start: 0.9023 (t) cc_final: 0.8500 (t) REVERT: A 273 LEU cc_start: 0.9689 (mt) cc_final: 0.9442 (mt) REVERT: A 274 ASP cc_start: 0.9017 (t0) cc_final: 0.8701 (t0) REVERT: A 352 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8650 (tm-30) REVERT: A 357 PHE cc_start: 0.9219 (m-80) cc_final: 0.8859 (m-10) REVERT: A 483 MET cc_start: 0.9441 (tmm) cc_final: 0.8811 (tmm) REVERT: B 16 ASP cc_start: 0.9024 (t0) cc_final: 0.8769 (t0) REVERT: B 41 TYR cc_start: 0.8887 (t80) cc_final: 0.8668 (t80) REVERT: B 51 LEU cc_start: 0.8851 (tp) cc_final: 0.8500 (tt) REVERT: B 103 GLU cc_start: 0.8857 (mp0) cc_final: 0.8549 (mp0) REVERT: B 105 ARG cc_start: 0.8685 (mtm110) cc_final: 0.8430 (ptp-110) REVERT: B 158 ILE cc_start: 0.8988 (mm) cc_final: 0.8757 (mm) REVERT: B 179 MET cc_start: 0.7408 (pp-130) cc_final: 0.7064 (pp-130) REVERT: B 274 ASP cc_start: 0.8963 (t0) cc_final: 0.8601 (t0) REVERT: B 277 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9007 (tm-30) REVERT: B 309 GLN cc_start: 0.9266 (pm20) cc_final: 0.8828 (pm20) REVERT: B 335 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 409 LYS cc_start: 0.8473 (mttp) cc_final: 0.7529 (mmtt) REVERT: B 467 SER cc_start: 0.9464 (p) cc_final: 0.9245 (p) REVERT: B 487 GLU cc_start: 0.9078 (tt0) cc_final: 0.8680 (tt0) REVERT: C 21 GLN cc_start: 0.8822 (pp30) cc_final: 0.8362 (pp30) REVERT: C 25 ASN cc_start: 0.8712 (t0) cc_final: 0.8137 (t0) REVERT: C 28 ASP cc_start: 0.8730 (m-30) cc_final: 0.8518 (m-30) REVERT: C 48 GLN cc_start: 0.9030 (mt0) cc_final: 0.8399 (mt0) REVERT: C 94 ASN cc_start: 0.9230 (t0) cc_final: 0.8648 (t0) REVERT: C 105 ARG cc_start: 0.8746 (mtm110) cc_final: 0.8186 (ttp80) REVERT: C 110 TYR cc_start: 0.8768 (t80) cc_final: 0.8322 (t80) REVERT: C 182 ARG cc_start: 0.8316 (tpm170) cc_final: 0.7939 (tpp-160) REVERT: C 200 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8668 (mt) REVERT: C 206 LYS cc_start: 0.9185 (tppp) cc_final: 0.8688 (tppp) REVERT: C 210 PRO cc_start: 0.9303 (Cg_exo) cc_final: 0.9085 (Cg_endo) REVERT: C 216 ASP cc_start: 0.7862 (t0) cc_final: 0.7597 (t0) REVERT: C 224 ARG cc_start: 0.9008 (ttt-90) cc_final: 0.8511 (ttm-80) REVERT: C 238 LYS cc_start: 0.8916 (mppt) cc_final: 0.8588 (mmmm) REVERT: C 262 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9143 (tt) REVERT: C 277 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8021 (tm-30) REVERT: C 296 ASN cc_start: 0.8716 (p0) cc_final: 0.8400 (m-40) REVERT: C 343 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 386 MET cc_start: 0.8500 (mpm) cc_final: 0.8125 (mpm) REVERT: C 461 ILE cc_start: 0.9219 (pp) cc_final: 0.8814 (pp) REVERT: C 465 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8729 (pm20) REVERT: C 468 CYS cc_start: 0.8477 (t) cc_final: 0.8175 (t) REVERT: C 475 SER cc_start: 0.8755 (t) cc_final: 0.8410 (t) REVERT: C 483 MET cc_start: 0.9093 (tmm) cc_final: 0.8870 (tmm) REVERT: D 32 TYR cc_start: 0.9169 (m-10) cc_final: 0.8711 (m-10) REVERT: D 93 HIS cc_start: 0.8825 (p-80) cc_final: 0.8593 (p90) REVERT: D 112 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 327 SER cc_start: 0.8979 (p) cc_final: 0.8720 (p) REVERT: D 334 GLN cc_start: 0.8967 (mt0) cc_final: 0.8520 (mt0) REVERT: D 335 GLU cc_start: 0.7910 (tt0) cc_final: 0.7679 (tt0) REVERT: D 343 GLN cc_start: 0.8799 (tm130) cc_final: 0.8436 (tm-30) REVERT: D 400 TYR cc_start: 0.7644 (m-80) cc_final: 0.7442 (m-80) REVERT: D 450 LYS cc_start: 0.8853 (mmpt) cc_final: 0.8563 (mmmt) REVERT: D 482 MET cc_start: 0.9090 (mtp) cc_final: 0.8843 (mtp) REVERT: D 483 MET cc_start: 0.9744 (tmm) cc_final: 0.9527 (tmm) REVERT: D 510 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8169 (tm-30) REVERT: E 75 GLU cc_start: 0.8301 (mp0) cc_final: 0.7694 (mp0) REVERT: E 150 MET cc_start: 0.7322 (tmt) cc_final: 0.6779 (tmt) REVERT: E 174 PHE cc_start: 0.8976 (m-80) cc_final: 0.8457 (m-80) REVERT: E 241 LYS cc_start: 0.9224 (mptt) cc_final: 0.8932 (mmtm) REVERT: E 273 LEU cc_start: 0.9629 (mp) cc_final: 0.9425 (mp) REVERT: E 274 ASP cc_start: 0.9308 (t0) cc_final: 0.9037 (t0) REVERT: E 279 ASN cc_start: 0.8555 (t0) cc_final: 0.8285 (t0) REVERT: E 285 ASN cc_start: 0.8976 (m110) cc_final: 0.8536 (m110) REVERT: E 296 ASN cc_start: 0.8503 (p0) cc_final: 0.8117 (t0) REVERT: E 382 SER cc_start: 0.9635 (m) cc_final: 0.9391 (t) REVERT: E 385 MET cc_start: 0.8972 (ttp) cc_final: 0.8741 (ttm) REVERT: E 455 LYS cc_start: 0.8969 (tppt) cc_final: 0.8489 (mmmt) REVERT: E 500 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8723 (tm-30) REVERT: F 16 ASP cc_start: 0.8842 (t0) cc_final: 0.8475 (t0) REVERT: F 51 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8669 (tm) REVERT: F 103 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8676 (mp0) REVERT: F 105 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8444 (mtm110) REVERT: F 110 TYR cc_start: 0.8662 (t80) cc_final: 0.8230 (t80) REVERT: F 114 PHE cc_start: 0.9189 (m-10) cc_final: 0.8753 (m-80) REVERT: F 132 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: F 206 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8888 (mtpt) REVERT: F 283 GLN cc_start: 0.9050 (tt0) cc_final: 0.8739 (tt0) REVERT: F 319 ASP cc_start: 0.8022 (t0) cc_final: 0.7569 (t0) REVERT: F 335 GLU cc_start: 0.8452 (tt0) cc_final: 0.8191 (tt0) REVERT: F 409 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8538 (tttt) REVERT: F 483 MET cc_start: 0.9408 (tmm) cc_final: 0.8999 (tmm) REVERT: F 487 GLU cc_start: 0.9120 (tt0) cc_final: 0.8771 (tt0) REVERT: G 75 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8055 (mt-10) REVERT: G 95 CYS cc_start: 0.8379 (p) cc_final: 0.8028 (p) REVERT: G 98 GLU cc_start: 0.8605 (pm20) cc_final: 0.8219 (pm20) REVERT: G 100 GLN cc_start: 0.8580 (pm20) cc_final: 0.8248 (pm20) REVERT: G 105 ARG cc_start: 0.8885 (mtm110) cc_final: 0.8426 (ttp80) REVERT: G 200 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8559 (mp) REVERT: G 277 GLN cc_start: 0.8673 (tm130) cc_final: 0.8094 (tm130) REVERT: G 296 ASN cc_start: 0.8773 (p0) cc_final: 0.8470 (m-40) REVERT: G 343 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7821 (tm-30) REVERT: G 355 ARG cc_start: 0.9402 (ptt180) cc_final: 0.9195 (ptt90) REVERT: G 362 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9144 (tp) REVERT: G 369 ASN cc_start: 0.8975 (p0) cc_final: 0.8771 (p0) REVERT: G 383 THR cc_start: 0.9762 (p) cc_final: 0.9508 (p) REVERT: G 386 MET cc_start: 0.8537 (mmp) cc_final: 0.8233 (mmm) REVERT: G 461 ILE cc_start: 0.9162 (pp) cc_final: 0.8722 (pp) REVERT: G 465 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8726 (pm20) REVERT: G 499 VAL cc_start: 0.9273 (p) cc_final: 0.9000 (p) REVERT: H 32 TYR cc_start: 0.9050 (m-10) cc_final: 0.8594 (m-10) REVERT: H 93 HIS cc_start: 0.8869 (p-80) cc_final: 0.8648 (p90) REVERT: H 103 GLU cc_start: 0.8541 (mp0) cc_final: 0.8306 (mp0) REVERT: H 228 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8408 (tmtt) REVERT: H 277 GLN cc_start: 0.8757 (tm130) cc_final: 0.8440 (tm130) REVERT: H 281 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7747 (pp) REVERT: H 327 SER cc_start: 0.8869 (p) cc_final: 0.8517 (p) REVERT: H 334 GLN cc_start: 0.9067 (mt0) cc_final: 0.8853 (mt0) REVERT: H 343 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8594 (tm-30) REVERT: H 364 ASP cc_start: 0.8495 (m-30) cc_final: 0.8147 (m-30) REVERT: H 385 MET cc_start: 0.8611 (ttm) cc_final: 0.8403 (ttm) REVERT: H 386 MET cc_start: 0.8526 (mtm) cc_final: 0.8308 (mtm) REVERT: H 393 THR cc_start: 0.8250 (p) cc_final: 0.7643 (p) REVERT: H 395 GLU cc_start: 0.8646 (mp0) cc_final: 0.8267 (mp0) outliers start: 105 outliers final: 22 residues processed: 1216 average time/residue: 0.1827 time to fit residues: 364.4796 Evaluate side-chains 929 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 897 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 314 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.0050 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 overall best weight: 0.6608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS A 230 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 93 HIS B 137 HIS B 243 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 92 HIS C 243 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN D 22 GLN D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN E 230 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 HIS F 22 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN F 507 HIS G 22 GLN G 25 ASN G 48 GLN G 94 ASN G 277 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 253 HIS H 277 GLN H 285 ASN H 298 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN H 478 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.097435 restraints weight = 52113.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.101388 restraints weight = 26521.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104084 restraints weight = 16738.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.105821 restraints weight = 12062.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.107091 restraints weight = 9629.236| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32073 Z= 0.167 Angle : 0.846 14.497 43488 Z= 0.423 Chirality : 0.051 0.293 4968 Planarity : 0.005 0.050 5448 Dihedral : 10.039 89.221 4534 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.28 % Favored : 93.55 % Rotamer: Outliers : 5.10 % Allowed : 20.45 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.12), residues: 3968 helix: -2.33 (0.12), residues: 1272 sheet: -2.32 (0.22), residues: 428 loop : -2.15 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 105 TYR 0.026 0.002 TYR A 353 PHE 0.025 0.002 PHE D 131 HIS 0.009 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (32072) covalent geometry : angle 0.84648 / 0.42 (43488) hydrogen bonds : bond 0.04608 / 3.03 ( 961) hydrogen bonds : angle 6.44778 / 4.49 ( 2700) Misc. bond : bond 0.00149 / 0.08 ( 1) *********************** 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 1244 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1077 time to evaluate : 1.251 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: A 34 ASP cc_start: 0.8332 (t70) cc_final: 0.8086 (t70) REVERT: A 100 GLN cc_start: 0.9393 (tt0) cc_final: 0.9149 (tt0) REVERT: A 105 ARG cc_start: 0.8818 (mtp-110) cc_final: 0.8111 (ttm-80) REVERT: A 108 LYS cc_start: 0.9283 (mtpt) cc_final: 0.9017 (mmtt) REVERT: A 145 THR cc_start: 0.8900 (p) cc_final: 0.8588 (t) REVERT: A 173 CYS cc_start: 0.5268 (m) cc_final: 0.4967 (m) REVERT: A 238 LYS cc_start: 0.8423 (mtmp) cc_final: 0.8140 (mtmm) REVERT: A 335 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 352 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8710 (tm-30) REVERT: A 409 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8640 (ttmm) REVERT: A 496 SER cc_start: 0.9241 (m) cc_final: 0.9026 (p) REVERT: A 500 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8813 (tm-30) REVERT: B 64 PRO cc_start: 0.9494 (Cg_endo) cc_final: 0.9267 (Cg_exo) REVERT: B 78 MET cc_start: 0.8990 (tmt) cc_final: 0.8505 (tmt) REVERT: B 103 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: B 105 ARG cc_start: 0.8731 (mtm110) cc_final: 0.8416 (ptp-110) REVERT: B 158 ILE cc_start: 0.8982 (mm) cc_final: 0.8777 (mm) REVERT: B 160 SER cc_start: 0.8591 (t) cc_final: 0.7899 (m) REVERT: B 179 MET cc_start: 0.7334 (pp-130) cc_final: 0.6984 (pp-130) REVERT: B 231 ARG cc_start: 0.8885 (mmt-90) cc_final: 0.8681 (mmp80) REVERT: B 274 ASP cc_start: 0.9013 (t0) cc_final: 0.8661 (t0) REVERT: B 312 ASN cc_start: 0.9381 (m-40) cc_final: 0.8542 (t0) REVERT: B 334 GLN cc_start: 0.8972 (mt0) cc_final: 0.8518 (mt0) REVERT: B 335 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7444 (tm-30) REVERT: B 343 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8045 (tp-100) REVERT: B 355 ARG cc_start: 0.9116 (ttp-170) cc_final: 0.8839 (ttp80) REVERT: B 395 GLU cc_start: 0.8699 (mp0) cc_final: 0.8467 (mp0) REVERT: B 408 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8244 (pp) REVERT: B 409 LYS cc_start: 0.8170 (mttp) cc_final: 0.7714 (mmtt) REVERT: B 487 GLU cc_start: 0.9131 (tt0) cc_final: 0.8624 (tt0) REVERT: B 498 GLN cc_start: 0.8280 (mm110) cc_final: 0.8003 (mm110) REVERT: C 25 ASN cc_start: 0.8670 (t0) cc_final: 0.8203 (t0) REVERT: C 36 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8840 (pp) REVERT: C 105 ARG cc_start: 0.8710 (mtm110) cc_final: 0.8256 (ttp80) REVERT: C 110 TYR cc_start: 0.8631 (t80) cc_final: 0.8140 (t80) REVERT: C 134 LYS cc_start: 0.9316 (ptmm) cc_final: 0.9050 (tptt) REVERT: C 149 ARG cc_start: 0.8539 (tmm-80) cc_final: 0.8002 (tmm-80) REVERT: C 182 ARG cc_start: 0.8140 (tpm170) cc_final: 0.7666 (tpp-160) REVERT: C 206 LYS cc_start: 0.9103 (tppp) cc_final: 0.8788 (mmmm) REVERT: C 224 ARG cc_start: 0.8957 (ttt-90) cc_final: 0.8348 (ttm-80) REVERT: C 277 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7821 (tm-30) REVERT: C 279 ASN cc_start: 0.9009 (t0) cc_final: 0.8590 (t0) REVERT: C 297 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9118 (tm) REVERT: C 327 SER cc_start: 0.9077 (p) cc_final: 0.8874 (p) REVERT: C 355 ARG cc_start: 0.9268 (ptt90) cc_final: 0.9014 (ptm-80) REVERT: C 369 ASN cc_start: 0.8660 (p0) cc_final: 0.8114 (p0) REVERT: C 386 MET cc_start: 0.8429 (mpm) cc_final: 0.7967 (mpm) REVERT: C 409 LYS cc_start: 0.8087 (ptpt) cc_final: 0.7847 (ptpt) REVERT: C 468 CYS cc_start: 0.8686 (t) cc_final: 0.8356 (t) REVERT: C 480 ARG cc_start: 0.9018 (mtm-85) cc_final: 0.8814 (mtt90) REVERT: C 483 MET cc_start: 0.9207 (tmm) cc_final: 0.8676 (tmm) REVERT: D 32 TYR cc_start: 0.8948 (m-10) cc_final: 0.8349 (m-10) REVERT: D 65 LEU cc_start: 0.9450 (mm) cc_final: 0.9239 (mm) REVERT: D 75 GLU cc_start: 0.7653 (pp20) cc_final: 0.7373 (pp20) REVERT: D 103 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: D 106 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8773 (ttpt) REVERT: D 199 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8852 (tm-30) REVERT: D 227 LEU cc_start: 0.9092 (mp) cc_final: 0.8832 (mm) REVERT: D 230 ASN cc_start: 0.7799 (t0) cc_final: 0.7098 (t0) REVERT: D 285 ASN cc_start: 0.9152 (m110) cc_final: 0.8931 (m110) REVERT: D 327 SER cc_start: 0.9101 (p) cc_final: 0.8756 (t) REVERT: D 482 MET cc_start: 0.9252 (mtp) cc_final: 0.8938 (mtp) REVERT: D 483 MET cc_start: 0.9831 (tmm) cc_final: 0.9446 (tmm) REVERT: D 510 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8128 (tm-30) REVERT: E 13 VAL cc_start: 0.9592 (t) cc_final: 0.9307 (p) REVERT: E 16 ASP cc_start: 0.8877 (t70) cc_final: 0.8290 (t0) REVERT: E 72 THR cc_start: 0.9536 (OUTLIER) cc_final: 0.9184 (t) REVERT: E 75 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: E 150 MET cc_start: 0.6989 (tmt) cc_final: 0.6302 (tmt) REVERT: E 179 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6648 (ppp) REVERT: E 230 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8878 (t0) REVERT: E 238 LYS cc_start: 0.8297 (mtmm) cc_final: 0.8017 (mtmm) REVERT: E 241 LYS cc_start: 0.9231 (mptt) cc_final: 0.8892 (mmtm) REVERT: E 274 ASP cc_start: 0.9107 (t0) cc_final: 0.8858 (t0) REVERT: E 279 ASN cc_start: 0.8688 (t0) cc_final: 0.7696 (t0) REVERT: E 296 ASN cc_start: 0.8422 (p0) cc_final: 0.8066 (t0) REVERT: E 335 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8282 (tm-30) REVERT: E 395 GLU cc_start: 0.8661 (mp0) cc_final: 0.8433 (mp0) REVERT: E 466 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.7944 (t-90) REVERT: E 480 ARG cc_start: 0.9280 (mtm-85) cc_final: 0.9076 (mtt90) REVERT: E 482 MET cc_start: 0.8789 (mtm) cc_final: 0.8570 (mtp) REVERT: E 483 MET cc_start: 0.9427 (tmm) cc_final: 0.8789 (tmm) REVERT: E 500 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8787 (tm-30) REVERT: F 16 ASP cc_start: 0.8818 (t0) cc_final: 0.8383 (t0) REVERT: F 51 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8338 (tm) REVERT: F 105 ARG cc_start: 0.8737 (mtm110) cc_final: 0.8429 (ptp-110) REVERT: F 110 TYR cc_start: 0.8707 (t80) cc_final: 0.8304 (t80) REVERT: F 114 PHE cc_start: 0.9087 (m-10) cc_final: 0.8660 (m-80) REVERT: F 121 LEU cc_start: 0.8281 (tt) cc_final: 0.8043 (tt) REVERT: F 179 MET cc_start: 0.7653 (pp-130) cc_final: 0.7433 (pp-130) REVERT: F 203 ARG cc_start: 0.8982 (mtm110) cc_final: 0.8776 (mtm110) REVERT: F 279 ASN cc_start: 0.8675 (t0) cc_final: 0.8312 (t0) REVERT: F 283 GLN cc_start: 0.9057 (tt0) cc_final: 0.8827 (tt0) REVERT: F 309 GLN cc_start: 0.9018 (pm20) cc_final: 0.8795 (pm20) REVERT: F 319 ASP cc_start: 0.8073 (t0) cc_final: 0.7844 (m-30) REVERT: F 409 LYS cc_start: 0.8552 (ttmm) cc_final: 0.7488 (tttt) REVERT: F 412 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7191 (ptt90) REVERT: F 482 MET cc_start: 0.8784 (mtp) cc_final: 0.8367 (mtp) REVERT: G 75 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8052 (mm-30) REVERT: G 94 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8662 (t0) REVERT: G 105 ARG cc_start: 0.8809 (mtm110) cc_final: 0.8361 (ttp80) REVERT: G 195 LYS cc_start: 0.9237 (pmmt) cc_final: 0.8501 (tttt) REVERT: G 277 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7693 (tm-30) REVERT: G 355 ARG cc_start: 0.9270 (ptt180) cc_final: 0.9042 (ptt180) REVERT: G 386 MET cc_start: 0.8743 (mmp) cc_final: 0.8504 (mmm) REVERT: G 390 LEU cc_start: 0.9042 (mp) cc_final: 0.8549 (mp) REVERT: G 450 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8182 (ptpp) REVERT: G 478 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7753 (pp30) REVERT: G 510 GLU cc_start: 0.8292 (mp0) cc_final: 0.8057 (mp0) REVERT: H 32 TYR cc_start: 0.8712 (m-10) cc_final: 0.8220 (m-10) REVERT: H 33 ASN cc_start: 0.8360 (t0) cc_final: 0.7608 (t0) REVERT: H 75 GLU cc_start: 0.8350 (mp0) cc_final: 0.8122 (mp0) REVERT: H 93 HIS cc_start: 0.8890 (p-80) cc_final: 0.8589 (p90) REVERT: H 131 PHE cc_start: 0.9173 (m-80) cc_final: 0.8533 (m-80) REVERT: H 228 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8110 (tmtt) REVERT: H 231 ARG cc_start: 0.8525 (mmp80) cc_final: 0.8239 (mmp-170) REVERT: H 274 ASP cc_start: 0.9085 (t70) cc_final: 0.8678 (t70) REVERT: H 286 MET cc_start: 0.8528 (mtp) cc_final: 0.8288 (mtp) REVERT: H 325 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8440 (ptt) REVERT: H 327 SER cc_start: 0.8624 (p) cc_final: 0.8377 (p) REVERT: H 343 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7683 (tm-30) REVERT: H 395 GLU cc_start: 0.8592 (mp0) cc_final: 0.8391 (mp0) REVERT: H 465 GLN cc_start: 0.8917 (mt0) cc_final: 0.8628 (mt0) REVERT: H 510 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8104 (tm-30) REVERT: K 4 TYR cc_start: 0.9189 (t80) cc_final: 0.8987 (t80) outliers start: 167 outliers final: 89 residues processed: 1152 average time/residue: 0.1934 time to fit residues: 365.7928 Evaluate side-chains 1019 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 916 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 230 ASN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 475 SER Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 470 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain J residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 281 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 0.4980 chunk 391 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 369 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 387 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 137 HIS ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 93 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** D 92 HIS ** 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 ** 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 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 137 HIS H 243 GLN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** 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 = 0.3549 r_free = 0.3549 target = 0.138818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.095407 restraints weight = 52422.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.099304 restraints weight = 27232.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.101895 restraints weight = 17363.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.103783 restraints weight = 12655.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104938 restraints weight = 10100.947| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32073 Z= 0.157 Angle : 0.799 14.520 43488 Z= 0.395 Chirality : 0.050 0.342 4968 Planarity : 0.004 0.044 5448 Dihedral : 9.220 89.223 4499 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.38 % Favored : 92.46 % Rotamer: Outliers : 6.57 % Allowed : 22.80 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.12), residues: 3968 helix: -1.79 (0.13), residues: 1276 sheet: -2.18 (0.23), residues: 414 loop : -2.02 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 105 TYR 0.028 0.002 TYR F 484 PHE 0.021 0.001 PHE D 165 HIS 0.009 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (32072) covalent geometry : angle 0.79929 / 0.40 (43488) hydrogen bonds : bond 0.04111 / 2.73 ( 961) hydrogen bonds : angle 6.04213 / 4.21 ( 2700) Misc. bond : bond 0.00159 / 0.08 ( 1) *********************** 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 1232 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 1017 time to evaluate : 1.196 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: A 34 ASP cc_start: 0.8287 (t70) cc_final: 0.8079 (t70) REVERT: A 82 MET cc_start: 0.9402 (mmm) cc_final: 0.9165 (tpp) REVERT: A 100 GLN cc_start: 0.9333 (tt0) cc_final: 0.9016 (tt0) REVERT: A 105 ARG cc_start: 0.8763 (mtp-110) cc_final: 0.8239 (ttm-80) REVERT: A 125 ASP cc_start: 0.7722 (p0) cc_final: 0.7479 (p0) REVERT: A 229 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8512 (mtpt) REVERT: A 230 ASN cc_start: 0.9181 (t0) cc_final: 0.8945 (t0) REVERT: A 238 LYS cc_start: 0.8423 (mtmp) cc_final: 0.8109 (mtmm) REVERT: A 279 ASN cc_start: 0.8708 (t0) cc_final: 0.7877 (t0) REVERT: A 352 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8335 (tm-30) REVERT: A 364 ASP cc_start: 0.9354 (t70) cc_final: 0.9086 (t0) REVERT: A 404 ASP cc_start: 0.8568 (t70) cc_final: 0.8265 (t0) REVERT: A 409 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8737 (ttmm) REVERT: A 412 ARG cc_start: 0.7413 (ttp80) cc_final: 0.6987 (ptt90) REVERT: A 478 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: A 489 LYS cc_start: 0.9293 (mttt) cc_final: 0.9057 (mmtp) REVERT: A 496 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 500 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8808 (tm-30) REVERT: B 64 PRO cc_start: 0.9478 (Cg_endo) cc_final: 0.9252 (Cg_exo) REVERT: B 78 MET cc_start: 0.9020 (tmt) cc_final: 0.8571 (tmt) REVERT: B 92 HIS cc_start: 0.8810 (p90) cc_final: 0.8602 (p90) REVERT: B 105 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8412 (ptp-110) REVERT: B 160 SER cc_start: 0.8513 (t) cc_final: 0.7822 (m) REVERT: B 179 MET cc_start: 0.7249 (pp-130) cc_final: 0.6926 (pp-130) REVERT: B 231 ARG cc_start: 0.8921 (mmt-90) cc_final: 0.8695 (mmp80) REVERT: B 259 ARG cc_start: 0.8871 (mtp-110) cc_final: 0.8188 (ttm-80) REVERT: B 274 ASP cc_start: 0.8980 (t0) cc_final: 0.8672 (t0) REVERT: B 277 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8717 (tm-30) REVERT: B 334 GLN cc_start: 0.8984 (mt0) cc_final: 0.8511 (mt0) REVERT: B 335 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 395 GLU cc_start: 0.8750 (mp0) cc_final: 0.8544 (mp0) REVERT: B 408 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8183 (pp) REVERT: B 409 LYS cc_start: 0.8137 (mttp) cc_final: 0.7723 (mmtt) REVERT: B 487 GLU cc_start: 0.9139 (tt0) cc_final: 0.8625 (tt0) REVERT: B 498 GLN cc_start: 0.8313 (mm110) cc_final: 0.8093 (mm-40) REVERT: C 25 ASN cc_start: 0.8583 (t0) cc_final: 0.8142 (t0) REVERT: C 36 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8827 (pp) REVERT: C 105 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8237 (ttp80) REVERT: C 108 LYS cc_start: 0.8563 (tptp) cc_final: 0.7945 (tptp) REVERT: C 134 LYS cc_start: 0.9328 (ptmm) cc_final: 0.9046 (tptt) REVERT: C 150 MET cc_start: 0.7889 (tpp) cc_final: 0.7604 (tpp) REVERT: C 153 ARG cc_start: 0.8941 (tpt-90) cc_final: 0.8720 (tpt-90) REVERT: C 164 ASP cc_start: 0.6463 (m-30) cc_final: 0.6125 (m-30) REVERT: C 182 ARG cc_start: 0.8143 (tpm170) cc_final: 0.7664 (tpp-160) REVERT: C 206 LYS cc_start: 0.9144 (tppp) cc_final: 0.8726 (mmmm) REVERT: C 218 LEU cc_start: 0.9495 (pt) cc_final: 0.9015 (tt) REVERT: C 224 ARG cc_start: 0.8932 (ttt-90) cc_final: 0.8236 (ttm-80) REVERT: C 258 TYR cc_start: 0.8038 (t80) cc_final: 0.7825 (t80) REVERT: C 277 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 279 ASN cc_start: 0.8938 (t0) cc_final: 0.8572 (t0) REVERT: C 386 MET cc_start: 0.8427 (mpm) cc_final: 0.7959 (mpm) REVERT: C 400 TYR cc_start: 0.7126 (m-80) cc_final: 0.6697 (m-10) REVERT: C 450 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8560 (ptpp) REVERT: C 468 CYS cc_start: 0.8781 (t) cc_final: 0.8298 (t) REVERT: C 478 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: C 480 ARG cc_start: 0.9062 (mtm-85) cc_final: 0.8855 (mtt90) REVERT: C 483 MET cc_start: 0.9188 (tmm) cc_final: 0.8777 (tmm) REVERT: C 509 TYR cc_start: 0.9124 (p90) cc_final: 0.8791 (p90) REVERT: D 34 ASP cc_start: 0.7943 (t0) cc_final: 0.7702 (m-30) REVERT: D 103 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8145 (tp30) REVERT: D 199 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8864 (tm-30) REVERT: D 231 ARG cc_start: 0.7514 (mmp-170) cc_final: 0.7084 (mmp-170) REVERT: D 285 ASN cc_start: 0.9208 (m110) cc_final: 0.8929 (m110) REVERT: D 327 SER cc_start: 0.9072 (p) cc_final: 0.8775 (t) REVERT: D 359 VAL cc_start: 0.9311 (t) cc_final: 0.9092 (p) REVERT: D 482 MET cc_start: 0.9258 (mtp) cc_final: 0.8940 (mtp) REVERT: D 483 MET cc_start: 0.9830 (tmm) cc_final: 0.9454 (tmm) REVERT: E 16 ASP cc_start: 0.8924 (t70) cc_final: 0.8256 (t0) REVERT: E 75 GLU cc_start: 