Starting phenix.real_space_refine on Thu Mar 21 23:48:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8r_20690/03_2024/6u8r_20690_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8r_20690/03_2024/6u8r_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8r_20690/03_2024/6u8r_20690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8r_20690/03_2024/6u8r_20690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8r_20690/03_2024/6u8r_20690_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8r_20690/03_2024/6u8r_20690_updated.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ARG 407": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 15.64, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 12.50 Conformation dependent library (CDL) restraints added in 6.1 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... running ksdssp... Secondary structure from input PDB file: 152 helices and 45 sheets defined 31.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 removed outlier: 3.807A pdb=" N ASN A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N CYS A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 128 through 137 removed outlier: 3.697A pdb=" N ARG A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.578A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 343 through 356 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) removed outlier: 4.555A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.528A pdb=" N LEU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 476 through 485 removed outlier: 3.719A pdb=" N ARG A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 128 through 136 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 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.588A pdb=" N LYS B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.799A pdb=" N TYR B 258 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 262 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 307 through 314 removed outlier: 4.026A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 351 through 357 removed outlier: 4.528A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 456 through 471 Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 495 through 501 removed outlier: 3.827A pdb=" N GLU B 500 " --> pdb=" O SER B 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 26 removed outlier: 4.306A pdb=" N ASN C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 removed outlier: 3.536A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 108 removed outlier: 3.724A pdb=" N ARG C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 136 removed outlier: 3.736A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.503A pdb=" N LYS C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 224 through 228' Processing helix chain 'C' and resid 254 through 266 removed outlier: 4.010A pdb=" N TYR C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 262 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 264 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 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 307 through 314 Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 344 through 356 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) removed outlier: 4.046A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 377 Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid 21 through 26 removed outlier: 5.070A pdb=" N CYS D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 128 through 136 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.576A pdb=" N LYS D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 258 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 262 " --> pdb=" O ARG D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 356 removed outlier: 4.161A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 498 through 501 No H-bonds generated for 'chain 'D' and resid 498 through 501' Processing helix chain 'E' and resid 20 through 24 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 128 through 136 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 194 through 202 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.509A pdb=" N LYS E 257 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 291 Processing helix chain 'E' and resid 307 through 314 Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 356 removed outlier: 3.545A pdb=" N TYR E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 378 Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 500 removed outlier: 3.618A pdb=" N VAL E 499 " --> pdb=" O SER E 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 24 through 26 No H-bonds generated for 'chain 'F' and resid 24 through 26' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 76 through 85 removed outlier: 3.583A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 128 through 136 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 194 through 204 removed outlier: 4.124A pdb=" N GLU F 199 " --> pdb=" O LYS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 227 No H-bonds generated for 'chain 'F' and resid 224 through 227' Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.562A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU F 262 " --> pdb=" O ARG F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 Processing helix chain 'F' and resid 307 through 314 removed outlier: 4.108A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 356 removed outlier: 4.059A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 456 through 471 Processing helix chain 'F' and resid 476 through 484 Processing helix chain 'F' and resid 497 through 501 removed outlier: 3.732A pdb=" N GLY F 501 " --> pdb=" O ALA F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 497 through 501' Processing helix chain 'G' and resid 20 through 26 removed outlier: 3.788A pdb=" N ASN G 25 " --> pdb=" O GLN G 21 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N CYS G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.752A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 108 removed outlier: 3.880A pdb=" N ARG G 105 " --> pdb=" O ALA G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 136 Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.770A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN G 265 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 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 307 through 314 Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 344 through 356 removed outlier: 3.878A pdb=" N LYS G 349 " --> pdb=" O THR G 345 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 379 Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid 21 through 26 removed outlier: 5.081A pdb=" N CYS H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.988A pdb=" N ALA H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 128 through 136 removed outlier: 3.549A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 229 removed outlier: 4.372A pdb=" N LYS H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS H 229 " --> pdb=" O THR H 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 224 through 229' Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.666A pdb=" N LYS H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR H 258 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU H 262 " --> pdb=" O ARG H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 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 307 through 314 Processing helix chain 'H' and resid 343 through 356 removed outlier: 4.154A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 417 through 419 No H-bonds generated for 'chain 'H' and resid 417 through 419' Processing helix chain 'H' and resid 453 through 455 No H-bonds generated for 'chain 'H' and resid 453 through 455' Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 498 through 501 No H-bonds generated for 'chain 'H' and resid 498 through 501' Processing helix chain 'M' and resid 4 through 7 No H-bonds generated for 'chain 'M' and resid 4 through 7' Processing helix chain 'N' and resid 2 through 5 No H-bonds generated for 'chain 'N' and resid 2 through 5' Processing helix chain 'O' and resid 2 through 5 No H-bonds generated for 'chain 'O' and resid 2 through 5' Processing helix chain 'I' and resid 3 through 7 removed outlier: 3.929A pdb=" N ILE I 6 " --> pdb=" O ASP I 3 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER I 7 " --> pdb=" O TYR I 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 7' Processing helix chain 'J' and resid 2 through 5 No H-bonds generated for 'chain 'J' and resid 2 through 5' Processing helix chain 'K' and resid 2 through 5 No H-bonds generated for 'chain 'K' and resid 2 through 5' Processing sheet with id= A, 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= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.230A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 383 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.847A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, 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) Processing sheet with id= E, first strand: chain 'A' and resid 143 through 145 Processing sheet with