0.8180 (mp0) cc_final: 0.7826 (mp0) REVERT: E 150 MET cc_start: 0.7096 (tmt) cc_final: 0.6449 (tmt) REVERT: E 230 ASN cc_start: 0.8906 (t0) cc_final: 0.8649 (t0) REVERT: E 241 LYS cc_start: 0.9205 (mptt) cc_final: 0.8848 (mmtm) REVERT: E 274 ASP cc_start: 0.9056 (t0) cc_final: 0.8817 (t0) REVERT: E 279 ASN cc_start: 0.8692 (t0) cc_final: 0.7751 (t0) REVERT: E 285 ASN cc_start: 0.8862 (m110) cc_final: 0.8404 (m110) REVERT: E 296 ASN cc_start: 0.8334 (p0) cc_final: 0.8056 (t0) REVERT: E 364 ASP cc_start: 0.8918 (m-30) cc_final: 0.8657 (t70) REVERT: E 461 ILE cc_start: 0.8872 (pp) cc_final: 0.8509 (mp) REVERT: E 466 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.8038 (t-90) REVERT: E 500 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8837 (tm-30) REVERT: F 16 ASP cc_start: 0.8790 (t0) cc_final: 0.8362 (t0) REVERT: F 51 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8145 (tm) REVERT: F 105 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8433 (ptp-110) REVERT: F 110 TYR cc_start: 0.8684 (t80) cc_final: 0.8375 (t80) REVERT: F 121 LEU cc_start: 0.8306 (tt) cc_final: 0.8086 (tt) REVERT: F 179 MET cc_start: 0.7691 (pp-130) cc_final: 0.7434 (pp-130) REVERT: F 203 ARG cc_start: 0.9080 (mtm110) cc_final: 0.8861 (mtm110) REVERT: F 319 ASP cc_start: 0.8045 (t0) cc_final: 0.7734 (m-30) REVERT: F 359 VAL cc_start: 0.9272 (t) cc_final: 0.8990 (p) REVERT: F 409 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8088 (mttt) REVERT: F 412 ARG cc_start: 0.8123 (ttp80) cc_final: 0.6917 (ptt90) REVERT: F 482 MET cc_start: 0.8777 (mtp) cc_final: 0.7959 (ttm) REVERT: F 487 GLU cc_start: 0.9199 (tt0) cc_final: 0.8440 (tt0) REVERT: G 75 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8138 (mm-30) REVERT: G 78 MET cc_start: 0.8526 (tpp) cc_final: 0.8289 (mpp) REVERT: G 80 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8422 (tt) REVERT: G 84 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8140 (pt) REVERT: G 105 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8506 (ttp80) REVERT: G 153 ARG cc_start: 0.7935 (tpt170) cc_final: 0.7699 (tpp80) REVERT: G 195 LYS cc_start: 0.9282 (pmmt) cc_final: 0.8572 (tttt) REVERT: G 277 GLN cc_start: 0.8282 (tm-30) cc_final: 0.8031 (tm-30) REVERT: G 355 ARG cc_start: 0.9310 (ptt180) cc_final: 0.8706 (ttp-170) REVERT: G 369 ASN cc_start: 0.8666 (p0) cc_final: 0.8420 (p0) REVERT: G 386 MET cc_start: 0.8896 (mmp) cc_final: 0.8623 (mmm) REVERT: G 400 TYR cc_start: 0.7169 (m-80) cc_final: 0.6368 (m-80) REVERT: G 475 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8514 (t) REVERT: G 478 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7397 (pp30) REVERT: G 484 TYR cc_start: 0.9119 (m-80) cc_final: 0.8723 (m-10) REVERT: G 510 GLU cc_start: 0.8186 (mp0) cc_final: 0.7896 (mp0) REVERT: H 32 TYR cc_start: 0.8709 (m-10) cc_final: 0.8443 (m-10) REVERT: H 33 ASN cc_start: 0.8292 (t0) cc_final: 0.7676 (t0) REVERT: H 75 GLU cc_start: 0.8425 (mp0) cc_final: 0.8130 (mp0) REVERT: H 93 HIS cc_start: 0.8931 (p-80) cc_final: 0.8615 (p90) REVERT: H 131 PHE cc_start: 0.9166 (m-80) cc_final: 0.8605 (m-80) REVERT: H 228 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8274 (tmtt) REVERT: H 230 ASN cc_start: 0.8166 (t0) cc_final: 0.7162 (t0) REVERT: H 231 ARG cc_start: 0.8537 (mmp80) cc_final: 0.8230 (mmp-170) REVERT: H 274 ASP cc_start: 0.9106 (t70) cc_final: 0.8703 (t70) REVERT: H 286 MET cc_start: 0.8494 (mtp) cc_final: 0.8153 (mtp) REVERT: H 309 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: H 343 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7604 (tm-30) REVERT: H 383 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8235 (t) REVERT: H 395 GLU cc_start: 0.8612 (mp0) cc_final: 0.8326 (mp0) REVERT: H 400 TYR cc_start: 0.7575 (m-10) cc_final: 0.7312 (m-10) REVERT: H 493 ARG cc_start: 0.9091 (ttp-170) cc_final: 0.8605 (ttp-170) REVERT: H 510 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8084 (tm-30) REVERT: O 7 SER cc_start: 0.9175 (m) cc_final: 0.8931 (p) REVERT: K 4 TYR cc_start: 0.9184 (t80) cc_final: 0.8926 (t80) outliers start: 215 outliers final: 127 residues processed: 1131 average time/residue: 0.1877 time to fit residues: 349.7958 Evaluate side-chains 1059 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 917 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 475 SER Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain J residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 38 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 311 optimal weight: 0.0010 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 129 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 303 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** 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 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN F 285 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 279 ASN ** G 478 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 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097268 restraints weight = 51667.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.101252 restraints weight = 26840.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.103979 restraints weight = 17059.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105761 restraints weight = 12355.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.107045 restraints weight = 9880.427| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32073 Z= 0.138 Angle : 0.771 15.409 43488 Z= 0.375 Chirality : 0.049 0.420 4968 Planarity : 0.004 0.052 5448 Dihedral : 8.790 88.266 4495 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.16 % Favored : 92.82 % Rotamer: Outliers : 6.97 % Allowed : 24.36 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.12), residues: 3968 helix: -1.42 (0.14), residues: 1278 sheet: -1.99 (0.24), residues: 398 loop : -1.90 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 203 TYR 0.030 0.002 TYR E 110 PHE 0.020 0.001 PHE D 165 HIS 0.011 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (32072) covalent geometry : angle 0.77108 / 0.37 (43488) hydrogen bonds : bond 0.03736 / 2.51 ( 961) hydrogen bonds : angle 5.78768 / 4.04 ( 2700) Misc. bond : bond 0.00101 / 0.05 ( 1) *********************** 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 1223 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 995 time to evaluate : 1.174 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: A 34 ASP cc_start: 0.8261 (t70) cc_final: 0.8029 (t70) REVERT: A 105 ARG cc_start: 0.8720 (mtp-110) cc_final: 0.8175 (ttm-80) REVERT: A 110 TYR cc_start: 0.8154 (t80) cc_final: 0.7304 (t80) REVERT: A 229 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8535 (mtpp) REVERT: A 230 ASN cc_start: 0.9072 (t0) cc_final: 0.8852 (t0) REVERT: A 238 LYS cc_start: 0.8364 (mtmp) cc_final: 0.8083 (mtmm) REVERT: A 279 ASN cc_start: 0.8630 (t0) cc_final: 0.7588 (t0) REVERT: A 319 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7178 (t0) REVERT: A 352 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 364 ASP cc_start: 0.9276 (t70) cc_final: 0.9026 (t0) REVERT: A 404 ASP cc_start: 0.8493 (t70) cc_final: 0.8215 (t0) REVERT: A 409 LYS cc_start: 0.9182 (ttmm) cc_final: 0.8650 (ttmm) REVERT: A 412 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6980 (ptt90) REVERT: A 461 ILE cc_start: 0.9260 (mm) cc_final: 0.9034 (mp) REVERT: A 478 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8346 (pt0) REVERT: A 487 GLU cc_start: 0.8394 (tt0) cc_final: 0.8187 (tt0) REVERT: A 489 LYS cc_start: 0.9301 (mttt) cc_final: 0.8880 (mmtp) REVERT: A 500 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8796 (tm-30) REVERT: B 78 MET cc_start: 0.8972 (tmt) cc_final: 0.8549 (tmt) REVERT: B 92 HIS cc_start: 0.8733 (p90) cc_final: 0.8495 (p90) REVERT: B 160 SER cc_start: 0.8513 (t) cc_final: 0.7822 (m) REVERT: B 231 ARG cc_start: 0.8902 (mmt-90) cc_final: 0.8660 (mmp80) REVERT: B 259 ARG cc_start: 0.8700 (mtp-110) cc_final: 0.8167 (ttm-80) REVERT: B 332 ILE cc_start: 0.8720 (pp) cc_final: 0.8441 (pt) REVERT: B 334 GLN cc_start: 0.8940 (mt0) cc_final: 0.8448 (mt0) REVERT: B 335 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 408 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8088 (pp) REVERT: B 409 LYS cc_start: 0.8140 (mttp) cc_final: 0.7692 (mmtt) REVERT: B 412 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7291 (ptt90) REVERT: B 448 GLN cc_start: 0.8539 (tt0) cc_final: 0.8284 (pm20) REVERT: B 482 MET cc_start: 0.8705 (mtp) cc_final: 0.8217 (ttm) REVERT: B 487 GLU cc_start: 0.9083 (tt0) cc_final: 0.8375 (tt0) REVERT: C 25 ASN cc_start: 0.8515 (t0) cc_final: 0.7969 (t0) REVERT: C 36 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8870 (pp) REVERT: C 75 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: C 98 GLU cc_start: 0.8557 (mp0) cc_final: 0.8297 (mp0) REVERT: C 102 ASN cc_start: 0.8370 (p0) cc_final: 0.7767 (p0) REVERT: C 105 ARG cc_start: 0.8604 (mtm110) cc_final: 0.8189 (ttp80) REVERT: C 150 MET cc_start: 0.8019 (tpp) cc_final: 0.7697 (tpp) REVERT: C 164 ASP cc_start: 0.6694 (m-30) cc_final: 0.6289 (m-30) REVERT: C 179 MET cc_start: 0.7442 (pp-130) cc_final: 0.7237 (pp-130) REVERT: C 182 ARG cc_start: 0.8141 (tpm170) cc_final: 0.7609 (tpp-160) REVERT: C 206 LYS cc_start: 0.9147 (tppp) cc_final: 0.8727 (mmmm) REVERT: C 218 LEU cc_start: 0.9491 (pt) cc_final: 0.9010 (tt) REVERT: C 224 ARG cc_start: 0.8945 (ttt-90) cc_final: 0.8293 (ttm-80) REVERT: C 279 ASN cc_start: 0.8912 (t0) cc_final: 0.8582 (t0) REVERT: C 369 ASN cc_start: 0.8626 (p0) cc_final: 0.8218 (p0) REVERT: C 386 MET cc_start: 0.8564 (mpm) cc_final: 0.8061 (mpm) REVERT: C 468 CYS cc_start: 0.8791 (t) cc_final: 0.8322 (t) REVERT: C 478 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: C 483 MET cc_start: 0.9231 (tmm) cc_final: 0.8681 (tmm) REVERT: C 484 TYR cc_start: 0.9020 (m-80) cc_final: 0.8564 (m-10) REVERT: D 32 TYR cc_start: 0.8679 (m-10) cc_final: 0.8358 (m-10) REVERT: D 102 ASN cc_start: 0.9196 (t0) cc_final: 0.8980 (t0) REVERT: D 103 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8092 (tp30) REVERT: D 111 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7334 (mm-30) REVERT: D 199 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8934 (tm-30) REVERT: D 235 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7941 (pp) REVERT: D 277 GLN cc_start: 0.8945 (tp40) cc_final: 0.8724 (mm110) REVERT: D 285 ASN cc_start: 0.9219 (m110) cc_final: 0.8883 (m110) REVERT: D 319 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.6928 (t0) REVERT: D 327 SER cc_start: 0.9015 (p) cc_final: 0.8767 (t) REVERT: D 343 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8265 (tm-30) REVERT: D 359 VAL cc_start: 0.9327 (t) cc_final: 0.9090 (p) REVERT: D 400 TYR cc_start: 0.6928 (m-80) cc_final: 0.5467 (m-80) REVERT: D 482 MET cc_start: 0.9234 (mtp) cc_final: 0.8925 (mtp) REVERT: D 483 MET cc_start: 0.9810 (tmm) cc_final: 0.9422 (tmm) REVERT: E 70 MET cc_start: 0.8527 (mtm) cc_final: 0.7951 (mtt) REVERT: E 75 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7860 (mp0) REVERT: E 105 ARG cc_start: 0.8687 (mtp-110) cc_final: 0.7853 (ttm-80) REVERT: E 110 TYR cc_start: 0.8061 (t80) cc_final: 0.7586 (t80) REVERT: E 149 ARG cc_start: 0.8145 (mpt180) cc_final: 0.7941 (mpp80) REVERT: E 150 MET cc_start: 0.7038 (tmt) cc_final: 0.6378 (tmt) REVERT: E 181 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8349 (mmtt) REVERT: E 238 LYS cc_start: 0.8322 (mtmm) cc_final: 0.8061 (mtmm) REVERT: E 241 LYS cc_start: 0.9189 (mptt) cc_final: 0.8779 (ttmm) REVERT: E 274 ASP cc_start: 0.9026 (t0) cc_final: 0.8798 (t0) REVERT: E 279 ASN cc_start: 0.8549 (t0) cc_final: 0.7543 (t0) REVERT: E 296 ASN cc_start: 0.8202 (p0) cc_final: 0.7991 (t0) REVERT: E 335 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8252 (tm-30) REVERT: E 364 ASP cc_start: 0.8984 (m-30) cc_final: 0.8728 (t70) REVERT: E 466 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8170 (t-90) REVERT: E 500 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8855 (tm-30) REVERT: F 16 ASP cc_start: 0.8767 (t0) cc_final: 0.8373 (t0) REVERT: F 78 MET cc_start: 0.9145 (tpp) cc_final: 0.8941 (tpp) REVERT: F 105 ARG cc_start: 0.8771 (mtm110) cc_final: 0.8560 (mtt-85) REVERT: F 110 TYR cc_start: 0.8678 (t80) cc_final: 0.8422 (t80) REVERT: F 114 PHE cc_start: 0.9053 (m-10) cc_final: 0.8760 (m-80) REVERT: F 203 ARG cc_start: 0.9083 (mtm110) cc_final: 0.8739 (mtm110) REVERT: F 259 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8121 (ttm-80) REVERT: F 299 VAL cc_start: 0.8699 (m) cc_final: 0.8414 (m) REVERT: F 319 ASP cc_start: 0.8110 (t0) cc_final: 0.7693 (t0) REVERT: F 409 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8058 (mttt) REVERT: F 412 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7689 (ptt90) REVERT: G 75 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7988 (mm-30) REVERT: G 78 MET cc_start: 0.8457 (tpp) cc_final: 0.8215 (tpp) REVERT: G 84 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8095 (pt) REVERT: G 105 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8518 (ttp80) REVERT: G 106 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8546 (ttpt) REVERT: G 153 ARG cc_start: 0.8063 (tpt170) cc_final: 0.7853 (tpp80) REVERT: G 195 LYS cc_start: 0.9280 (pmmt) cc_final: 0.8635 (tttt) REVERT: G 277 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7926 (tm-30) REVERT: G 322 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7256 (ttt-90) REVERT: G 342 PRO cc_start: 0.9361 (Cg_exo) cc_final: 0.9154 (Cg_endo) REVERT: G 369 ASN cc_start: 0.8673 (p0) cc_final: 0.8269 (p0) REVERT: G 386 MET cc_start: 0.9010 (mmp) cc_final: 0.8704 (mmm) REVERT: G 390 LEU cc_start: 0.8984 (mp) cc_final: 0.8742 (mp) REVERT: G 400 TYR cc_start: 0.7154 (m-80) cc_final: 0.5582 (m-80) REVERT: G 510 GLU cc_start: 0.8139 (mp0) cc_final: 0.7824 (mp0) REVERT: H 32 TYR cc_start: 0.8650 (m-10) cc_final: 0.8436 (m-10) REVERT: H 33 ASN cc_start: 0.8284 (t0) cc_final: 0.7774 (t0) REVERT: H 65 LEU cc_start: 0.9054 (mt) cc_final: 0.8813 (mt) REVERT: H 75 GLU cc_start: 0.8308 (mp0) cc_final: 0.7932 (mp0) REVERT: H 93 HIS cc_start: 0.8957 (p-80) cc_final: 0.8628 (p90) REVERT: H 99 PHE cc_start: 0.9253 (t80) cc_final: 0.8975 (t80) REVERT: H 131 PHE cc_start: 0.9088 (m-80) cc_final: 0.8543 (m-80) REVERT: H 228 LYS cc_start: 0.8625 (mtmm) cc_final: 0.8277 (tmtt) REVERT: H 230 ASN cc_start: 0.8202 (t0) cc_final: 0.7289 (t0) REVERT: H 231 ARG cc_start: 0.8540 (mmp80) cc_final: 0.8247 (mmp-170) REVERT: H 274 ASP cc_start: 0.9067 (t70) cc_final: 0.8733 (t70) REVERT: H 309 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: H 343 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7656 (tm-30) REVERT: H 359 VAL cc_start: 0.9266 (t) cc_final: 0.8859 (p) REVERT: H 395 GLU cc_start: 0.8564 (mp0) cc_final: 0.8322 (mp0) REVERT: H 493 ARG cc_start: 0.8957 (ttp-170) cc_final: 0.8712 (ttp-170) REVERT: H 510 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8102 (tm-30) REVERT: K 4 TYR cc_start: 0.9110 (t80) cc_final: 0.8834 (t80) outliers start: 228 outliers final: 139 residues processed: 1107 average time/residue: 0.1905 time to fit residues: 348.2808 Evaluate side-chains 1076 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 924 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 363 optimal weight: 3.9990 chunk 274 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 64 optimal weight: 0.0370 chunk 328 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 243 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN F 285 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 465 GLN G 478 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.097367 restraints weight = 51975.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.101299 restraints weight = 27169.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104006 restraints weight = 17392.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105784 restraints weight = 12624.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107147 restraints weight = 10103.653| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32073 Z= 0.142 Angle : 0.768 15.741 43488 Z= 0.370 Chirality : 0.049 0.432 4968 Planarity : 0.004 0.068 5448 Dihedral : 8.451 84.196 4488 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.74 % Favored : 92.24 % Rotamer: Outliers : 7.33 % Allowed : 25.73 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.13), residues: 3968 helix: -1.14 (0.14), residues: 1268 sheet: -1.67 (0.25), residues: 384 loop : -1.84 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 203 TYR 0.028 0.002 TYR E 110 PHE 0.018 0.001 PHE D 165 HIS 0.011 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (32072) covalent geometry : angle 0.76794 / 0.37 (43488) hydrogen bonds : bond 0.03583 / 2.40 ( 961) hydrogen bonds : angle 5.68660 / 3.98 ( 2700) Misc. bond : bond 0.00124 / 0.07 ( 1) *********************** 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 1217 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 977 time to evaluate : 1.260 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: A 34 ASP cc_start: 0.8307 (t70) cc_final: 0.8071 (t70) REVERT: A 102 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8691 (p0) REVERT: A 103 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8707 (tp30) REVERT: A 105 ARG cc_start: 0.8741 (mtp-110) cc_final: 0.8185 (ttm-80) REVERT: A 229 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8711 (mtpp) REVERT: A 230 ASN cc_start: 0.9131 (t0) cc_final: 0.8861 (t0) REVERT: A 238 LYS cc_start: 0.8394 (mtmp) cc_final: 0.8111 (mtmm) REVERT: A 274 ASP cc_start: 0.8905 (t0) cc_final: 0.8513 (t0) REVERT: A 279 ASN cc_start: 0.8585 (t0) cc_final: 0.7643 (t0) REVERT: A 319 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7113 (t0) REVERT: A 352 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8313 (tm-30) REVERT: A 353 TYR cc_start: 0.9004 (t80) cc_final: 0.8688 (t80) REVERT: A 364 ASP cc_start: 0.9320 (t70) cc_final: 0.9116 (t0) REVERT: A 404 ASP cc_start: 0.8565 (t70) cc_final: 0.8108 (t0) REVERT: A 409 LYS cc_start: 0.9212 (ttmm) cc_final: 0.8694 (ttmm) REVERT: A 412 ARG cc_start: 0.7359 (ttp80) cc_final: 0.7009 (ptt90) REVERT: A 414 MET cc_start: 0.9167 (mmp) cc_final: 0.8934 (mmm) REVERT: A 461 ILE cc_start: 0.9228 (mm) cc_final: 0.9017 (mp) REVERT: A 478 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: A 487 GLU cc_start: 0.8419 (tt0) cc_final: 0.8214 (tt0) REVERT: A 489 LYS cc_start: 0.9301 (mttt) cc_final: 0.8874 (mmtp) REVERT: A 500 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8784 (tm-30) REVERT: B 92 HIS cc_start: 0.8755 (p90) cc_final: 0.8454 (p90) REVERT: B 103 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: B 160 SER cc_start: 0.8519 (t) cc_final: 0.7734 (m) REVERT: B 231 ARG cc_start: 0.8908 (mmt-90) cc_final: 0.8660 (mmp80) REVERT: B 259 ARG cc_start: 0.8603 (mtp-110) cc_final: 0.8269 (ttm-80) REVERT: B 334 GLN cc_start: 0.8961 (mt0) cc_final: 0.8546 (mt0) REVERT: B 335 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 352 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7843 (pp20) REVERT: B 385 MET cc_start: 0.8508 (ttm) cc_final: 0.8045 (ttp) REVERT: B 408 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8107 (pp) REVERT: B 409 LYS cc_start: 0.8218 (mttp) cc_final: 0.7675 (mmtp) REVERT: B 412 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7223 (ptt90) REVERT: B 482 MET cc_start: 0.8661 (mtp) cc_final: 0.8050 (ttm) REVERT: B 487 GLU cc_start: 0.9051 (tt0) cc_final: 0.8260 (tt0) REVERT: C 25 ASN cc_start: 0.8512 (t0) cc_final: 0.7971 (t0) REVERT: C 36 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8670 (pp) REVERT: C 75 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8093 (mm-30) REVERT: C 105 ARG cc_start: 0.8592 (mtm110) cc_final: 0.8200 (ttp80) REVERT: C 134 LYS cc_start: 0.9343 (ptmm) cc_final: 0.9030 (tppt) REVERT: C 150 MET cc_start: 0.7917 (tpp) cc_final: 0.6817 (tpp) REVERT: C 164 ASP cc_start: 0.6623 (m-30) cc_final: 0.6235 (m-30) REVERT: C 179 MET cc_start: 0.7502 (pp-130) cc_final: 0.7242 (pp-130) REVERT: C 182 ARG cc_start: 0.8142 (tpm170) cc_final: 0.7625 (tpp-160) REVERT: C 206 LYS cc_start: 0.9135 (tppp) cc_final: 0.8817 (mmmm) REVERT: C 218 LEU cc_start: 0.9490 (pt) cc_final: 0.9011 (tt) REVERT: C 224 ARG cc_start: 0.8990 (ttt-90) cc_final: 0.8527 (ttm-80) REVERT: C 277 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7598 (tm-30) REVERT: C 279 ASN cc_start: 0.8878 (t0) cc_final: 0.8438 (t0) REVERT: C 355 ARG cc_start: 0.9230 (ptm-80) cc_final: 0.8807 (ptm-80) REVERT: C 369 ASN cc_start: 0.8623 (p0) cc_final: 0.8142 (p0) REVERT: C 386 MET cc_start: 0.8454 (mpm) cc_final: 0.7953 (mpm) REVERT: C 400 TYR cc_start: 0.7122 (m-80) cc_final: 0.6288 (m-80) REVERT: C 450 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8640 (ptpp) REVERT: C 468 CYS cc_start: 0.8835 (t) cc_final: 0.8333 (t) REVERT: C 478 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: C 483 MET cc_start: 0.9260 (tmm) cc_final: 0.8683 (tmm) REVERT: C 484 TYR cc_start: 0.9105 (m-80) cc_final: 0.8648 (m-10) REVERT: C 510 GLU cc_start: 0.8368 (mp0) cc_final: 0.8164 (mp0) REVERT: D 32 TYR cc_start: 0.8714 (m-10) cc_final: 0.8301 (m-10) REVERT: D 103 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: D 105 ARG cc_start: 0.8714 (mtm110) cc_final: 0.8426 (ptt180) REVERT: D 111 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7419 (mm-30) REVERT: D 199 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8923 (tm-30) REVERT: D 231 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7558 (mmm160) REVERT: D 277 GLN cc_start: 0.8970 (tp40) cc_final: 0.8738 (mm110) REVERT: D 285 ASN cc_start: 0.9234 (m110) cc_final: 0.8861 (m110) REVERT: D 319 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.6877 (t0) REVERT: D 327 SER cc_start: 0.8951 (p) cc_final: 0.8748 (t) REVERT: D 343 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8397 (tm-30) REVERT: D 359 VAL cc_start: 0.9322 (t) cc_final: 0.9105 (p) REVERT: D 482 MET cc_start: 0.9248 (mtp) cc_final: 0.8929 (mtp) REVERT: D 483 MET cc_start: 0.9810 (tmm) cc_final: 0.9454 (tmm) REVERT: E 70 MET cc_start: 0.8493 (mtm) cc_final: 0.8212 (mtt) REVERT: E 75 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7680 (mp0) REVERT: E 149 ARG cc_start: 0.8163 (mpt180) cc_final: 0.7949 (mpp80) REVERT: E 150 MET cc_start: 0.6984 (tmt) cc_final: 0.6333 (tmt) REVERT: E 238 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7999 (mtmm) REVERT: E 241 LYS cc_start: 0.9181 (mptt) cc_final: 0.8799 (ttmm) REVERT: E 279 ASN cc_start: 0.8482 (t0) cc_final: 0.7612 (t0) REVERT: E 364 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8731 (t70) REVERT: E 466 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8123 (t-90) REVERT: E 483 MET cc_start: 0.9475 (tmm) cc_final: 0.9232 (tmm) REVERT: E 500 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8868 (tm-30) REVERT: F 16 ASP cc_start: 0.8787 (t0) cc_final: 0.8396 (t0) REVERT: F 92 HIS cc_start: 0.8817 (p90) cc_final: 0.8521 (p-80) REVERT: F 98 GLU cc_start: 0.9347 (mp0) cc_final: 0.8896 (pm20) REVERT: F 103 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: F 110 TYR cc_start: 0.8705 (t80) cc_final: 0.8505 (t80) REVERT: F 114 PHE cc_start: 0.9053 (m-10) cc_final: 0.8710 (m-80) REVERT: F 199 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: F 203 ARG cc_start: 0.9069 (mtm110) cc_final: 0.8776 (mtm110) REVERT: F 319 ASP cc_start: 0.8106 (t0) cc_final: 0.7681 (t0) REVERT: F 408 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8417 (pp) REVERT: F 409 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8040 (mmtt) REVERT: F 412 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7677 (ptt90) REVERT: G 75 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8025 (mm-30) REVERT: G 84 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8019 (pt) REVERT: G 105 ARG cc_start: 0.8769 (mtm110) cc_final: 0.8522 (ttp80) REVERT: G 132 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8107 (mm-30) REVERT: G 195 LYS cc_start: 0.9312 (pmmt) cc_final: 0.8623 (tttt) REVERT: G 232 ASP cc_start: 0.8401 (t70) cc_final: 0.7916 (t0) REVERT: G 277 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7895 (tm-30) REVERT: G 369 ASN cc_start: 0.8660 (p0) cc_final: 0.8258 (p0) REVERT: G 478 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7429 (pp30) REVERT: G 510 GLU cc_start: 0.8148 (mp0) cc_final: 0.7811 (mp0) REVERT: H 33 ASN cc_start: 0.8335 (t0) cc_final: 0.7800 (t0) REVERT: H 65 LEU cc_start: 0.9199 (mt) cc_final: 0.8959 (mt) REVERT: H 75 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7857 (pm20) REVERT: H 93 HIS cc_start: 0.8950 (p-80) cc_final: 0.8611 (p90) REVERT: H 99 PHE cc_start: 0.9237 (t80) cc_final: 0.8926 (t80) REVERT: H 131 PHE cc_start: 0.9096 (m-80) cc_final: 0.8752 (m-80) REVERT: H 228 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8355 (tmtt) REVERT: H 230 ASN cc_start: 0.8185 (t0) cc_final: 0.7291 (t0) REVERT: H 231 ARG cc_start: 0.8538 (mmp80) cc_final: 0.8230 (mmp-170) REVERT: H 274 ASP cc_start: 0.9061 (t70) cc_final: 0.8768 (t70) REVERT: H 319 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6512 (t0) REVERT: H 343 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7644 (tm-30) REVERT: H 359 VAL cc_start: 0.9317 (t) cc_final: 0.8951 (p) REVERT: H 510 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8085 (tm-30) REVERT: O 1 MET cc_start: 0.5462 (pmm) cc_final: 0.4876 (pmm) REVERT: K 1 MET cc_start: 0.5866 (pmm) cc_final: 0.5178 (pmm) REVERT: K 4 TYR cc_start: 0.9065 (t80) cc_final: 0.8759 (t80) outliers start: 240 outliers final: 160 residues processed: 1102 average time/residue: 0.1915 time to fit residues: 349.8521 Evaluate side-chains 1097 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 916 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 300 optimal weight: 0.0170 chunk 212 optimal weight: 5.9990 chunk 220 optimal weight: 0.6980 chunk 340 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 230 optimal weight: 0.6980 chunk 255 optimal weight: 10.0000 chunk 369 optimal weight: 0.4980 chunk 181 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 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 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 171 HIS H 478 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115873 restraints weight = 52027.