id= F, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= G, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.908A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (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) Processing sheet with id= H, first strand: chain 'B' and resid 120 through 122 Processing sheet with id= I, first strand: chain 'B' and resid 248 through 250 removed outlier: 6.304A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 401 through 403 Processing sheet with id= K, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= L, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= M, first strand: chain 'C' and resid 187 through 189 removed outlier: 7.779A pdb=" N ALA C 188 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 209 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 211 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.686A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 362 through 364 removed outlier: 6.902A pdb=" N THR C 383 " --> pdb=" O ALA C 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= Q, first strand: chain 'C' and resid 143 through 145 Processing sheet with id= R, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= S, first strand: chain 'D' and resid 65 through 67 removed outlier: 5.888A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 187 through 189 removed outlier: 8.447A pdb=" N ALA D 188 " --> pdb=" O LYS D 208 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 209 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.566A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 401 through 403 removed outlier: 3.505A pdb=" N SER D 403 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.520A pdb=" N ILE D 142 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 158 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= X, 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= Y, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.068A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 247 through 250 removed outlier: 7.162A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, 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= AB, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= AC, 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= AD, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AE, first strand: chain 'F' and resid 65 through 67 removed outlier: 5.964A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 383 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.728A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 401 through 403 Processing sheet with id= AH, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AI, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AJ, first strand: chain 'G' and resid 65 through 67 removed outlier: 5.560A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 187 through 189 removed outlier: 8.755A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU G 209 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE G 211 " --> pdb=" O ALA G 220 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.725A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL G 272 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, 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) Processing sheet with id= AN, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AO, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.925A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR H 383 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 248 through 250 removed outlier: 6.879A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 401 through 403 removed outlier: 3.513A pdb=" N SER H 403 " --> pdb=" O ILE H 406 " (cutoff:3.500A) Processing sheet with id= AR, 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= AS, first strand: chain 'H' and resid 208 through 213 removed outlier: 3.620A pdb=" N LEU H 209 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASN H 213 " --> pdb=" O LEU H 218 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU H 218 " --> pdb=" O ASN H 213 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 1929 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: 10.20 Time building geometry restraints manager: 13.57 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: 92.16 - 102.35: 184 102.35 - 112.54: 16875 112.54 - 122.73: 23402 122.73 - 132.92: 2952 132.92 - 143.11: 75 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: 17886 20.57 - 41.15: 1471 41.15 - 61.72: 370 61.72 - 82.30: 112 82.30 - 102.87: 17 Dihedral angle restraints: 19856 sinusoidal: 8448 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 19853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4350 0.122 - 0.244: 562 0.244 - 0.366: 50 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: 4631 2.73 - 3.27: 31011 3.27 - 3.82: 56010 3.82 - 4.36: 63653 4.36 - 4.90: 104318 Nonbonded interactions: 259623 Sorted by model distance: nonbonded pdb=" OG SER A 329 " pdb=" O HIS B 504 " model vdw 2.188 2.440 nonbonded pdb=" OG1 THR H 147 " pdb=" OG SER H 152 " model vdw 2.231 2.440 nonbonded pdb=" OD1 ASP G 50 " pdb=" OG SER G 475 " model vdw 2.232 2.440 nonbonded pdb=" OD2 ASP D 364 " pdb=" O2' IMP D 603 " model vdw 2.238 2.440 nonbonded pdb=" OG SER E 159 " pdb=" O1B ATP E 603 " model vdw 2.242 2.440 ... (remaining 259618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.240 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 81.630 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.300 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 32072 Z= 1.255 Angle : 1.845 23.084 43488 Z= 1.144 Chirality : 0.085 0.610 4968 Planarity : 0.008 0.081 5448 Dihedral : 17.004 102.870 12576 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.017 0.003 HIS H 504 PHE 0.044 0.005 PHE F 174 TYR 0.058 0.004 TYR C 411 ARG 0.021 0.002 ARG B 355 *********************** 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 fitting. rotamer outliers: 105 poor density : 1179 time to evaluate : 3.405 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 34 ASP cc_start: 0.8392 (t70) cc_final: 0.8182 (t70) REVERT: A 173 CYS cc_start: 0.5872 (m) cc_final: 0.5472 (m) REVERT: A 195 LYS cc_start: 0.8384 (mmmm) cc_final: 0.8114 (tptt) REVERT: A 224 ARG cc_start: 0.8592 (ttt-90) cc_final: 0.8260 (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: 0.8498 (t) REVERT: A 273 LEU cc_start: 0.9689 (mt) cc_final: 0.9443 (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: 0.8651 (tm-30) REVERT: A 357 PHE cc_start: 0.9219 (m-80) cc_final: 0.8860 (m-10) REVERT: A 483 MET cc_start: 0.9441 (tmm) cc_final: 0.8818 (tmm) REVERT: B 16 ASP cc_start: 0.9024 (t0) cc_final: 0.8768 (t0) REVERT: B 51 LEU cc_start: 0.8851 (tp) cc_final: 0.8498 (tt) REVERT: B 103 GLU cc_start: 0.8857 (mp0) cc_final: 0.8551 (mp0) REVERT: B 105 ARG cc_start: 0.8685 (mtm110) cc_final: 0.8375 (ptp-110) REVERT: B 158 ILE cc_start: 0.8988 (mm) cc_final: 0.8758 (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: 0.8604 (t0) REVERT: B 277 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9010 (tm-30) REVERT: B 309 GLN cc_start: 0.9266 (pm20) cc_final: 0.8823 (pm20) REVERT: B 335 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 364 ASP cc_start: 0.8286 (m-30) cc_final: 0.6632 (m-30) REVERT: B 385 MET cc_start: 0.8679 (ttp) cc_final: 0.7786 (ttp) REVERT: B 409 LYS cc_start: 0.8473 (mttp) cc_final: 0.7532 (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: 0.8364 (pp30) REVERT: C 25 ASN cc_start: 0.8712 (t0) cc_final: 0.8139 (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: 0.8647 (t0) REVERT: C 105 ARG cc_start: 0.8746 (mtm110) cc_final: 0.8214 (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: 0.8625 (tppp) REVERT: C 210 PRO cc_start: 0.9303 (Cg_exo) cc_final: 0.9084 (Cg_endo) REVERT: C 216 ASP cc_start: 0.7862 (t0) cc_final: 0.7619 (t0) REVERT: C 224 ARG cc_start: 0.9008 (ttt-90) cc_final: 0.8474 (ttm-80) REVERT: C 238 LYS cc_start: 0.8916 (mppt) cc_final: 0.8587 (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: 0.8019 (tm-30) REVERT: C 296 ASN cc_start: 0.8716 (p0) cc_final: 0.8401 (m-40) REVERT: C 343 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7921 (tm-30) REVERT: C 386 MET cc_start: 0.8500 (mpm) cc_final: 0.8126 (mpm) REVERT: C 461 ILE cc_start: 0.9219 (pp) cc_final: 0.8815 (pp) REVERT: C 465 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: C 468 CYS cc_start: 0.8477 (t) cc_final: 0.8174 (t) REVERT: C 475 SER cc_start: 0.8755 (t) cc_final: 0.8407 (t) REVERT: C 483 MET cc_start: 0.9093 (tmm) cc_final: 0.8849 (tmm) REVERT: D 32 TYR cc_start: 0.9169 (m-10) cc_final: 0.8693 (m-10) REVERT: D 93 HIS cc_start: 0.8825 (p-80) cc_final: 0.8596 (p90) REVERT: D 112 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8348 (tm-30) REVERT: D 131 PHE cc_start: 0.9094 (m-80) cc_final: 0.8839 (m-80) REVERT: D 327 SER cc_start: 0.8979 (p) cc_final: 0.8707 (p) REVERT: D 334 GLN cc_start: 0.8967 (mt0) cc_final: 0.8534 (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: 0.8419 (tm-30) REVERT: D 400 TYR cc_start: 0.7644 (m-80) cc_final: 0.7436 (m-80) REVERT: D 450 LYS cc_start: 0.8853 (mmpt) cc_final: 0.8565 (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: 0.8166 (tm-30) REVERT: E 75 GLU cc_start: 0.8301 (mp0) cc_final: 0.7680 (mp0) REVERT: E 150 MET cc_start: 0.7322 (tmt) cc_final: 0.6781 (tmt) REVERT: E 174 PHE cc_start: 0.8976 (m-80) cc_final: 0.8456 (m-80) REVERT: E 241 LYS cc_start: 0.9224 (mptt) cc_final: 0.8931 (mmtm) REVERT: E 274 ASP cc_start: 0.9308 (t0) cc_final: 0.9040 (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: 0.8537 (m110) REVERT: E 296 ASN cc_start: 0.8503 (p0) cc_final: 0.8118 (t0) REVERT: E 382 SER cc_start: 0.9635 (m) cc_final: 0.9388 (t) REVERT: E 385 MET cc_start: 0.8972 (ttp) cc_final: 0.8743 (ttm) REVERT: E 455 LYS cc_start: 0.8969 (tppt) cc_final: 0.8485 (mmmt) REVERT: E 500 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8721 (tm-30) REVERT: F 16 ASP cc_start: 0.8842 (t0) cc_final: 0.8476 (t0) REVERT: F 51 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8668 (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: 0.8443 (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: 0.8564 (mp0) REVERT: F 139 PHE cc_start: 0.8102 (p90) cc_final: 0.7469 (p90) REVERT: F 246 CYS cc_start: 0.8888 (t) cc_final: 0.8688 (t) 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: 0.7568 (t0) REVERT: F 335 GLU cc_start: 0.8452 (tt0) cc_final: 0.8189 (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: 0.9000 (tmm) REVERT: F 487 GLU cc_start: 0.9120 (tt0) cc_final: 0.8770 (tt0) REVERT: G 75 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8060 (mt-10) REVERT: G 95 CYS cc_start: 0.8379 (p) cc_final: 0.8029 (p) REVERT: G 98 GLU cc_start: 0.8605 (pm20) cc_final: 0.8218 (pm20) REVERT: G 100 GLN cc_start: 0.8580 (pm20) cc_final: 0.8247 (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: 0.8557 (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: 0.8469 (m-40) REVERT: G 343 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7822 (tm-30) REVERT: G 362 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9134 (tp) REVERT: G 369 ASN cc_start: 0.8975 (p0) cc_final: 0.8772 (p0) REVERT: G 383 THR cc_start: 0.9762 (p) cc_final: 0.9506 (p) REVERT: G 386 MET cc_start: 0.8537 (mmp) cc_final: 0.8335 (mmp) REVERT: G 461 ILE cc_start: 0.9162 (pp) cc_final: 0.8706 (pp) REVERT: G 465 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8728 (pm20) REVERT: G 499 VAL cc_start: 0.9273 (p) cc_final: 0.8999 (p) REVERT: H 32 TYR cc_start: 0.9050 (m-10) cc_final: 0.8592 (m-10) REVERT: H 93 HIS cc_start: 0.8869 (p-80) cc_final: 0.8644 (p90) REVERT: H 103 GLU cc_start: 0.8541 (mp0) cc_final: 0.8308 (mp0) REVERT: H 105 ARG cc_start: 0.8858 (ptt-90) cc_final: 0.8505 (ptt90) REVERT: H 228 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8362 (tmtt) REVERT: H 277 GLN cc_start: 0.8757 (tm130) cc_final: 0.8443 (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: 0.8516 (p) REVERT: H 334 GLN cc_start: 0.9067 (mt0) cc_final: 0.8851 (mt0) REVERT: H 343 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8593 (tm-30) REVERT: H 364 ASP cc_start: 0.8495 (m-30) cc_final: 0.8148 (m-30) REVERT: H 385 MET cc_start: 0.8611 (ttm) cc_final: 0.8406 (ttm) REVERT: H 386 MET cc_start: 0.8526 (mtm) cc_final: 0.8311 (mtm) REVERT: H 393 THR cc_start: 0.8250 (p) cc_final: 0.7645 (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: 0.3981 time to fit residues: 780.5673 Evaluate side-chains 931 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 899 time to evaluate : 3.388 ------------------------------------------------------------------------------- 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 331 optimal weight: 3.9990 chunk 297 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 355 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 137 HIS A 230 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 478 GLN B 93 HIS B 137 HIS B 243 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 334 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 230 ASN D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN E 94 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS F 243 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN F 466 HIS 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 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 277 GLN H 285 ASN H 298 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN H 478 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32072 Z= 0.349 Angle : 0.840 14.311 43488 Z= 0.425 Chirality : 0.051 0.303 4968 Planarity : 0.005 0.054 5448 Dihedral : 15.574 89.607 5430 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.01 % Favored : 92.74 % Rotamer: Outliers : 6.20 % Allowed : 20.45 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.12), residues: 3968 helix: -2.41 (0.12), residues: 1234 sheet: -2.37 (0.22), residues: 448 loop : -2.20 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 92 PHE 0.022 0.002 PHE D 165 TYR 0.026 0.002 TYR A 353 ARG 0.006 0.001 ARG D 182 *********************** 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 1204 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1001 time to evaluate : 3.377 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 125 ASP cc_start: 0.7717 (p0) cc_final: 0.7458 (p0) REVERT: A 173 CYS cc_start: 0.5669 (m) cc_final: 0.5303 (m) REVERT: A 224 ARG cc_start: 0.8632 (ttt-90) cc_final: 0.7907 (tpp80) REVERT: A 230 ASN cc_start: 0.9317 (t0) cc_final: 0.9072 (t0) REVERT: A 274 ASP cc_start: 0.8858 (t0) cc_final: 0.8535 (t0) REVERT: A 352 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8660 (tm-30) REVERT: A 404 ASP cc_start: 0.8599 (t70) cc_final: 0.8312 (t0) REVERT: A 482 MET cc_start: 0.8703 (mtm) cc_final: 0.8432 (mtp) REVERT: A 500 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8874 (tm-30) REVERT: B 16 ASP cc_start: 0.8981 (t0) cc_final: 0.8669 (t0) REVERT: B 103 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: B 160 SER cc_start: 0.8669 (t) cc_final: 0.7968 (m) REVERT: B 179 MET cc_start: 0.7636 (pp-130) cc_final: 0.7281 (pp-130) REVERT: B 334 GLN cc_start: 0.8960 (mt0) cc_final: 0.8595 (mt0) REVERT: B 335 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 408 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8344 (pp) REVERT: B 409 LYS cc_start: 0.8318 (mttp) cc_final: 0.7788 (mmtt) REVERT: B 487 GLU cc_start: 0.9048 (tt0) cc_final: 0.8677 (tt0) REVERT: B 510 GLU cc_start: 0.8301 (tt0) cc_final: 0.8041 (tt0) REVERT: C 21 GLN cc_start: 0.8866 (pp30) cc_final: 0.8666 (tm-30) REVERT: C 25 ASN cc_start: 0.8579 (t0) cc_final: 0.8125 (t0) REVERT: C 36 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9028 (pp) REVERT: C 48 GLN cc_start: 0.8982 (mt0) cc_final: 0.8363 (mt0) REVERT: C 105 ARG cc_start: 0.8750 (mtm110) cc_final: 0.8275 (tmm-80) REVERT: C 108 LYS cc_start: 0.8525 (tptp) cc_final: 0.7878 (tptp) REVERT: C 110 TYR cc_start: 0.8609 (t80) cc_final: 0.8055 (t80) REVERT: C 149 ARG cc_start: 0.8364 (tmm-80) cc_final: 0.8006 (tmm-80) REVERT: C 182 ARG cc_start: 0.8181 (tpm170) cc_final: 0.7737 (tpp-160) REVERT: C 206 LYS cc_start: 0.9117 (tppp) cc_final: 0.8001 (mmmm) REVERT: C 216 ASP cc_start: 0.7359 (t0) cc_final: 0.6346 (m-30) REVERT: C 218 LEU cc_start: 0.9495 (pt) cc_final: 0.8939 (tt) REVERT: C 224 ARG cc_start: 0.9012 (ttt-90) cc_final: 0.7773 (ttm170) REVERT: C 238 LYS cc_start: 0.9017 (mppt) cc_final: 0.8607 (mmmm) REVERT: C 277 GLN cc_start: 0.8304 (tm-30) cc_final: 0.8071 (tm-30) REVERT: C 297 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9019 (tm) REVERT: C 343 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 386 MET cc_start: 0.8362 (mpm) cc_final: 0.8069 (mpm) REVERT: C 400 TYR cc_start: 0.7158 (m-80) cc_final: 0.6921 (m-80) REVERT: C 468 CYS cc_start: 0.8367 (t) cc_final: 0.7923 (t) REVERT: C 483 MET cc_start: 0.9152 (tmm) cc_final: 0.8733 (tmm) REVERT: D 32 TYR cc_start: 0.8922 (m-10) cc_final: 0.8654 (m-10) REVERT: D 75 GLU cc_start: 0.7967 (pp20) cc_final: 0.7741 (pp20) REVERT: D 82 MET cc_start: 0.9033 (mtm) cc_final: 0.8569 (mtp) REVERT: D 93 HIS cc_start: 0.8845 (p-80) cc_final: 0.8628 (p90) REVERT: D 103 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: D 106 LYS cc_start: 0.9078 (ttmt) cc_final: 0.8872 (ttpt) REVERT: D 199 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8868 (tm-30) REVERT: D 277 GLN cc_start: 0.9056 (tp40) cc_final: 0.8517 (tp40) REVERT: D 327 SER cc_start: 0.9182 (p) cc_final: 0.8589 (t) REVERT: D 343 GLN cc_start: 0.8706 (tm-30) cc_final: 0.7994 (tm-30) REVERT: D 482 MET cc_start: 0.9109 (mtp) cc_final: 0.8826 (mtp) REVERT: D 510 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8182 (tm-30) REVERT: E 16 ASP cc_start: 0.8855 (t70) cc_final: 0.8421 (t0) REVERT: E 21 GLN cc_start: 0.8189 (pp30) cc_final: 0.7824 (pp30) REVERT: E 75 GLU cc_start: 0.8206 (mp0) cc_final: 0.7755 (mp0) REVERT: E 110 TYR cc_start: 0.8228 (t80) cc_final: 0.7517 (t80) REVERT: E 150 MET cc_start: 0.7234 (tmt) cc_final: 0.6606 (tmt) REVERT: E 241 LYS cc_start: 0.9232 (mptt) cc_final: 0.8917 (mmtm) REVERT: E 296 ASN cc_start: 0.8560 (p0) cc_final: 0.8139 (t0) REVERT: E 395 GLU cc_start: 0.8651 (mp0) cc_final: 0.8444 (mp0) REVERT: E 466 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.8221 (t-90) REVERT: E 480 ARG cc_start: 0.9460 (mtm-85) cc_final: 0.9201 (mtt90) REVERT: E 483 MET cc_start: 0.9354 (tmm) cc_final: 0.8740 (tmm) REVERT: E 500 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8699 (tm-30) REVERT: F 16 ASP cc_start: 0.8765 (t0) cc_final: 0.8470 (t0) REVERT: F 51 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8461 (tm) REVERT: F 95 CYS cc_start: 0.7983 (p) cc_final: 0.7454 (p) REVERT: F 105 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8567 (mtp85) REVERT: F 132 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: F 203 ARG cc_start: 0.9031 (mtm110) cc_final: 0.8827 (mtm110) REVERT: F 224 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.7813 (ttt-90) REVERT: F 279 ASN cc_start: 0.8558 (t0) cc_final: 0.8164 (t0) REVERT: F 283 GLN cc_start: 0.8959 (tt0) cc_final: 0.8744 (tt0) REVERT: F 309 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8675 (pm20) REVERT: F 319 ASP cc_start: 0.7926 (t0) cc_final: 0.7536 (t0) REVERT: F 409 LYS cc_start: 0.8743 (ttmm) cc_final: 0.7725 (tttt) REVERT: F 412 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7259 (ptt90) REVERT: F 487 GLU cc_start: 0.9090 (tt0) cc_final: 0.8780 (tt0) REVERT: G 75 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8218 (mt-10) REVERT: G 94 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8659 (t0) REVERT: G 105 ARG cc_start: 0.8831 (mtm110) cc_final: 0.8469 (tmm-80) REVERT: G 111 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8096 (mm-30) REVERT: G 195 LYS cc_start: 0.9278 (pmmt) cc_final: 0.8479 (tttt) REVERT: G 277 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8184 (tm-30) REVERT: G 343 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7382 (tm-30) REVERT: G 409 LYS cc_start: 0.8383 (ptpt) cc_final: 0.8180 (ptpt) REVERT: G 478 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7642 (pp30) REVERT: G 491 GLU cc_start: 0.8515 (tp30) cc_final: 0.8201 (tp30) REVERT: H 32 TYR cc_start: 0.8838 (m-10) cc_final: 0.8499 (m-10) REVERT: H 93 HIS cc_start: 0.8883 (p-80) cc_final: 0.8553 (p90) REVERT: H 228 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8307 (tmtt) REVERT: H 231 ARG cc_start: 0.8547 (mmp80) cc_final: 0.8302 (mmp-170) REVERT: H 274 ASP cc_start: 0.8923 (t70) cc_final: 0.8383 (t70) REVERT: H 343 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8016 (tm-30) REVERT: H 393 THR cc_start: 0.8288 (p) cc_final: 0.7903 (p) REVERT: H 395 GLU cc_start: 0.8631 (mp0) cc_final: 0.8398 (mp0) REVERT: H 450 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8714 (mmmt) REVERT: H 465 GLN cc_start: 0.8951 (mt0) cc_final: 0.8667 (mt0) REVERT: H 483 MET cc_start: 0.9704 (tmm) cc_final: 0.9412 (tmm) REVERT: H 510 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8165 (tm-30) outliers start: 203 outliers final: 132 residues processed: 1102 average time/residue: 0.3934 time to fit residues: 708.9485 Evaluate side-chains 1042 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 899 time to evaluate : 3.412 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ILE 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 250 ILE Chi-restraints excluded: chain B residue 263 LEU 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 297 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 361 VAL 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 B residue 416 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 47 ASP 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 263 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 275 SER 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 345 THR 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 447 VAL Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 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 225 THR 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 369 ASN Chi-restraints excluded: chain D residue 370 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 E residue 15 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 66 VAL 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 224 ARG Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 334 GLN Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL 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 E residue 499 VAL Chi-restraints excluded: chain F residue 19 THR 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 132 GLU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 222 ILE 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 309 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 384 VAL 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 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 269 ASP Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 345 THR 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 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 142 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 470 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 Chi-restraints excluded: chain K residue 10 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 296 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 356 optimal weight: 0.8980 chunk 385 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 chunk 353 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 286 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN A 343 GLN B 309 GLN B 334 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 469 GLN E 137 HIS E 198 ASN ** 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 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 465 GLN G 478 GLN H 137 HIS H 171 HIS H 243 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32072 Z= 0.218 Angle : 0.757 14.349 43488 Z= 0.374 Chirality : 0.048 0.357 4968 Planarity : 0.004 0.045 5448 Dihedral : 14.315 88.724 5400 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 6.54 % Allowed : 23.32 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.12), residues: 3968 helix: -1.82 (0.13), residues: 1244 sheet: -2.22 (0.24), residues: 386 loop : -2.02 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS H 137 PHE 0.018 0.001 PHE D 165 TYR 0.026 0.002 TYR F 484 ARG 0.005 0.000 ARG G 407 *********************** 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 1235 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1021 time to evaluate : 3.830 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 105 ARG cc_start: 0.8861 (mtp-110) cc_final: 0.8162 (ttm-80) REVERT: A 125 ASP cc_start: 0.7732 (p0) cc_final: 0.7447 (p0) REVERT: A 224 ARG cc_start: 0.8586 (ttt-90) cc_final: 0.7834 (tpp80) REVERT: A 230 ASN cc_start: 0.9190 (t0) cc_final: 0.8905 (t0) REVERT: A 274 ASP cc_start: 0.8781 (t0) cc_final: 0.8531 (t0) REVERT: A 277 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 352 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8702 (tm-30) REVERT: A 404 ASP cc_start: 0.8529 (t70) cc_final: 0.8230 (t0) REVERT: A 478 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: A 500 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8939 (tm-30) REVERT: B 103 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: B 160 SER cc_start: 0.8763 (t) cc_final: 0.8109 (m) REVERT: B 179 MET cc_start: 0.7607 (pp-130) cc_final: 0.7397 (pp-130) REVERT: B 259 ARG cc_start: 0.8771 (mtp-110) cc_final: 0.8335 (ttm-80) REVERT: B 274 ASP cc_start: 0.8774 (t0) cc_final: 0.8436 (t0) REVERT: B 309 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8675 (pm20) REVERT: B 334 GLN cc_start: 0.8955 (mt0) cc_final: 0.8565 (mt0) REVERT: B 335 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 352 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8108 (pp20) REVERT: B 395 GLU cc_start: 0.8690 (mp0) cc_final: 0.8317 (mp0) REVERT: B 408 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8230 (pp) REVERT: B 409 LYS cc_start: 0.8274 (mttp) cc_final: 0.7745 (mmtp) REVERT: B 448 GLN cc_start: 0.8607 (tt0) cc_final: 0.8294 (pm20) REVERT: B 453 ILE cc_start: 0.9293 (tt) cc_final: 0.9039 (mt) REVERT: B 487 GLU cc_start: 0.9049 (tt0) cc_final: 0.8489 (tt0) REVERT: B 510 GLU cc_start: 0.8284 (tt0) cc_final: 0.8024 (tt0) REVERT: C 25 ASN cc_start: 0.8478 (t0) cc_final: 0.8109 (t0) REVERT: C 36 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8944 (pp) REVERT: C 75 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8281 (mt-10) REVERT: C 105 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8288 (tmm-80) REVERT: C 108 LYS cc_start: 0.8538 (tptp) cc_final: 0.7786 (tptp) REVERT: C 111 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8522 (tp30) REVERT: C 134 LYS cc_start: 0.9237 (ptmm) cc_final: 0.8886 (tptt) REVERT: C 164 ASP cc_start: 0.6465 (m-30) cc_final: 0.5761 (m-30) REVERT: C 182 ARG cc_start: 0.8063 (tpm170) cc_final: 0.7607 (tpp-160) REVERT: C 206 LYS cc_start: 0.9128 (tppp) cc_final: 0.8891 (mmmm) REVERT: C 218 LEU cc_start: 0.9478 (pt) cc_final: 0.9049 (tt) REVERT: C 224 ARG cc_start: 0.8965 (ttt-90) cc_final: 0.8492 (ttm-80) REVERT: C 297 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9036 (tm) REVERT: C 386 MET cc_start: 0.8313 (mpm) cc_final: 0.7961 (mpm) REVERT: C 468 CYS cc_start: 0.8365 (t) cc_final: 0.7928 (t) REVERT: C 483 MET cc_start: 0.9131 (tmm) cc_final: 0.8685 (tmm) REVERT: D 75 GLU cc_start: 0.7817 (pp20) cc_final: 0.7450 (pp20) REVERT: D 93 HIS cc_start: 0.8811 (p-80) cc_final: 0.8530 (p90) REVERT: D 103 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: D 131 PHE cc_start: 