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120348 restraints weight = 25701.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123381 restraints weight = 15806.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125374 restraints weight = 11166.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126516 restraints weight = 8775.234| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32073 Z= 0.132 Angle : 0.781 16.389 43488 Z= 0.372 Chirality : 0.049 0.457 4968 Planarity : 0.004 0.056 5448 Dihedral : 8.271 87.035 4488 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.26 % Favored : 92.72 % Rotamer: Outliers : 7.03 % Allowed : 27.44 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.13), residues: 3968 helix: -1.00 (0.14), residues: 1274 sheet: -1.57 (0.26), residues: 380 loop : -1.79 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 149 TYR 0.026 0.002 TYR G 484 PHE 0.018 0.001 PHE F 131 HIS 0.009 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (32072) covalent geometry : angle 0.78065 / 0.37 (43488) hydrogen bonds : bond 0.03493 / 2.35 ( 961) hydrogen bonds : angle 5.64557 / 3.95 ( 2700) Misc. bond : bond 0.00092 / 0.05 ( 1) *********************** 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 1209 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 979 time to evaluate : 1.207 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: A 34 ASP cc_start: 0.8271 (t70) cc_final: 0.8033 (t70) REVERT: A 102 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8651 (p0) REVERT: A 103 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8739 (tp30) REVERT: A 105 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8218 (ttm-80) REVERT: A 110 TYR cc_start: 0.7393 (t80) cc_final: 0.7108 (t80) REVERT: A 112 GLN cc_start: 0.7479 (mp10) cc_final: 0.7128 (mp10) REVERT: A 238 LYS cc_start: 0.8396 (mtmp) cc_final: 0.8175 (mtmm) REVERT: A 242 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7595 (mmtt) REVERT: A 274 ASP cc_start: 0.8946 (t0) cc_final: 0.8589 (t0) REVERT: A 279 ASN cc_start: 0.8554 (t0) cc_final: 0.7804 (t0) REVERT: A 296 ASN cc_start: 0.8723 (p0) cc_final: 0.8229 (t0) REVERT: A 319 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7139 (t0) REVERT: A 353 TYR cc_start: 0.8977 (t80) cc_final: 0.8718 (t80) REVERT: A 364 ASP cc_start: 0.9338 (t0) cc_final: 0.9132 (t0) REVERT: A 404 ASP cc_start: 0.8610 (t70) cc_final: 0.8147 (t0) REVERT: A 409 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8689 (ttmm) REVERT: A 412 ARG cc_start: 0.7346 (ttp80) cc_final: 0.6893 (ptt90) REVERT: A 478 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8348 (pt0) REVERT: A 487 GLU cc_start: 0.8434 (tt0) cc_final: 0.8200 (tt0) REVERT: A 489 LYS cc_start: 0.9275 (mttt) cc_final: 0.8847 (mmtp) REVERT: A 500 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8764 (tm-30) REVERT: B 22 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8596 (pm20) REVERT: B 92 HIS cc_start: 0.8730 (p90) cc_final: 0.8420 (p90) REVERT: B 98 GLU cc_start: 0.9079 (pm20) cc_final: 0.8766 (pm20) REVERT: B 103 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: B 160 SER cc_start: 0.8308 (t) cc_final: 0.7624 (m) REVERT: B 231 ARG cc_start: 0.8891 (mmt-90) cc_final: 0.8624 (mmp80) REVERT: B 259 ARG cc_start: 0.8466 (mtp-110) cc_final: 0.8068 (ttm-80) REVERT: B 277 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8449 (tt0) REVERT: B 312 ASN cc_start: 0.9363 (m-40) cc_final: 0.8878 (t0) REVERT: B 334 GLN cc_start: 0.8934 (mt0) cc_final: 0.8491 (mt0) REVERT: B 335 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 343 GLN cc_start: 0.8596 (tp40) cc_final: 0.8371 (tp-100) REVERT: B 400 TYR cc_start: 0.8196 (m-80) cc_final: 0.7931 (m-10) REVERT: B 408 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8202 (pp) REVERT: B 412 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7565 (ptt90) REVERT: B 482 MET cc_start: 0.8587 (mtp) cc_final: 0.8092 (ttm) REVERT: B 487 GLU cc_start: 0.9033 (tt0) cc_final: 0.8277 (tt0) REVERT: C 25 ASN cc_start: 0.8499 (t0) cc_final: 0.7971 (t0) REVERT: C 36 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8646 (pp) REVERT: C 37 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8297 (pt) REVERT: C 75 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8130 (mm-30) REVERT: C 105 ARG cc_start: 0.8577 (mtm110) cc_final: 0.8200 (ttp80) REVERT: C 134 LYS cc_start: 0.9347 (ptmm) cc_final: 0.9046 (tppt) REVERT: C 150 MET cc_start: 0.7816 (tpp) cc_final: 0.7599 (tpp) REVERT: C 153 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8454 (tpp80) REVERT: C 164 ASP cc_start: 0.6697 (m-30) cc_final: 0.6107 (m-30) REVERT: C 179 MET cc_start: 0.7515 (pp-130) cc_final: 0.7234 (pp-130) REVERT: C 206 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8465 (mmmm) REVERT: C 218 LEU cc_start: 0.9536 (pt) cc_final: 0.9116 (tt) REVERT: C 224 ARG cc_start: 0.9019 (ttt-90) cc_final: 0.8322 (ttt-90) REVERT: C 355 ARG cc_start: 0.9204 (ptm-80) cc_final: 0.8826 (ptm-80) REVERT: C 386 MET cc_start: 0.8448 (mpm) cc_final: 0.7939 (mpm) REVERT: C 468 CYS cc_start: 0.8855 (t) cc_final: 0.8292 (t) REVERT: C 478 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: C 483 MET cc_start: 0.9271 (tmm) cc_final: 0.8707 (tmm) REVERT: C 484 TYR cc_start: 0.9101 (m-80) cc_final: 0.8680 (m-10) REVERT: C 510 GLU cc_start: 0.8360 (mp0) cc_final: 0.8126 (mp0) REVERT: D 25 ASN cc_start: 0.8282 (m-40) cc_final: 0.7965 (m-40) REVERT: D 32 TYR cc_start: 0.8695 (m-10) cc_final: 0.8267 (m-10) REVERT: D 103 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: D 105 ARG cc_start: 0.8668 (mtm110) cc_final: 0.8453 (ptt180) REVERT: D 111 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7565 (mm-30) REVERT: D 199 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8890 (tm-30) REVERT: D 231 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7827 (mmm160) REVERT: D 277 GLN cc_start: 0.8901 (tp40) cc_final: 0.8316 (tp40) REVERT: D 309 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: D 319 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6836 (t0) REVERT: D 343 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8240 (tm-30) REVERT: D 359 VAL cc_start: 0.9328 (t) cc_final: 0.9114 (p) REVERT: D 482 MET cc_start: 0.9233 (mtp) cc_final: 0.8914 (mtp) REVERT: D 483 MET cc_start: 0.9808 (tmm) cc_final: 0.9468 (tmm) REVERT: E 149 ARG cc_start: 0.8180 (mpt180) cc_final: 0.7952 (mpp80) REVERT: E 150 MET cc_start: 0.7008 (tmt) cc_final: 0.6378 (tmt) REVERT: E 229 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7661 (pttm) REVERT: E 238 LYS cc_start: 0.8266 (mtmm) cc_final: 0.8063 (mtmm) REVERT: E 241 LYS cc_start: 0.9182 (mptt) cc_final: 0.8802 (ttmm) REVERT: E 279 ASN cc_start: 0.8349 (t0) cc_final: 0.7753 (t0) REVERT: E 382 SER cc_start: 0.9535 (m) cc_final: 0.9266 (t) REVERT: E 412 ARG cc_start: 0.7346 (ttp80) cc_final: 0.6543 (ptt90) REVERT: E 466 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.8056 (t-90) REVERT: F 16 ASP cc_start: 0.8753 (t0) cc_final: 0.8355 (t0) REVERT: F 82 MET cc_start: 0.8215 (ppp) cc_final: 0.7536 (tmm) REVERT: F 92 HIS cc_start: 0.8865 (p90) cc_final: 0.8582 (p-80) REVERT: F 98 GLU cc_start: 0.9326 (mp0) cc_final: 0.8909 (pm20) REVERT: F 103 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: F 114 PHE cc_start: 0.9082 (m-10) cc_final: 0.8739 (m-80) REVERT: F 199 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: F 203 ARG cc_start: 0.9066 (mtm110) cc_final: 0.8763 (mtm110) REVERT: F 319 ASP cc_start: 0.8146 (t0) cc_final: 0.7755 (t0) REVERT: F 352 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7790 (pp20) REVERT: F 409 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8003 (mmtt) REVERT: F 412 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7674 (ptt90) REVERT: G 75 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8037 (mm-30) REVERT: G 84 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7998 (pt) REVERT: G 103 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7977 (mm-30) REVERT: G 105 ARG cc_start: 0.8730 (mtm110) cc_final: 0.8469 (ttp80) REVERT: G 179 MET cc_start: 0.4190 (ppp) cc_final: 0.3898 (ppp) REVERT: G 182 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.7645 (mmm160) REVERT: G 195 LYS cc_start: 0.9317 (pmmt) cc_final: 0.8689 (mttt) REVERT: G 232 ASP cc_start: 0.8352 (t70) cc_final: 0.7852 (t0) REVERT: G 238 LYS cc_start: 0.9259 (mttp) cc_final: 0.8750 (mtpp) REVERT: G 355 ARG cc_start: 0.9180 (ptt90) cc_final: 0.8927 (ptm-80) REVERT: G 478 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7358 (pp30) REVERT: G 510 GLU cc_start: 0.8128 (mp0) cc_final: 0.7772 (mp0) REVERT: H 33 ASN cc_start: 0.8295 (t0) cc_final: 0.7780 (t0) REVERT: H 65 LEU cc_start: 0.9200 (mt) cc_final: 0.8944 (mt) REVERT: H 75 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: H 93 HIS cc_start: 0.8944 (p-80) cc_final: 0.8576 (p90) REVERT: H 99 PHE cc_start: 0.9250 (t80) cc_final: 0.8940 (t80) REVERT: H 131 PHE cc_start: 0.8961 (m-80) cc_final: 0.8576 (m-80) REVERT: H 230 ASN cc_start: 0.8130 (t0) cc_final: 0.7286 (t0) REVERT: H 231 ARG cc_start: 0.8566 (mmp80) cc_final: 0.8308 (mmp-170) REVERT: H 274 ASP cc_start: 0.9093 (t70) cc_final: 0.8613 (t70) REVERT: H 319 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6454 (t0) REVERT: H 343 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7279 (tm-30) REVERT: H 359 VAL cc_start: 0.9310 (t) cc_final: 0.8931 (p) REVERT: H 399 GLU cc_start: 0.8419 (mp0) cc_final: 0.8213 (mp0) REVERT: H 510 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8121 (tm-30) REVERT: O 1 MET cc_start: 0.5473 (pmm) cc_final: 0.4925 (pmm) REVERT: K 1 MET cc_start: 0.6232 (pmm) cc_final: 0.5667 (pmm) REVERT: K 4 TYR cc_start: 0.9025 (t80) cc_final: 0.8750 (t80) outliers start: 230 outliers final: 158 residues processed: 1091 average time/residue: 0.1888 time to fit residues: 342.7306 Evaluate side-chains 1099 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 919 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 271 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 358 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 179 optimal weight: 0.5980 chunk 288 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 369 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** A 465 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 285 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 469 GLN D 33 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 478 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112889 restraints weight = 52681.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117189 restraints weight = 26415.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120006 restraints weight = 16457.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122052 restraints weight = 11800.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123219 restraints weight = 9290.751| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32073 Z= 0.177 Angle : 0.805 18.186 43488 Z= 0.388 Chirality : 0.050 0.525 4968 Planarity : 0.004 0.051 5448 Dihedral : 8.098 87.741 4488 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.91 % Favored : 92.06 % Rotamer: Outliers : 7.33 % Allowed : 28.15 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.13), residues: 3968 helix: -0.89 (0.14), residues: 1274 sheet: -1.47 (0.25), residues: 406 loop : -1.75 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 203 TYR 0.028 0.002 TYR G 484 PHE 0.025 0.001 PHE D 165 HIS 0.011 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (32072) covalent geometry : angle 0.80456 / 0.39 (43488) hydrogen bonds : bond 0.03619 / 2.42 ( 961) hydrogen bonds : angle 5.64803 / 3.95 ( 2700) Misc. bond : bond 0.00171 / 0.09 ( 1) *********************** 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 1201 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 961 time to evaluate : 1.178 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: A 102 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8665 (p0) REVERT: A 103 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8617 (tp30) REVERT: A 105 ARG cc_start: 0.8636 (mtp-110) cc_final: 0.8201 (ttm-80) REVERT: A 274 ASP cc_start: 0.8920 (t0) cc_final: 0.8622 (t0) REVERT: A 277 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 279 ASN cc_start: 0.8674 (t0) cc_final: 0.8018 (t0) REVERT: A 296 ASN cc_start: 0.8623 (p0) cc_final: 0.8120 (t0) REVERT: A 319 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7228 (t0) REVERT: A 352 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8382 (tm-30) REVERT: A 404 ASP cc_start: 0.8507 (t70) cc_final: 0.8119 (t0) REVERT: A 409 LYS cc_start: 0.9275 (ttmm) cc_final: 0.8749 (ttmm) REVERT: A 478 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: A 487 GLU cc_start: 0.8280 (tt0) cc_final: 0.8068 (tt0) REVERT: A 489 LYS cc_start: 0.9332 (mttt) cc_final: 0.9132 (mmtp) REVERT: B 92 HIS cc_start: 0.8685 (p90) cc_final: 0.8387 (p90) REVERT: B 103 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: B 160 SER cc_start: 0.8517 (t) cc_final: 0.7837 (m) REVERT: B 205 LYS cc_start: 0.9302 (mmpt) cc_final: 0.8949 (mmtt) REVERT: B 231 ARG cc_start: 0.8772 (mmt-90) cc_final: 0.8545 (mmp80) REVERT: B 259 ARG cc_start: 0.8362 (mtp-110) cc_final: 0.8039 (ttm-80) REVERT: B 277 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8477 (tt0) REVERT: B 309 GLN cc_start: 0.9264 (pt0) cc_final: 0.8994 (pt0) REVERT: B 312 ASN cc_start: 0.9370 (m-40) cc_final: 0.8897 (t0) REVERT: B 334 GLN cc_start: 0.8852 (mt0) cc_final: 0.8458 (mt0) REVERT: B 335 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 343 GLN cc_start: 0.8802 (tp40) cc_final: 0.8574 (tp-100) REVERT: B 352 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7979 (pp20) REVERT: B 408 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8354 (pp) REVERT: B 409 LYS cc_start: 0.8328 (mttp) cc_final: 0.7872 (mmtt) REVERT: B 412 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7546 (ptt90) REVERT: B 487 GLU cc_start: 0.8956 (tt0) cc_final: 0.8678 (tt0) REVERT: B 492 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8424 (ttmt) REVERT: B 513 LEU cc_start: 0.8585 (mp) cc_final: 0.8207 (tp) REVERT: C 25 ASN cc_start: 0.8384 (t0) cc_final: 0.7906 (t0) REVERT: C 36 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8943 (pp) REVERT: C 37 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8631 (pt) REVERT: C 75 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8193 (mm-30) REVERT: C 105 ARG cc_start: 0.8547 (mtm110) cc_final: 0.8233 (tmm-80) REVERT: C 134 LYS cc_start: 0.9368 (ptmm) cc_final: 0.9040 (tppt) REVERT: C 150 MET cc_start: 0.7874 (tpp) cc_final: 0.7634 (tpp) REVERT: C 164 ASP cc_start: 0.6716 (m-30) cc_final: 0.6364 (m-30) REVERT: C 174 PHE cc_start: 0.6943 (m-80) cc_final: 0.6509 (m-80) REVERT: C 179 MET cc_start: 0.7776 (pp-130) cc_final: 0.7439 (pp-130) REVERT: C 182 ARG cc_start: 0.8244 (tpm170) cc_final: 0.7664 (tpp-160) REVERT: C 192 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8609 (mt) REVERT: C 203 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8220 (ttp80) REVERT: C 218 LEU cc_start: 0.9477 (pt) cc_final: 0.9090 (tt) REVERT: C 355 ARG cc_start: 0.9273 (ptm-80) cc_final: 0.8961 (ptm-80) REVERT: C 369 ASN cc_start: 0.8556 (p0) cc_final: 0.8075 (p0) REVERT: C 386 MET cc_start: 0.8463 (mpm) cc_final: 0.8015 (mpm) REVERT: C 468 CYS cc_start: 0.8731 (t) cc_final: 0.8282 (t) REVERT: C 478 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: C 483 MET cc_start: 0.9196 (tmm) cc_final: 0.8722 (tmm) REVERT: C 484 TYR cc_start: 0.9178 (m-80) cc_final: 0.8770 (m-10) REVERT: D 25 ASN cc_start: 0.8438 (m-40) cc_final: 0.8146 (m-40) REVERT: D 32 TYR cc_start: 0.8772 (m-10) cc_final: 0.8409 (m-10) REVERT: D 111 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7740 (mm-30) REVERT: D 199 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8870 (tm-30) REVERT: D 231 ARG cc_start: 0.8298 (mmm160) cc_final: 0.7874 (mmm160) REVERT: D 285 ASN cc_start: 0.9270 (m-40) cc_final: 0.8991 (m110) REVERT: D 319 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6934 (t0) REVERT: D 343 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 400 TYR cc_start: 0.6790 (m-10) cc_final: 0.6523 (m-10) REVERT: D 482 MET cc_start: 0.9148 (mtp) cc_final: 0.8857 (mtp) REVERT: D 483 MET cc_start: 0.9754 (tmm) cc_final: 0.9550 (tmm) REVERT: E 105 ARG cc_start: 0.8687 (mtp-110) cc_final: 0.8049 (ttm-80) REVERT: E 111 GLU cc_start: 0.8578 (mp0) cc_final: 0.7995 (mp0) REVERT: E 150 MET cc_start: 0.6892 (tmt) cc_final: 0.6225 (tmt) REVERT: E 229 LYS cc_start: 0.8365 (ptpt) cc_final: 0.7786 (pttm) REVERT: E 241 LYS cc_start: 0.9193 (mptt) cc_final: 0.8841 (ttmm) REVERT: E 279 ASN cc_start: 0.8381 (t0) cc_final: 0.7716 (t0) REVERT: E 343 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7286 (tm-30) REVERT: E 364 ASP cc_start: 0.9202 (t70) cc_final: 0.8829 (t0) REVERT: E 466 HIS cc_start: 0.8954 (OUTLIER) cc_final: 0.8289 (t-90) REVERT: E 483 MET cc_start: 0.9426 (tmm) cc_final: 0.9196 (tmm) REVERT: F 16 ASP cc_start: 0.8740 (t0) cc_final: 0.8427 (t0) REVERT: F 82 MET cc_start: 0.8225 (ppp) cc_final: 0.7719 (tmm) REVERT: F 92 HIS cc_start: 0.8793 (p90) cc_final: 0.8443 (p-80) REVERT: F 103 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: F 114 PHE cc_start: 0.9024 (m-10) cc_final: 0.8667 (m-80) REVERT: F 199 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: F 203 ARG cc_start: 0.9066 (mtm110) cc_final: 0.8758 (mtm110) REVERT: F 335 GLU cc_start: 0.8267 (tt0) cc_final: 0.7581 (tt0) REVERT: F 352 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7858 (pp20) REVERT: F 409 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8163 (mmtt) REVERT: F 412 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7817 (ptt90) REVERT: F 470 ASP cc_start: 0.9173 (m-30) cc_final: 0.8960 (t0) REVERT: F 487 GLU cc_start: 0.8925 (tt0) cc_final: 0.8660 (tt0) REVERT: G 84 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7968 (pt) REVERT: G 105 ARG cc_start: 0.8814 (mtm110) cc_final: 0.8546 (ttp80) REVERT: G 192 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8254 (mm) REVERT: G 195 LYS cc_start: 0.9339 (pmmt) cc_final: 0.8704 (mttt) REVERT: G 232 ASP cc_start: 0.8372 (t70) cc_final: 0.7895 (t0) REVERT: G 238 LYS cc_start: 0.9224 (mttp) cc_final: 0.8874 (mtpp) REVERT: G 355 ARG cc_start: 0.8723 (ptt90) cc_final: 0.8424 (ptm160) REVERT: G 369 ASN cc_start: 0.8736 (p0) cc_final: 0.8496 (p0) REVERT: G 420 MET cc_start: 0.4476 (OUTLIER) cc_final: 0.3462 (tpp) REVERT: G 478 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7721 (pp30) REVERT: G 510 GLU cc_start: 0.8078 (mp0) cc_final: 0.7558 (mp0) REVERT: H 33 ASN cc_start: 0.8415 (t0) cc_final: 0.8035 (t0) REVERT: H 75 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: H 93 HIS cc_start: 0.8994 (p-80) cc_final: 0.8612 (p90) REVERT: H 99 PHE cc_start: 0.9212 (t80) cc_final: 0.8943 (t80) REVERT: H 131 PHE cc_start: 0.8891 (m-80) cc_final: 0.8378 (m-80) REVERT: H 230 ASN cc_start: 0.8023 (t0) cc_final: 0.7113 (t0) REVERT: H 274 ASP cc_start: 0.9152 (t70) cc_final: 0.8781 (t70) REVERT: H 343 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7573 (tm-30) REVERT: H 359 VAL cc_start: 0.9323 (t) cc_final: 0.8998 (p) REVERT: H 399 GLU cc_start: 0.8310 (mp0) cc_final: 0.8068 (mp0) REVERT: H 510 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8181 (tm-30) REVERT: O 1 MET cc_start: 0.6148 (pmm) cc_final: 0.5640 (pmm) REVERT: K 1 MET cc_start: 0.6013 (pmm) cc_final: 0.5516 (pmm) REVERT: K 4 TYR cc_start: 0.8918 (t80) cc_final: 0.8688 (t80) outliers start: 240 outliers final: 168 residues processed: 1079 average time/residue: 0.1831 time to fit residues: 328.6688 Evaluate side-chains 1103 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 913 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 293 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 188 optimal weight: 3.9990 chunk 324 optimal weight: 0.2980 chunk 219 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 307 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 352 optimal weight: 0.0970 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 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** ** B 94 ASN ** 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 285 ASN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 283 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113446 restraints weight = 52349.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117820 restraints weight = 26435.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120768 restraints weight = 16460.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122653 restraints weight = 11739.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124095 restraints weight = 9299.350| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32073 Z= 0.133 Angle : 0.811 18.327 43488 Z= 0.385 Chirality : 0.050 0.563 4968 Planarity : 0.004 0.048 5448 Dihedral : 7.966 87.977 4488 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.14 % Allowed : 30.13 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3968 helix: -0.78 (0.14), residues: 1276 sheet: -1.39 (0.25), residues: 400 loop : -1.72 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 105 TYR 0.032 0.002 TYR F 110 PHE 0.021 0.001 PHE F 131 HIS 0.010 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (32072) covalent geometry : angle 0.81110 / 0.39 (43488) hydrogen bonds : bond 0.03402 / 2.27 ( 961) hydrogen bonds : angle 5.61619 / 3.92 ( 2700) Misc. bond : bond 0.00097 / 0.05 ( 1) *********************** 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 1196 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 995 time to evaluate : 1.199 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: A 102 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8667 (p0) REVERT: A 103 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8739 (tp30) REVERT: A 105 ARG cc_start: 0.8728 (mtp-110) cc_final: 0.8280 (ttm-80) REVERT: A 112 GLN cc_start: 0.7659 (mp10) cc_final: 0.7386 (mp10) REVERT: A 274 ASP cc_start: 0.8917 (t0) cc_final: 0.8628 (t0) REVERT: A 277 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 279 ASN cc_start: 0.8451 (t0) cc_final: 0.7721 (t0) REVERT: A 296 ASN cc_start: 0.8675 (p0) cc_final: 0.8220 (t0) REVERT: A 319 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7239 (t0) REVERT: A 335 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8247 (tm-30) REVERT: A 404 ASP cc_start: 0.8541 (t70) cc_final: 0.8126 (t0) REVERT: A 409 LYS cc_start: 0.9174 (ttmm) cc_final: 0.8714 (ttmm) REVERT: A 478 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: A 483 MET cc_start: 0.9457 (tmm) cc_final: 0.9228 (tmm) REVERT: A 487 GLU cc_start: 0.8568 (tt0) cc_final: 0.8261 (tt0) REVERT: A 489 LYS cc_start: 0.9255 (mttt) cc_final: 0.8855 (mmtp) REVERT: A 491 GLU cc_start: 0.8101 (pt0) cc_final: 0.7886 (pt0) REVERT: B 92 HIS cc_start: 0.8742 (p90) cc_final: 0.8452 (p90) REVERT: B 98 GLU cc_start: 0.9060 (pm20) cc_final: 0.8740 (pm20) REVERT: B 103 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: B 160 SER cc_start: 0.8417 (t) cc_final: 0.7744 (m) REVERT: B 231 ARG cc_start: 0.8837 (mmt-90) cc_final: 0.8581 (mmp80) REVERT: B 259 ARG cc_start: 0.8429 (mtp-110) cc_final: 0.8023 (ttm-80) REVERT: B 277 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8435 (tt0) REVERT: B 309 GLN cc_start: 0.9280 (pt0) cc_final: 0.8893 (pt0) REVERT: B 312 ASN cc_start: 0.9370 (m-40) cc_final: 0.8892 (t0) REVERT: B 334 GLN cc_start: 0.8864 (mt0) cc_final: 0.8359 (mt0) REVERT: B 335 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 352 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7999 (pp20) REVERT: B 408 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 409 LYS cc_start: 0.8157 (mttp) cc_final: 0.7687 (mmtt) REVERT: B 412 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7419 (ttp80) REVERT: B 487 GLU cc_start: 0.8926 (tt0) cc_final: 0.8550 (tt0) REVERT: B 492 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8199 (ttmt) REVERT: C 25 ASN cc_start: 0.8569 (t0) cc_final: 0.8079 (t0) REVERT: C 75 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8139 (mm-30) REVERT: C 105 ARG cc_start: 0.8542 (mtm110) cc_final: 0.8220 (tmm-80) REVERT: C 134 LYS cc_start: 0.9357 (ptmm) cc_final: 0.9050 (tptt) REVERT: C 153 ARG cc_start: 0.8688 (tpp80) cc_final: 0.8035 (tpp80) REVERT: C 164 ASP cc_start: 0.6646 (m-30) cc_final: 0.6329 (m-30) REVERT: C 174 PHE cc_start: 0.7159 (m-80) cc_final: 0.6737 (m-80) REVERT: C 179 MET cc_start: 0.7670 (pp-130) cc_final: 0.7363 (pp-130) REVERT: C 182 ARG cc_start: 0.8206 (tpm170) cc_final: 0.7637 (tpp-160) REVERT: C 218 LEU cc_start: 0.9546 (pt) cc_final: 0.9161 (tt) REVERT: C 224 ARG cc_start: 0.8825 (ttt-90) cc_final: 0.8297 (ttm-80) REVERT: C 355 ARG cc_start: 0.9217 (ptm-80) cc_final: 0.8949 (ptm-80) REVERT: C 369 ASN cc_start: 0.8433 (p0) cc_final: 0.7942 (p0) REVERT: C 386 MET cc_start: 0.8519 (mpm) cc_final: 0.8096 (mpm) REVERT: C 468 CYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8166 (t) REVERT: C 478 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: C 483 MET cc_start: 0.9287 (tmm) cc_final: 0.8730 (tmm) REVERT: C 484 TYR cc_start: 0.9144 (m-80) cc_final: 0.8728 (m-10) REVERT: C 509 TYR cc_start: 0.9181 (p90) cc_final: 0.8866 (p90) REVERT: C 510 GLU cc_start: 0.8366 (mp0) cc_final: 0.8131 (mp0) REVERT: D 32 TYR cc_start: 0.8815 (m-10) cc_final: 0.8435 (m-10) REVERT: D 103 GLU cc_start: 0.8437 (tp30) cc_final: 0.8162 (mm-30) REVERT: D 111 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7705 (mm-30) REVERT: D 199 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8892 (tm-30) REVERT: D 231 ARG cc_start: 0.8402 (mmm160) cc_final: 0.7868 (mmm160) REVERT: D 285 ASN cc_start: 0.9241 (m-40) cc_final: 0.8956 (m110) REVERT: D 343 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8040 (tm-30) REVERT: D 377 LEU cc_start: 0.9308 (mt) cc_final: 0.9043 (mt) REVERT: D 482 MET cc_start: 0.9227 (mtp) cc_final: 0.8906 (mtp) REVERT: E 105 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8057 (ttm-80) REVERT: E 150 MET cc_start: 0.7043 (tmt) cc_final: 0.6411 (tmt) REVERT: E 230 ASN cc_start: 0.8924 (t0) cc_final: 0.8660 (t0) REVERT: E 241 LYS cc_start: 0.9171 (mptt) cc_final: 0.8810 (ttmm) REVERT: E 279 ASN cc_start: 0.8159 (t0) cc_final: 0.7509 (t0) REVERT: E 343 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7007 (tm-30) REVERT: E 364 ASP cc_start: 0.9365 (t70) cc_final: 0.8906 (t0) REVERT: E 386 MET cc_start: 0.9480 (pmm) cc_final: 0.9228 (pmm) REVERT: E 412 ARG cc_start: 0.7047 (ttp80) cc_final: 0.6002 (ptt90) REVERT: E 466 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8025 (t-90) REVERT: E 483 MET cc_start: 0.9459 (tmm) cc_final: 0.9229 (tmm) REVERT: F 16 ASP cc_start: 0.8725 (t0) cc_final: 0.8344 (t0) REVERT: F 78 MET cc_start: 0.9384 (tpp) cc_final: 0.9160 (tpp) REVERT: F 82 MET cc_start: 0.8145 (ppp) cc_final: 0.7852 (tmm) REVERT: F 92 HIS cc_start: 0.8809 (p90) cc_final: 0.8391 (p-80) REVERT: F 103 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: F 114 PHE cc_start: 0.9038 (m-10) cc_final: 0.8656 (m-80) REVERT: F 139 PHE cc_start: 0.8230 (p90) cc_final: 0.7795 (p90) REVERT: F 199 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: F 352 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7712 (pp20) REVERT: F 409 LYS cc_start: 0.8548 (ttmm) cc_final: 0.7989 (mmtt) REVERT: F 412 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7654 (ptt90) REVERT: F 487 GLU cc_start: 0.9020 (tt0) cc_final: 0.8670 (tt0) REVERT: G 32 TYR cc_start: 0.8099 (m-10) cc_final: 0.7865 (m-10) REVERT: G 103 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8021 (mm-30) REVERT: G 111 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7093 (tp30) REVERT: G 192 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8219 (mm) REVERT: G 195 LYS cc_start: 0.9312 (pmmt) cc_final: 0.8687 (mttt) REVERT: G 232 ASP cc_start: 0.8364 (t70) cc_final: 0.7859 (t0) REVERT: G 238 LYS cc_start: 0.9253 (mttp) cc_final: 0.8818 (mtpp) REVERT: G 279 ASN cc_start: 0.8031 (t0) cc_final: 0.7809 (t0) REVERT: G 420 MET cc_start: 0.4344 (OUTLIER) cc_final: 0.3463 (tpp) REVERT: G 478 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7105 (pp30) REVERT: G 510 GLU cc_start: 0.8186 (mp0) cc_final: 0.7578 (mp0) REVERT: H 33 ASN cc_start: 0.8324 (t0) cc_final: 0.7827 (t0) REVERT: H 75 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: H 93 HIS cc_start: 0.8949 (p-80) cc_final: 0.8593 (p90) REVERT: H 99 PHE cc_start: 0.9242 (t80) cc_final: 0.8925 (t80) REVERT: H 111 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7551 (mm-30) REVERT: H 131 PHE cc_start: 0.8877 (m-80) cc_final: 0.8475 (m-80) REVERT: H 274 ASP cc_start: 0.9172 (t70) cc_final: 0.8769 (t70) REVERT: H 277 GLN cc_start: 0.8598 (tp40) cc_final: 0.8284 (tp40) REVERT: H 343 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7260 (tm-30) REVERT: H 359 VAL cc_start: 0.9338 (t) cc_final: 0.8997 (p) REVERT: H 399 GLU cc_start: 0.8474 (mp0) cc_final: 0.8214 (mp0) REVERT: H 510 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8084 (tm-30) REVERT: O 1 MET cc_start: 0.5785 (pmm) cc_final: 0.5370 (pmm) REVERT: K 1 MET cc_start: 0.6023 (pmm) cc_final: 0.5518 (pmm) REVERT: K 4 TYR cc_start: 0.8991 (t80) cc_final: 0.8743 (t80) outliers start: 201 outliers final: 149 residues processed: 1090 average time/residue: 0.1802 time to fit residues: 327.0030 Evaluate side-chains 1100 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 933 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 478 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 155 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 chunk 120 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 37 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 383 optimal weight: 0.9990 chunk 172 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 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 334 GLN B 279 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN E 283 GLN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 478 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118174 restraints weight = 52259.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122652 restraints weight = 25944.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125671 restraints weight = 15989.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127697 restraints weight = 11286.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128970 restraints weight = 8829.190| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32073 Z= 0.136 Angle : 0.827 17.315 43488 Z= 0.393 Chirality : 0.049 0.579 4968 Planarity : 0.004 0.061 5448 Dihedral : 7.864 86.957 4488 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 5.53 % Allowed : 30.53 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.13), residues: 3968 helix: -0.80 (0.14), residues: 1288 sheet: -1.59 (0.25), residues: 408 loop : -1.70 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 105 TYR 0.027 0.002 TYR A 110 PHE 0.019 0.001 PHE D 165 HIS 0.009 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (32072) covalent geometry : angle 0.82735 / 0.39 (43488) hydrogen bonds : bond 0.03457 / 2.32 ( 961) hydrogen bonds : angle 5.65217 / 3.95 ( 2700) Misc. bond : bond 0.00116 / 0.06 ( 1) *********************** 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 1157 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 976 time to evaluate : 1.159 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: A 102 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8657 (p0) REVERT: A 103 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8683 (tp30) REVERT: A 105 ARG cc_start: 0.8644 (mtp-110) cc_final: 0.8204 (ttm-80) REVERT: A 111 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8499 (mm-30) REVERT: A 112 GLN cc_start: 0.7732 (mp10) cc_final: 0.7291 (mp10) REVERT: A 230 ASN cc_start: 0.9060 (t0) cc_final: 0.8825 (t0) REVERT: A 242 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7644 (mmtt) REVERT: A 274 ASP cc_start: 0.8899 (t0) cc_final: 0.8684 (t0) REVERT: A 277 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 279 ASN cc_start: 0.8267 (t0) cc_final: 0.7762 (t0) REVERT: A 296 ASN cc_start: 0.8631 (p0) cc_final: 0.8186 (t0) REVERT: A 335 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 375 LYS cc_start: 0.9353 (mtmm) cc_final: 0.9070 (ttmt) REVERT: A 404 ASP cc_start: 0.8452 (t70) cc_final: 0.8090 (t0) REVERT: A 409 LYS cc_start: 0.9168 (ttmm) cc_final: 0.8736 (ttmm) REVERT: A 478 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8366 (pt0) REVERT: A 487 GLU cc_start: 0.8450 (tt0) cc_final: 0.8191 (tt0) REVERT: A 489 LYS cc_start: 0.9194 (mttt) cc_final: 0.8787 (mmtp) REVERT: B 92 HIS cc_start: 0.8716 (p90) cc_final: 0.8461 (p90) REVERT: B 103 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: B 160 SER cc_start: 0.8592 (t) cc_final: 0.7945 (m) REVERT: B 259 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.8022 (ttm-80) REVERT: B 277 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8439 (tt0) REVERT: B 312 ASN cc_start: 0.9282 (m-40) cc_final: 0.8918 (t0) REVERT: B 334 GLN cc_start: 0.8810 (mt0) cc_final: 0.8364 (mt0) REVERT: B 335 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 408 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8338 (pp) REVERT: B 409 LYS cc_start: 0.8198 (mttp) cc_final: 0.7734 (mmtt) REVERT: B 412 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7237 (ttp80) REVERT: B 487 GLU cc_start: 0.8815 (tt0) cc_final: 0.8447 (tt0) REVERT: B 492 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8310 (ttmt) REVERT: B 513 LEU cc_start: 0.8616 (mp) cc_final: 0.8223 (tp) REVERT: C 25 ASN cc_start: 0.8467 (t0) cc_final: 0.7983 (t0) REVERT: C 36 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8573 (pp) REVERT: C 105 ARG cc_start: 0.8475 (mtm110) cc_final: 0.8184 (tmm-80) REVERT: C 134 LYS cc_start: 0.9390 (ptmm) cc_final: 0.9106 (tptt) REVERT: C 164 ASP cc_start: 0.6530 (m-30) cc_final: 0.6227 (p0) REVERT: C 179 MET cc_start: 0.7802 (pp-130) cc_final: 0.7509 (pp-130) REVERT: C 182 ARG cc_start: 0.8197 (tpm170) cc_final: 0.7617 (tpp-160) REVERT: C 192 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8585 (mt) REVERT: C 203 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8250 (ttp80) REVERT: C 218 LEU cc_start: 0.9528 (pt) cc_final: 0.9068 (tt) REVERT: C 224 ARG cc_start: 0.8847 (ttt-90) cc_final: 0.8388 (ttm-80) REVERT: C 238 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8330 (mmmm) REVERT: C 311 LYS cc_start: 0.8671 (tmtt) cc_final: 0.8281 (tmtt) REVERT: C 355 ARG cc_start: 0.9120 (ptm-80) cc_final: 0.8876 (ptm-80) REVERT: C 369 ASN cc_start: 0.8325 (p0) cc_final: 0.7621 (p0) REVERT: C 386 MET cc_start: 0.8392 (mpm) cc_final: 0.8047 (mpm) REVERT: C 468 CYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8203 (t) REVERT: C 478 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: C 483 MET cc_start: 0.9259 (tmm) cc_final: 0.8726 (tmm) REVERT: C 484 TYR cc_start: 0.9173 (m-80) cc_final: 0.8767 (m-10) REVERT: C 509 TYR cc_start: 0.9197 (p90) cc_final: 0.8892 (p90) REVERT: C 510 GLU cc_start: 0.8337 (mp0) cc_final: 0.8104 (mp0) REVERT: D 25 ASN cc_start: 0.8376 (m-40) cc_final: 0.8127 (m-40) REVERT: D 32 TYR cc_start: 0.8762 (m-10) cc_final: 0.8388 (m-10) REVERT: D 99 PHE cc_start: 0.9364 (t80) cc_final: 0.9033 (t80) REVERT: D 105 ARG cc_start: 0.8781 (mtm110) cc_final: 0.8484 (ptt180) REVERT: D 111 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7715 (mm-30) REVERT: D 199 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8877 (tm-30) REVERT: D 231 ARG cc_start: 0.8333 (mmm160) cc_final: 0.7648 (mmm160) REVERT: D 285 ASN cc_start: 0.9265 (m-40) cc_final: 0.8933 (m110) REVERT: D 343 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8047 (tm-30) REVERT: D 377 LEU cc_start: 0.9346 (mt) cc_final: 0.9078 (mt) REVERT: D 482 MET cc_start: 0.9143 (mtp) cc_final: 0.8902 (mtp) REVERT: E 105 ARG cc_start: 0.8683 (mtp-110) cc_final: 0.8098 (ttm-80) REVERT: E 150 MET cc_start: 0.6960 (tmt) cc_final: 0.6313 (tmt) REVERT: E 229 LYS cc_start: 0.8294 (ptpt) cc_final: 0.7663 (pttm) REVERT: E 230 ASN cc_start: 0.8914 (t0) cc_final: 0.8668 (t0) REVERT: E 241 LYS cc_start: 0.9175 (mptt) cc_final: 0.8814 (ttmm) REVERT: E 279 ASN cc_start: 0.8122 (t0) cc_final: 0.7531 (t0) REVERT: E 343 GLN cc_start: 0.7523 (tm-30) cc_final: 0.6920 (tm-30) REVERT: E 386 MET cc_start: 0.9478 (pmm) cc_final: 0.9274 (pmm) REVERT: E 466 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.8125 (t-90) REVERT: E 483 MET cc_start: 0.9425 (tmm) cc_final: 0.9174 (tmm) REVERT: F 16 ASP cc_start: 0.8739 (t0) cc_final: 0.8333 (t0) REVERT: F 78 MET cc_start: 0.9333 (tpp) cc_final: 0.9086 (tpp) REVERT: F 82 MET cc_start: 0.8242 (ppp) cc_final: 0.7884 (tmm) REVERT: F 92 HIS cc_start: 0.8775 (p90) cc_final: 0.8394 (p-80) REVERT: F 103 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: F 139 PHE cc_start: 0.8266 (p90) cc_final: 0.7882 (p90) REVERT: F 199 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: F 352 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7732 (pp20) REVERT: F 355 ARG cc_start: 0.9234 (ptt90) cc_final: 0.8602 (ptm-80) REVERT: F 362 ILE cc_start: 0.9169 (mt) cc_final: 0.8946 (mm) REVERT: F 409 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8039 (mmtt) REVERT: F 487 GLU cc_start: 0.8947 (tt0) cc_final: 0.8635 (tt0) REVERT: G 103 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8291 (mm-30) REVERT: G 192 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8232 (mm) REVERT: G 195 LYS cc_start: 0.9305 (pmmt) cc_final: 0.8710 (mttt) REVERT: G 232 ASP cc_start: 0.8306 (t70) cc_final: 0.7925 (t0) REVERT: G 238 LYS cc_start: 0.9207 (mttp) cc_final: 0.8828 (mtpp) REVERT: G 342 PRO cc_start: 0.9455 (Cg_exo) cc_final: 0.9230 (Cg_endo) REVERT: G 420 MET cc_start: 0.4330 (OUTLIER) cc_final: 0.3536 (tpp) REVERT: G 478 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7801 (pp30) REVERT: G 482 MET cc_start: 0.8726 (ttm) cc_final: 0.8458 (ttp) REVERT: G 510 GLU cc_start: 0.8089 (mp0) cc_final: 0.7522 (mp0) REVERT: H 33 ASN cc_start: 0.8345 (t0) cc_final: 0.7866 (t0) REVERT: H 43 ASP cc_start: 0.8145 (p0) cc_final: 0.7855 (p0) REVERT: H 75 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: H 93 HIS cc_start: 0.8950 (p-80) cc_final: 0.8572 (p90) REVERT: H 99 PHE cc_start: 0.9190 (t80) cc_final: 0.8939 (t80) REVERT: H 111 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7659 (mm-30) REVERT: H 131 PHE cc_start: 0.8803 (m-80) cc_final: 0.8314 (m-80) REVERT: H 274 ASP cc_start: 0.9213 (t70) cc_final: 0.8850 (t70) REVERT: H 277 GLN cc_start: 0.8511 (tp40) cc_final: 0.8304 (tp40) REVERT: H 343 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7296 (tm-30) REVERT: H 359 VAL cc_start: 0.9330 (t) cc_final: 0.8984 (p) REVERT: H 399 GLU cc_start: 0.8454 (mp0) cc_final: 0.8190 (mp0) REVERT: O 1 MET cc_start: 0.5892 (pmm) cc_final: 0.5475 (pmm) REVERT: K 1 MET cc_start: 0.6224 (pmm) cc_final: 0.5782 (pmm) outliers start: 181 outliers final: 137 residues processed: 1059 average time/residue: 0.1814 time to fit residues: 318.2898 Evaluate side-chains 1085 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 929 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 452 SER Chi-restraints excluded: chain H residue 478 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 380 optimal weight: 4.9990 chunk 384 optimal weight: 0.0030 chunk 269 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 378 optimal weight: 0.0060 chunk 105 optimal weight: 1.9990 chunk 387 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 368 optimal weight: 2.