0.8790 (m-10) cc_final: 0.8475 (m-80) REVERT: D 199 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8891 (tm-30) REVERT: D 227 LEU cc_start: 0.9290 (mp) cc_final: 0.9083 (mm) REVERT: D 277 GLN cc_start: 0.8922 (tp40) cc_final: 0.8604 (tp40) REVERT: D 327 SER cc_start: 0.9015 (p) cc_final: 0.8724 (t) REVERT: D 343 GLN cc_start: 0.8447 (tm-30) cc_final: 0.7724 (tm-30) REVERT: E 13 VAL cc_start: 0.9499 (t) cc_final: 0.9254 (p) REVERT: E 16 ASP cc_start: 0.8814 (t70) cc_final: 0.8296 (t0) REVERT: E 75 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7781 (mp0) REVERT: E 150 MET cc_start: 0.7168 (tmt) cc_final: 0.6491 (tmt) REVERT: E 229 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8272 (ptmt) REVERT: E 238 LYS cc_start: 0.8438 (mtmm) cc_final: 0.8113 (mtmm) REVERT: E 241 LYS cc_start: 0.9222 (mptt) cc_final: 0.8894 (mmtm) REVERT: E 279 ASN cc_start: 0.8561 (t0) cc_final: 0.7599 (t0) REVERT: E 296 ASN cc_start: 0.8420 (p0) cc_final: 0.8197 (t0) REVERT: E 385 MET cc_start: 0.8724 (ttm) cc_final: 0.8515 (ttp) REVERT: E 389 LEU cc_start: 0.9279 (tp) cc_final: 0.9064 (tp) REVERT: E 395 GLU cc_start: 0.8560 (mp0) cc_final: 0.8275 (mp0) REVERT: E 466 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8224 (t-90) REVERT: E 483 MET cc_start: 0.9380 (tmm) cc_final: 0.8705 (tmm) REVERT: E 500 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8736 (tm-30) REVERT: F 16 ASP cc_start: 0.8641 (t0) cc_final: 0.8319 (t0) REVERT: F 51 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8261 (tm) REVERT: F 95 CYS cc_start: 0.7808 (p) cc_final: 0.7208 (p) REVERT: F 121 LEU cc_start: 0.8335 (tt) cc_final: 0.8117 (tt) REVERT: F 139 PHE cc_start: 0.8181 (p90) cc_final: 0.7542 (p90) REVERT: F 179 MET cc_start: 0.7656 (pp-130) cc_final: 0.7417 (pp-130) REVERT: F 224 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8122 (ttm-80) REVERT: F 409 LYS cc_start: 0.8633 (ttmm) cc_final: 0.7556 (tttt) REVERT: F 412 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7054 (ptt90) REVERT: G 75 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8218 (mt-10) REVERT: G 103 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8265 (mm-30) REVERT: G 105 ARG cc_start: 0.8707 (mtm110) cc_final: 0.8407 (tmm-80) REVERT: G 153 ARG cc_start: 0.8231 (tpt170) cc_final: 0.7952 (tpp80) REVERT: G 195 LYS cc_start: 0.9268 (pmmt) cc_final: 0.8446 (tttt) REVERT: G 243 GLN cc_start: 0.8151 (mp10) cc_final: 0.7943 (pm20) REVERT: G 277 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7741 (tm-30) REVERT: G 297 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9017 (tm) REVERT: G 400 TYR cc_start: 0.7086 (m-80) cc_final: 0.6152 (m-80) REVERT: G 478 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7507 (pp30) REVERT: H 32 TYR cc_start: 0.8704 (m-10) cc_final: 0.8390 (m-10) REVERT: H 33 ASN cc_start: 0.8288 (t0) cc_final: 0.7874 (t0) REVERT: H 70 MET cc_start: 0.8875 (mtm) cc_final: 0.8626 (mtm) REVERT: H 93 HIS cc_start: 0.8861 (p-80) cc_final: 0.8493 (p90) REVERT: H 228 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8286 (tmtt) REVERT: H 231 ARG cc_start: 0.8467 (mmp80) cc_final: 0.8211 (mmp-170) REVERT: H 274 ASP cc_start: 0.8971 (t70) cc_final: 0.8332 (t70) REVERT: H 309 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: H 343 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7755 (tm-30) REVERT: H 393 THR cc_start: 0.8212 (p) cc_final: 0.7458 (p) REVERT: H 395 GLU cc_start: 0.8553 (mp0) cc_final: 0.8086 (mp0) REVERT: H 400 TYR cc_start: 0.7565 (m-10) cc_final: 0.7214 (m-10) REVERT: H 450 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8711 (mmmt) REVERT: H 483 MET cc_start: 0.9653 (tmm) cc_final: 0.8883 (tmm) REVERT: H 484 TYR cc_start: 0.8905 (m-80) cc_final: 0.8581 (m-10) REVERT: H 510 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8139 (tm-30) REVERT: K 4 TYR cc_start: 0.9085 (t80) cc_final: 0.8880 (t80) outliers start: 214 outliers final: 132 residues processed: 1128 average time/residue: 0.3900 time to fit residues: 716.2961 Evaluate side-chains 1042 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 896 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 66 VAL 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 361 VAL Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 471 ILE 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 59 ILE 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 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 238 LYS Chi-restraints excluded: chain B residue 263 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 309 GLN Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 373 ILE 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 488 LEU 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 263 LEU Chi-restraints excluded: chain C residue 269 ASP 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 362 ILE 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 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 142 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL 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 199 GLU Chi-restraints excluded: chain E residue 201 LEU 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 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 386 MET 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 19 THR 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 132 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 272 VAL 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 382 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 103 GLU 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 269 ASP Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR 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 477 THR 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 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 327 SER Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 3 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 10.0000 chunk 268 optimal weight: 0.0970 chunk 185 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 239 optimal weight: 0.0570 chunk 357 optimal weight: 8.9990 chunk 378 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 339 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** 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 309 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** 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 ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 283 GLN G 465 GLN G 478 GLN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32072 Z= 0.249 Angle : 0.743 14.887 43488 Z= 0.367 Chirality : 0.048 0.388 4968 Planarity : 0.004 0.050 5448 Dihedral : 13.568 89.253 5396 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.33 % Favored : 92.49 % Rotamer: Outliers : 8.59 % Allowed : 24.66 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.12), residues: 3968 helix: -1.52 (0.14), residues: 1258 sheet: -2.19 (0.23), residues: 398 loop : -1.89 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 92 PHE 0.018 0.001 PHE D 165 TYR 0.036 0.002 TYR F 484 ARG 0.009 0.000 ARG F 203 *********************** 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 1263 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 982 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9256 (mmm) cc_final: 0.8737 (mmm) REVERT: A 105 ARG cc_start: 0.8926 (mtp-110) cc_final: 0.8244 (ttm-80) REVERT: A 112 GLN cc_start: 0.7672 (mp10) cc_final: 0.6907 (mp10) REVERT: A 125 ASP cc_start: 0.7809 (p0) cc_final: 0.7526 (p0) REVERT: A 224 ARG cc_start: 0.8468 (ttt-90) cc_final: 0.7652 (tpp80) REVERT: A 230 ASN cc_start: 0.9124 (t0) cc_final: 0.8835 (t0) REVERT: A 274 ASP cc_start: 0.8820 (t0) cc_final: 0.8577 (t0) REVERT: A 277 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 352 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 404 ASP cc_start: 0.8516 (t70) cc_final: 0.8032 (t0) REVERT: A 409 LYS cc_start: 0.9255 (ttmm) cc_final: 0.8717 (ttmm) REVERT: A 474 LYS cc_start: 0.9014 (pttt) cc_final: 0.8508 (pttp) REVERT: A 478 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: A 496 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8596 (p) REVERT: A 500 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8846 (tm-30) REVERT: B 32 TYR cc_start: 0.8714 (m-10) cc_final: 0.8412 (m-10) REVERT: B 78 MET cc_start: 0.8918 (tmt) cc_final: 0.8491 (tmt) REVERT: B 103 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: B 160 SER cc_start: 0.8867 (t) cc_final: 0.8250 (m) REVERT: B 179 MET cc_start: 0.7199 (pp-130) cc_final: 0.6771 (pp-130) REVERT: B 274 ASP cc_start: 0.8840 (t0) cc_final: 0.8444 (t0) REVERT: B 277 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8522 (tt0) REVERT: B 309 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: B 322 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7800 (ttt-90) REVERT: B 332 ILE cc_start: 0.9028 (pp) cc_final: 0.8821 (pt) REVERT: B 334 GLN cc_start: 0.8936 (mt0) cc_final: 0.8501 (mt0) REVERT: B 335 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7846 (tm-30) REVERT: B 343 GLN cc_start: 0.8996 (tp40) cc_final: 0.8696 (tp-100) REVERT: B 352 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8177 (pp20) REVERT: B 355 