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 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 334 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** 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 285 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 253 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115482 restraints weight = 52348.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119901 restraints weight = 26436.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122885 restraints weight = 16434.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124861 restraints weight = 11680.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126284 restraints weight = 9201.467| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32073 Z= 0.144 Angle : 0.840 17.982 43488 Z= 0.402 Chirality : 0.050 0.566 4968 Planarity : 0.004 0.062 5448 Dihedral : 7.790 86.023 4487 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 5.01 % Allowed : 31.91 % Favored : 63.08 % 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 are not related in a simple way. whole: -2.08 (0.13), residues: 3968 helix: -0.81 (0.14), residues: 1294 sheet: -1.64 (0.25), residues: 388 loop : -1.69 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 203 TYR 0.035 0.002 TYR G 484 PHE 0.024 0.001 PHE F 131 HIS 0.010 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (32072) covalent geometry : angle 0.84009 / 0.40 (43488) hydrogen bonds : bond 0.03490 / 2.32 ( 961) hydrogen bonds : angle 5.65415 / 3.96 ( 2700) Misc. bond : bond 0.00096 / 0.05 ( 1) ********************** 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 1117 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 953 time to evaluate : 1.207 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: A 102 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8648 (p0) REVERT: A 103 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8716 (tp30) REVERT: A 105 ARG cc_start: 0.8742 (mtp-110) cc_final: 0.8250 (ttm-80) REVERT: A 112 GLN cc_start: 0.7629 (mp10) cc_final: 0.7167 (mp10) REVERT: A 229 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8344 (ptpt) REVERT: A 242 LYS cc_start: 0.7965 (mmmm) cc_final: 0.7641 (mmtt) REVERT: A 274 ASP cc_start: 0.8920 (t0) cc_final: 0.8688 (t0) REVERT: A 277 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7250 (tm-30) REVERT: A 279 ASN cc_start: 0.8173 (t0) cc_final: 0.7778 (t0) REVERT: A 296 ASN cc_start: 0.8640 (p0) cc_final: 0.8231 (t0) REVERT: A 335 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 375 LYS cc_start: 0.9336 (mtmm) cc_final: 0.9076 (ttmt) REVERT: A 385 MET cc_start: 0.9214 (ttm) cc_final: 0.8688 (ttm) REVERT: A 404 ASP cc_start: 0.8503 (t70) cc_final: 0.8132 (t0) REVERT: A 409 LYS cc_start: 0.9167 (ttmm) cc_final: 0.8730 (ttmm) REVERT: A 478 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: A 487 GLU cc_start: 0.8487 (tt0) cc_final: 0.8209 (tt0) REVERT: B 92 HIS cc_start: 0.8737 (p90) cc_final: 0.8384 (p90) REVERT: B 98 GLU cc_start: 0.9044 (pm20) cc_final: 0.8715 (pm20) REVERT: B 160 SER cc_start: 0.8619 (t) cc_final: 0.7995 (m) REVERT: B 174 PHE cc_start: 0.8760 (m-10) cc_final: 0.8461 (m-10) REVERT: B 259 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.7980 (ttm-80) REVERT: B 309 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8706 (pt0) REVERT: B 312 ASN cc_start: 0.9237 (m-40) cc_final: 0.8937 (t0) REVERT: B 334 GLN cc_start: 0.8842 (mt0) cc_final: 0.8376 (mt0) REVERT: B 335 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7309 (tm-30) REVERT: B 355 ARG cc_start: 0.8575 (ttp-110) cc_final: 0.8372 (mtm110) REVERT: B 408 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8335 (pp) REVERT: B 409 LYS cc_start: 0.8184 (mttp) cc_final: 0.7633 (mmtt) REVERT: B 412 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7186 (ttp80) REVERT: B 487 GLU cc_start: 0.8838 (tt0) cc_final: 0.8541 (tt0) REVERT: B 492 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8329 (ttmt) REVERT: B 513 LEU cc_start: 0.8614 (mp) cc_final: 0.8257 (tp) REVERT: C 25 ASN cc_start: 0.8515 (t0) cc_final: 0.8031 (t0) REVERT: C 36 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8494 (pp) REVERT: C 105 ARG cc_start: 0.8459 (mtm110) cc_final: 0.8128 (tmm-80) REVERT: C 134 LYS cc_start: 0.9389 (ptmm) cc_final: 0.9096 (tptt) REVERT: C 163 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8685 (pt) REVERT: C 174 PHE cc_start: 0.7213 (m-80) cc_final: 0.6815 (m-80) REVERT: C 179 MET cc_start: 0.7787 (pp-130) cc_final: 0.7399 (pp-130) REVERT: C 182 ARG cc_start: 0.8178 (tpm170) cc_final: 0.7661 (tpp-160) REVERT: C 192 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8552 (mt) REVERT: C 203 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8235 (ttp80) REVERT: C 218 LEU cc_start: 0.9522 (pt) cc_final: 0.9091 (tt) REVERT: C 224 ARG cc_start: 0.8904 (ttt-90) cc_final: 0.8470 (ttm-80) REVERT: C 238 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8319 (mmmm) REVERT: C 355 ARG cc_start: 0.9104 (ptm-80) cc_final: 0.8872 (ptm-80) REVERT: C 369 ASN cc_start: 0.8278 (p0) cc_final: 0.7592 (p0) REVERT: C 386 MET cc_start: 0.8289 (mpm) cc_final: 0.8064 (mpm) REVERT: C 468 CYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8272 (t) REVERT: C 478 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: C 483 MET cc_start: 0.9280 (tmm) cc_final: 0.8754 (tmm) REVERT: C 484 TYR cc_start: 0.9144 (m-80) cc_final: 0.8818 (m-10) REVERT: C 509 TYR cc_start: 0.9181 (p90) cc_final: 0.8878 (p90) REVERT: C 510 GLU cc_start: 0.8328 (mp0) cc_final: 0.8080 (mp0) REVERT: D 25 ASN cc_start: 0.8440 (m-40) cc_final: 0.8180 (m-40) REVERT: D 32 TYR cc_start: 0.8742 (m-10) cc_final: 0.8352 (m-10) REVERT: D 99 PHE cc_start: 0.9382 (t80) cc_final: 0.8906 (t80) REVERT: D 103 GLU cc_start: 0.8558 (tp30) cc_final: 0.8171 (tp30) REVERT: D 105 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8434 (ptt-90) REVERT: D 111 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7689 (mm-30) REVERT: D 199 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8884 (tm-30) REVERT: D 231 ARG cc_start: 0.8418 (mmm160) cc_final: 0.7795 (mmm160) REVERT: D 285 ASN cc_start: 0.9264 (m-40) cc_final: 0.8915 (m110) REVERT: D 343 GLN cc_start: 0.8560 (tm-30) cc_final: 0.7985 (tm-30) REVERT: D 377 LEU cc_start: 0.9380 (mt) cc_final: 0.9068 (mt) REVERT: D 482 MET cc_start: 0.9181 (mtp) cc_final: 0.8908 (mtp) REVERT: E 105 ARG cc_start: 0.8672 (mtp-110) cc_final: 0.8102 (ttm-80) REVERT: E 150 MET cc_start: 0.7004 (tmt) cc_final: 0.6367 (tmt) REVERT: E 229 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7559 (pttm) REVERT: E 230 ASN cc_start: 0.8859 (t0) cc_final: 0.8635 (t0) REVERT: E 241 LYS cc_start: 0.9170 (mptt) cc_final: 0.8808 (ttmm) REVERT: E 279 ASN cc_start: 0.8242 (t0) cc_final: 0.7584 (t0) REVERT: E 306 THR cc_start: 0.8962 (t) cc_final: 0.8736 (t) REVERT: E 343 GLN cc_start: 0.7511 (tm-30) cc_final: 0.6888 (tm-30) REVERT: E 386 MET cc_start: 0.9471 (pmm) cc_final: 0.9237 (pmm) REVERT: E 466 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8086 (t-90) REVERT: E 483 MET cc_start: 0.9471 (tmm) cc_final: 0.9237 (tmm) REVERT: F 16 ASP cc_start: 0.8716 (t0) cc_final: 0.8500 (t0) REVERT: F 74 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7925 (t) REVERT: F 78 MET cc_start: 0.9376 (tpp) cc_final: 0.9067 (tpp) REVERT: F 82 MET cc_start: 0.8239 (ppp) cc_final: 0.7796 (tmm) REVERT: F 92 HIS cc_start: 0.8744 (p90) cc_final: 0.8344 (p-80) REVERT: F 103 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: F 110 TYR cc_start: 0.8607 (t80) cc_final: 0.8362 (t80) REVERT: F 139 PHE cc_start: 0.8240 (p90) cc_final: 0.7854 (p90) REVERT: F 335 GLU cc_start: 0.8324 (tt0) cc_final: 0.7992 (tt0) REVERT: F 352 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7674 (pp20) REVERT: F 355 ARG cc_start: 0.9155 (ptt90) cc_final: 0.8630 (ptm-80) REVERT: F 409 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8014 (mmtt) REVERT: G 103 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8325 (mm-30) REVERT: G 192 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8215 (mm) REVERT: G 195 LYS cc_start: 0.9307 (pmmt) cc_final: 0.8728 (mttt) REVERT: G 232 ASP cc_start: 0.8314 (t70) cc_final: 0.7933 (t0) REVERT: G 238 LYS cc_start: 0.9211 (mttp) cc_final: 0.8797 (mtpp) REVERT: G 342 PRO cc_start: 0.9447 (Cg_exo) cc_final: 0.9197 (Cg_endo) REVERT: G 352 GLU cc_start: 0.8741 (tp30) cc_final: 0.8316 (tp30) REVERT: G 355 ARG cc_start: 0.7935 (ptm160) cc_final: 0.7385 (ptm-80) REVERT: G 478 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7618 (pp30) REVERT: G 482 MET cc_start: 0.8727 (ttm) cc_final: 0.8365 (ttp) REVERT: G 510 GLU cc_start: 0.8117 (mp0) cc_final: 0.7546 (mp0) REVERT: H 33 ASN cc_start: 0.8356 (t0) cc_final: 0.8003 (t0) REVERT: H 43 ASP cc_start: 0.8180 (p0) cc_final: 0.7907 (p0) REVERT: H 75 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: H 93 HIS cc_start: 0.8956 (p-80) cc_final: 0.8582 (p90) REVERT: H 99 PHE cc_start: 0.9190 (t80) cc_final: 0.8811 (t80) REVERT: H 111 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7715 (mm-30) REVERT: H 131 PHE cc_start: 0.8674 (m-80) cc_final: 0.8153 (m-80) REVERT: H 274 ASP cc_start: 0.9169 (t70) cc_final: 0.8881 (t70) REVERT: H 343 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7286 (tm-30) REVERT: H 359 VAL cc_start: 0.9357 (t) cc_final: 0.9023 (p) REVERT: O 1 MET cc_start: 0.5665 (pmm) cc_final: 0.5259 (pmm) REVERT: K 1 MET cc_start: 0.6097 (pmm) cc_final: 0.5744 (pmm) outliers start: 164 outliers final: 129 residues processed: 1035 average time/residue: 0.1877 time to fit residues: 322.4317 Evaluate side-chains 1062 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 913 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 483 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 452 SER Chi-restraints excluded: chain H residue 478 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 236 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 346 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 106 optimal weight: 0.0270 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 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 334 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112556 restraints weight = 54001.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116926 restraints weight = 28181.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119937 restraints weight = 18029.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121969 restraints weight = 13098.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123239 restraints weight = 10471.538| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32073 Z= 0.156 Angle : 0.840 16.978 43488 Z= 0.405 Chirality : 0.050 0.527 4968 Planarity : 0.004 0.049 5448 Dihedral : 7.743 87.465 4487 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.04 % Allowed : 32.27 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.13), residues: 3968 helix: -0.79 (0.14), residues: 1296 sheet: -1.60 (0.25), residues: 394 loop : -1.70 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 203 TYR 0.033 0.002 TYR G 484 PHE 0.021 0.001 PHE A 114 HIS 0.008 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (32072) covalent geometry : angle 0.84028 / 0.40 (43488) hydrogen bonds : bond 0.03535 / 2.34 ( 961) hydrogen bonds : angle 5.65424 / 3.95 ( 2700) Misc. bond : bond 0.00123 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7231.00 seconds wall clock time: 125 minutes 26.94 seconds (7526.94 seconds total)