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8425 (ptm-80) REVERT: B 408 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8198 (pp) REVERT: B 409 LYS cc_start: 0.8237 (mttp) cc_final: 0.7794 (mmtp) REVERT: B 448 GLN cc_start: 0.8549 (tt0) cc_final: 0.8347 (pm20) REVERT: B 453 ILE cc_start: 0.9355 (tt) cc_final: 0.9148 (mt) REVERT: B 487 GLU cc_start: 0.8997 (tt0) cc_final: 0.8534 (tt0) REVERT: B 510 GLU cc_start: 0.8273 (tt0) cc_final: 0.7993 (tt0) REVERT: C 25 ASN cc_start: 0.8538 (t0) cc_final: 0.8028 (t0) REVERT: C 36 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8986 (pp) REVERT: C 37 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8818 (pt) REVERT: C 105 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8312 (ttp80) REVERT: C 108 LYS cc_start: 0.8487 (tptp) cc_final: 0.7636 (tptp) REVERT: C 134 LYS cc_start: 0.9240 (ptmm) cc_final: 0.8864 (tptt) REVERT: C 150 MET cc_start: 0.7985 (tpp) cc_final: 0.7718 (tpp) REVERT: C 179 MET cc_start: 0.7203 (pp-130) cc_final: 0.6966 (pp-130) REVERT: C 182 ARG cc_start: 0.8065 (tpm170) cc_final: 0.7436 (tpp-160) REVERT: C 206 LYS cc_start: 0.9128 (tppp) cc_final: 0.8567 (mmmm) REVERT: C 218 LEU cc_start: 0.9537 (pt) cc_final: 0.9024 (tt) REVERT: C 224 ARG cc_start: 0.8957 (ttt-90) cc_final: 0.8273 (ttt180) REVERT: C 279 ASN cc_start: 0.9085 (t0) cc_final: 0.8597 (t0) REVERT: C 296 ASN cc_start: 0.8662 (p0) cc_final: 0.8376 (m-40) REVERT: C 297 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8939 (tm) REVERT: C 369 ASN cc_start: 0.8635 (p0) cc_final: 0.8325 (p0) REVERT: C 395 GLU cc_start: 0.8360 (pm20) cc_final: 0.8001 (pm20) REVERT: C 468 CYS cc_start: 0.8473 (t) cc_final: 0.7962 (t) REVERT: C 478 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: C 483 MET cc_start: 0.9212 (tmm) cc_final: 0.8723 (tmm) REVERT: D 82 MET cc_start: 0.8994 (mtm) cc_final: 0.8735 (mtp) REVERT: D 93 HIS cc_start: 0.8841 (p-80) cc_final: 0.8530 (p90) REVERT: D 103 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: D 131 PHE cc_start: 0.8712 (m-10) cc_final: 0.8413 (m-80) REVERT: D 199 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8853 (tm-30) REVERT: D 235 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8062 (pp) REVERT: D 327 SER cc_start: 0.9085 (p) cc_final: 0.8638 (t) REVERT: D 343 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D 483 MET cc_start: 0.9731 (tmm) cc_final: 0.9434 (tmm) REVERT: E 13 VAL cc_start: 0.9498 (t) cc_final: 0.9228 (p) REVERT: E 16 ASP cc_start: 0.8868 (t70) cc_final: 0.8251 (t0) REVERT: E 105 ARG cc_start: 0.8880 (mtp-110) cc_final: 0.8238 (ttm-80) REVERT: E 150 MET cc_start: 0.7269 (tmt) cc_final: 0.6661 (tmt) REVERT: E 199 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.9093 (mt-10) REVERT: E 238 LYS cc_start: 0.8454 (mtmm) cc_final: 0.8221 (mtmm) REVERT: E 241 LYS cc_start: 0.9221 (mptt) cc_final: 0.8880 (mmtm) REVERT: E 279 ASN cc_start: 0.8519 (t0) cc_final: 0.7677 (t0) REVERT: E 420 MET cc_start: 0.5630 (mmm) cc_final: 0.5404 (mmm) REVERT: E 466 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8247 (t-90) REVERT: E 483 MET cc_start: 0.9412 (tmm) cc_final: 0.8700 (tmm) REVERT: E 500 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8724 (tm-30) REVERT: F 16 ASP cc_start: 0.8623 (t0) cc_final: 0.8319 (t0) REVERT: F 51 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8332 (tm) REVERT: F 55 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8132 (tt) REVERT: F 95 CYS cc_start: 0.7662 (p) cc_final: 0.7066 (p) REVERT: F 139 PHE cc_start: 0.8224 (p90) cc_final: 0.7573 (p90) REVERT: F 179 MET cc_start: 0.7897 (pp-130) cc_final: 0.7454 (pp-130) REVERT: F 224 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8025 (ttm-80) REVERT: F 343 GLN cc_start: 0.8700 (tp40) cc_final: 0.8450 (tp-100) REVERT: F 352 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7829 (pp20) REVERT: F 412 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7143 (ptt90) REVERT: G 75 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8125 (mm-30) REVERT: G 103 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: G 105 ARG cc_start: 0.8716 (mtm110) cc_final: 0.8357 (tmm-80) REVERT: G 153 ARG cc_start: 0.8267 (tpt170) cc_final: 0.8024 (tpp80) REVERT: G 195 LYS cc_start: 0.9251 (pmmt) cc_final: 0.8524 (tttt) REVERT: G 277 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7932 (tm-30) REVERT: G 386 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8738 (mmp) REVERT: G 478 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7434 (pp30) REVERT: H 32 TYR cc_start: 0.8715 (m-10) cc_final: 0.8470 (m-10) REVERT: H 33 ASN cc_start: 0.8337 (t0) cc_final: 0.7916 (t0) REVERT: H 93 HIS cc_start: 0.8941 (p-80) cc_final: 0.8544 (p90) REVERT: H 228 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8396 (tmtt) REVERT: H 231 ARG cc_start: 0.8482 (mmp80) cc_final: 0.8223 (mmp-170) REVERT: H 274 ASP cc_start: 0.8929 (t70) cc_final: 0.8448 (t70) REVERT: H 309 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: H 343 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7858 (tm-30) REVERT: H 359 VAL cc_start: 0.9361 (t) cc_final: 0.9040 (p) REVERT: H 393 THR cc_start: 0.8195 (p) cc_final: 0.7479 (p) REVERT: H 395 GLU cc_start: 0.8543 (mp0) cc_final: 0.8268 (mp0) REVERT: H 450 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8712 (mmmt) REVERT: H 483 MET cc_start: 0.9641 (tmm) cc_final: 0.8926 (tmm) REVERT: H 484 TYR cc_start: 0.8957 (m-80) cc_final: 0.8637 (m-10) REVERT: H 510 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8037 (tm-30) REVERT: K 4 TYR cc_start: 0.9080 (t80) cc_final: 0.8868 (t80) outliers start: 281 outliers final: 180 residues processed: 1112 average time/residue: 0.3822 time to fit residues: 695.4825 Evaluate side-chains 1124 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 921 time to evaluate : 3.517 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 496 SER 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 55 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL 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 194 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 238 LYS Chi-restraints excluded: chain B residue 263 LEU 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 309 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 362 ILE 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 37 ILE Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 269 ASP 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 450 LYS 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 33 ASN Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 37 ILE 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 66 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 235 LEU 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 325 MET Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 73 VAL 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 163 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 201 LEU 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 299 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 386 MET 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 19 THR 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 55 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 132 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 333 THR 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 444 SER Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 103 GLU 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 269 ASP Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR 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 362 ILE Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 386 MET 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 38 LEU Chi-restraints excluded: chain H residue 49 VAL 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 209 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain P 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 3 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 323 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** 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 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 B 309 GLN C 243 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 465 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN G 478 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32072 Z= 0.264 Angle : 0.747 14.830 43488 Z= 0.367 Chirality : 0.048 0.278 4968 Planarity : 0.004 0.045 5448 Dihedral : 13.170 89.952 5396 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.51 % Favored : 92.39 % Rotamer: Outliers : 8.89 % Allowed : 25.89 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.13), residues: 3968 helix: -1.31 (0.14), residues: 1250 sheet: -2.17 (0.23), residues: 430 loop : -1.79 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 92 PHE 0.024 0.001 PHE E 456 TYR 0.035 0.002 TYR F 484 ARG 0.007 0.000 ARG F 203 *********************** 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 1241 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 950 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8943 (mtp-110) cc_final: 0.8344 (ttm-80) REVERT: A 112 GLN cc_start: 0.7699 (mp10) cc_final: 0.6933 (mp10) REVERT: A 224 ARG cc_start: 0.8445 (ttt-90) cc_final: 0.7900 (tpp80) REVERT: A 230 ASN cc_start: 0.9142 (t0) cc_final: 0.8844 (t0) REVERT: A 233 TYR cc_start: 0.8493 (m-80) cc_final: 0.8249 (m-10) REVERT: A 274 ASP cc_start: 0.8873 (t0) cc_final: 0.8652 (t0) REVERT: A 277 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 352 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 404 ASP cc_start: 0.8508 (t70) cc_final: 0.8045 (t0) REVERT: A 409 LYS cc_start: 0.9249 (ttmm) cc_final: 0.8719 (ttmm) REVERT: A 478 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: A 496 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8679 (p) REVERT: A 500 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8831 (tm-30) REVERT: B 32 TYR cc_start: 0.8702 (m-10) cc_final: 0.8450 (m-10) REVERT: B 78 MET cc_start: 0.8924 (tmt) cc_final: 0.8493 (tmt) REVERT: B 103 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: B 160 SER cc_start: 0.8908 (t) cc_final: 0.8320 (m) REVERT: B 179 MET cc_start: 0.7064 (pp-130) cc_final: 0.6693 (pp-130) REVERT: B 259 ARG cc_start: 0.8751 (mtp-110) cc_final: 0.8180 (ttm-80) REVERT: B 274 ASP cc_start: 0.8818 (t0) cc_final: 0.8595 (t0) REVERT: B 277 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8606 (tt0) REVERT: B 309 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: B 334 GLN cc_start: 0.8937 (mt0) cc_final: 0.8510 (mt0) REVERT: B 335 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7904 (tm-30) REVERT: B 408 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8187 (pp) REVERT: B 409 LYS cc_start: 0.8265 (mttp) cc_final: 0.7767 (mmtt) REVERT: B 483 MET cc_start: 0.9165 (tmm) cc_final: 0.8807 (tmm) REVERT: B 492 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8568 (mttp) REVERT: B 510 GLU cc_start: 0.8265 (tt0) cc_final: 0.7988 (tt0) REVERT: C 25 ASN cc_start: 0.8563 (t0) cc_final: 0.8215 (t0) REVERT: C 36 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8917 (pp) REVERT: C 37 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8769 (pt) REVERT: C 105 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8280 (tmm-80) REVERT: C 134 LYS cc_start: 0.9251 (ptmm) cc_final: 0.8859 (tptt) REVERT: C 150 MET cc_start: 0.8045 (tpp) cc_final: 0.7071 (tpp) REVERT: C 163 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8528 (pt) REVERT: C 179 MET cc_start: 0.7264 (pp-130) cc_final: 0.6961 (pp-130) REVERT: C 182 ARG cc_start: 0.8064 (tpm170) cc_final: 0.7559 (tpp-160) REVERT: C 206 LYS cc_start: 0.9124 (tppp) cc_final: 0.8195 (mmmm) REVERT: C 218 LEU cc_start: 0.9540 (pt) cc_final: 0.9033 (tt) REVERT: C 224 ARG cc_start: 0.9008 (ttt-90) cc_final: 0.8114 (ttt180) REVERT: C 279 ASN cc_start: 0.9095 (t0) cc_final: 0.8605 (t0) REVERT: C 297 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9072 (tm) REVERT: C 468 CYS cc_start: 0.8540 (t) cc_final: 0.8059 (t) REVERT: C 469 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8233 (tp-100) REVERT: C 478 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: C 483 MET cc_start: 0.9219 (tmm) cc_final: 0.8741 (tmm) REVERT: D 82 MET cc_start: 0.9112 (mtm) cc_final: 0.8671 (mtp) REVERT: D 93 HIS cc_start: 0.8864 (p-80) cc_final: 0.8548 (p90) REVERT: D 103 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8203 (tp30) REVERT: D 105 ARG cc_start: 0.8889 (mtm110) cc_final: 0.8355 (ptp-170) REVERT: D 199 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8873 (tm-30) REVERT: D 235 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8066 (pp) REVERT: D 277 GLN cc_start: 0.9023 (tp40) cc_final: 0.8810 (tp40) REVERT: D 327 SER cc_start: 0.9031 (p) cc_final: 0.8575 (t) REVERT: D 343 GLN cc_start: 0.8620 (tm-30) cc_final: 0.7758 (tm-30) REVERT: D 483 MET cc_start: 0.9745 (tmm) cc_final: 0.9446 (tmm) REVERT: E 16 ASP cc_start: 0.8835 (t70) cc_final: 0.8631 (t0) REVERT: E 105 ARG cc_start: 0.8890 (mtp-110) cc_final: 0.8101 (ttm-80) REVERT: E 149 ARG cc_start: 0.8284 (mpt180) cc_final: 0.8025 (mpp80) REVERT: E 150 MET cc_start: 0.7121 (tmt) cc_final: 0.6523 (tmt) REVERT: E 179 MET cc_start: 0.6405 (ppp) cc_final: 0.5327 (ppp) REVERT: E 199 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9099 (mt-10) REVERT: E 238 LYS cc_start: 0.8456 (mtmm) cc_final: 0.8177 (mtmm) REVERT: E 241 LYS cc_start: 0.9227 (mptt) cc_final: 0.8895 (mmtm) REVERT: E 385 MET cc_start: 0.8808 (ttp) cc_final: 0.8576 (ttp) REVERT: E 420 MET cc_start: 0.5695 (mmm) cc_final: 0.5481 (mmm) REVERT: E 450 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8747 (ptmm) REVERT: E 466 HIS cc_start: 0.8889 (OUTLIER) cc_final: 0.8279 (t-90) REVERT: E 483 MET cc_start: 0.9423 (tmm) cc_final: 0.8728 (tmm) REVERT: E 500 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8730 (tm-30) REVERT: F 16 ASP cc_start: 0.8612 (t0) cc_final: 0.8322 (t0) REVERT: F 51 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8382 (tm) REVERT: F 55 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8194 (tt) REVERT: F 78 MET cc_start: 0.9187 (tpp) cc_final: 0.8892 (tpp) REVERT: F 95 CYS cc_start: 0.7635 (p) cc_final: 0.7038 (p) REVERT: F 103 GLU cc_start: 0.8800 (mp0) cc_final: 0.8267 (mp0) REVERT: F 139 PHE cc_start: 0.8270 (p90) cc_final: 0.7582 (p90) REVERT: F 153 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8007 (tpt170) REVERT: F 179 MET cc_start: 0.7935 (pp-130) cc_final: 0.7518 (pp-130) REVERT: F 199 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: F 224 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.7883 (ttt-90) REVERT: F 343 GLN cc_start: 0.8741 (tp40) cc_final: 0.8477 (tp-100) REVERT: F 352 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7871 (pp20) REVERT: F 412 ARG cc_start: 0.8169 (ttp80) cc_final: 0.6795 (ptt90) REVERT: G 75 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8176 (mm-30) REVERT: G 78 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8666 (tmm) REVERT: G 103 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: G 105 ARG cc_start: 0.8731 (mtm110) cc_final: 0.8397 (tmm-80) REVERT: G 153 ARG cc_start: 0.8357 (tpt170) cc_final: 0.8119 (tpp80) REVERT: G 182 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.8141 (mmm-85) REVERT: G 195 LYS cc_start: 0.9263 (pmmt) cc_final: 0.8519 (tttt) REVERT: G 277 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8012 (tm-30) REVERT: G 409 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7851 (ptpt) REVERT: G 478 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7777 (pp30) REVERT: G 500 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8954 (tm-30) REVERT: H 33 ASN cc_start: 0.8267 (t0) cc_final: 0.7935 (t0) REVERT: H 82 MET cc_start: 0.9224 (mtm) cc_final: 0.9001 (mtm) REVERT: H 93 HIS cc_start: 0.8939 (p-80) cc_final: 0.8573 (p90) REVERT: H 228 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8361 (tmtt) REVERT: H 231 ARG cc_start: 0.8495 (mmp80) cc_final: 0.8241 (mmp-170) REVERT: H 274 ASP cc_start: 0.8899 (t70) cc_final: 0.8236 (t70) REVERT: H 285 ASN cc_start: 0.9070 (m-40) cc_final: 0.8660 (m110) REVERT: H 343 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7957 (tm-30) REVERT: H 359 VAL cc_start: 0.9386 (t) cc_final: 0.9056 (p) REVERT: H 393 THR cc_start: 0.8193 (p) cc_final: 0.7374 (p) REVERT: H 395 GLU cc_start: 0.8552 (mp0) cc_final: 0.8265 (mp0) REVERT: H 450 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8717 (mmmt) REVERT: H 483 MET cc_start: 0.9621 (tmm) cc_final: 0.8955 (tmm) REVERT: H 484 TYR cc_start: 0.9006 (m-80) cc_final: 0.8682 (m-10) REVERT: H 510 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8056 (tm-30) REVERT: K 4 TYR cc_start: 0.9077 (t80) cc_final: 0.8844 (t80) outliers start: 291 outliers final: 194 residues processed: 1097 average time/residue: 0.3834 time to fit residues: 691.2234 Evaluate side-chains 1117 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 898 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP 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 103 GLU 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 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL 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 238 LYS Chi-restraints excluded: chain B residue 263 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 309 GLN Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 362 ILE 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 485 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 LYS 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 47 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 ILE 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 195 LYS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 269 ASP 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 417 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 469 GLN 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 33 ASN Chi-restraints excluded: chain D residue 34 ASP 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 66 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 221 ILE Chi-restraints excluded: chain D residue 235 LEU 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 325 MET Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 102 ASN 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 163 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 201 LEU 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 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 450 LYS 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 19 THR 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 55 LEU Chi-restraints excluded: chain F residue 59 ILE 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 109 LYS Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU 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 272 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 333 THR 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 444 SER Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 164 ASP 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 269 ASP Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 315 ASP 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 457 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 78 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 382 SER 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 P 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 1 MET Chi-restraints excluded: chain K residue 3 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.9980 chunk 341 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 379 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 0.4980 chunk 199 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 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 469 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN G 478 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32072 Z= 0.217 Angle : 0.741 17.053 43488 Z= 0.358 Chirality : 0.047 0.272 4968 Planarity : 0.004 0.044 5448 Dihedral : 12.701 88.759 5393 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.38 % Favored : 92.57 % Rotamer: Outliers : 8.34 % Allowed : 27.44 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 3968 helix: -1.13 (0.14), residues: 1232 sheet: -2.28 (0.24), residues: 420 loop : -1.69 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 92 PHE 0.019 0.001 PHE D 165 TYR 0.028 0.002 TYR C 110 ARG 0.007 0.000 ARG C 149 *********************** 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 1237 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 964 time to evaluate : 3.953 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 105 ARG cc_start: 0.8904 (mtp-110) cc_final: 0.8305 (ttm-80) REVERT: A 224 ARG cc_start: 0.8397 (ttt-90) cc_final: 0.7855 (tpp80) REVERT: A 230 ASN cc_start: 0.9066 (t0) cc_final: 0.8780 (t0) REVERT: A 274 ASP cc_start: 0.8843 (t0) cc_final: 0.8603 (t0) REVERT: A 277 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 296 ASN cc_start: 0.8710 (p0) cc_final: 0.7787 (t0) REVERT: A 298 GLN cc_start: 0.8045 (pm20) cc_final: 0.7762 (pm20) REVERT: A 404 ASP cc_start: 0.8498 (t70) cc_final: 0.8077 (t0) REVERT: A 409 LYS cc_start: 0.9228 (ttmm) cc_final: 0.8741 (ttmm) REVERT: A 478 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: A 491 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: A 500 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8829 (tm-30) REVERT: B 32 TYR cc_start: 0.8719 (m-10) cc_final: 0.8489 (m-10) REVERT: B 98 GLU cc_start: 0.9101 (pm20) cc_final: 0.8823 (pm20) REVERT: B 103 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: B 160 SER cc_start: 0.8930 (t) cc_final: 0.8309 (m) REVERT: B 179 MET cc_start: 0.6915 (pp-130) cc_final: 0.6624 (pp-130) REVERT: B 259 ARG cc_start: 0.8701 (mtp-110) cc_final: 0.8060 (ttm-80) REVERT: B 277 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8636 (tt0) REVERT: B 334 GLN cc_start: 0.8914 (mt0) cc_final: 0.8490 (mt0) REVERT: B 335 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 352 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: B 408 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8184 (pp) REVERT: B 409 LYS cc_start: 0.8257 (mttp) cc_final: 0.7670 (mmtt) REVERT: B 412 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7600 (ptt90) REVERT: B 483 MET cc_start: 0.9114 (tmm) cc_final: 0.8854 (tmm) REVERT: B 487 GLU cc_start: 0.8899 (tt0) cc_final: 0.8669 (tt0) REVERT: B 492 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8528 (mttp) REVERT: B 510 GLU cc_start: 0.8253 (tt0) cc_final: 0.8020 (tt0) REVERT: C 25 ASN cc_start: 0.8542 (t0) cc_final: 0.8050 (t0) REVERT: C 36 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8931 (pp) REVERT: C 37 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8733 (pt) REVERT: C 105 ARG cc_start: 0.8738 (mtm110) cc_final: 0.8275 (tmm-80) REVERT: C 163 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8520 (pt) REVERT: C 179 MET cc_start: 0.7404 (pp-130) cc_final: 0.7142 (pp-130) REVERT: C 206 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8877 (mmmm) REVERT: C 218 LEU cc_start: 0.9553 (pt) cc_final: 0.9092 (tt) REVERT: C 224 ARG cc_start: 0.9019 (ttt-90) cc_final: 0.8438 (ttt180) REVERT: C 238 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8631 (mmmm) REVERT: C 279 ASN cc_start: 0.9041 (t0) cc_final: 0.8623 (t0) REVERT: C 296 ASN cc_start: 0.8652 (p0) cc_final: 0.8407 (m-40) REVERT: C 297 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8926 (tm) REVERT: C 352 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (pp20) REVERT: C 369 ASN cc_start: 0.8566 (p0) cc_final: 0.8294 (p0) REVERT: C 468 CYS cc_start: 0.8507 (t) cc_final: 0.7958 (t) REVERT: C 478 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: C 483 MET cc_start: 0.9220 (tmm) cc_final: 0.8793 (tmm) REVERT: D 93 HIS cc_start: 0.8852 (p-80) cc_final: 0.8551 (p90) REVERT: D 102 ASN cc_start: 0.9256 (t0) cc_final: 0.8912 (t0) REVERT: D 103 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8137 (tp30) REVERT: D 105 ARG cc_start: 0.8834 (mtm110) cc_final: 0.8486 (ttp80) REVERT: D 111 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7464 (mm-30) REVERT: D 199 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8883 (tm-30) REVERT: D 235 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8056 (pp) REVERT: D 327 SER cc_start: 0.8960 (p) cc_final: 0.8712 (t) REVERT: D 343 GLN cc_start: 0.8589 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 400 TYR cc_start: 0.6959 (m-80) cc_final: 0.6314 (m-10) REVERT: D 483 MET cc_start: 0.9727 (tmm) cc_final: 0.9526 (tmm) REVERT: E 16 ASP cc_start: 0.9060 (t70) cc_final: 0.8679 (t0) REVERT: E 28 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8537 (p0) REVERT: E 30 LEU cc_start: 0.9405 (mm) cc_final: 0.8802 (mm) REVERT: E 149 ARG cc_start: 0.8277 (mpt180) cc_final: 0.8029 (mpp80) REVERT: E 150 MET cc_start: 0.7104 (tmt) cc_final: 0.6514 (tmt) REVERT: E 199 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9085 (mt-10) REVERT: E 238 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8195 (mtmm) REVERT: E 241 LYS cc_start: 0.9230 (mptt) cc_final: 0.8892 (mmtm) REVERT: E 279 ASN cc_start: 0.8470 (t0) cc_final: 0.7622 (t0) REVERT: E 298 GLN cc_start: 0.6982 (tt0) cc_final: 0.6725 (tt0) REVERT: E 385 MET cc_start: 0.8813 (ttp) cc_final: 0.8581 (ttp) REVERT: E 450 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8688 (ptmm) REVERT: E 466 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8196 (t-90) REVERT: E 483 MET cc_start: 0.9449 (tmm) cc_final: 0.8743 (tmm) REVERT: E 500 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8751 (tm-30) REVERT: F 16 ASP cc_start: 0.8540 (t0) cc_final: 0.8286 (t0) REVERT: F 51 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8330 (tm) REVERT: F 55 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8195 (tt) REVERT: F 78 MET cc_start: 0.9177 (tpp) cc_final: 0.8909 (tpp) REVERT: F 95 CYS cc_start: 0.7860 (p) cc_final: 0.7264 (p) REVERT: F 103 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: F 139 PHE cc_start: 0.8280 (p90) cc_final: 0.7584 (p90) REVERT: F 179 MET cc_start: 0.7815 (pp-130) cc_final: 0.7434 (pp-130) REVERT: F 199 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: F 224 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.7860 (ttm-80) REVERT: F 352 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7746 (pp20) REVERT: F 362 ILE cc_start: 0.9408 (mt) cc_final: 0.9156 (mm) REVERT: F 409 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8032 (mmtt) REVERT: F 412 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7583 (ptt90) REVERT: F 469 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8572 (tm-30) REVERT: G 78 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8673 (tmm) REVERT: G 103 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8271 (mm-30) REVERT: G 105 ARG cc_start: 0.8724 (mtm110) cc_final: 0.8343 (tmm-80) REVERT: G 195 LYS cc_start: 0.9252 (pmmt) cc_final: 0.8483 (tttt) REVERT: G 238 LYS cc_start: 0.9254 (mttm) cc_final: 0.8903 (mtpp) REVERT: G 420 MET cc_start: 0.4538 (OUTLIER) cc_final: 0.3456 (tpp) REVERT: G 478 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7679 (pp30) REVERT: G 500 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8948 (tm-30) REVERT: H 33 ASN cc_start: 0.8042 (t0) cc_final: 0.7798 (t0) REVERT: H 93 HIS cc_start: 0.8872 (p-80) cc_final: 0.8509 (p90) REVERT: H 228 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8347 (tmtt) REVERT: H 231 ARG cc_start: 0.8453 (mmp80) cc_final: 0.8216 (mmp-170) REVERT: H 274 ASP cc_start: 0.8902 (t70) cc_final: 0.8183 (t70) REVERT: H 285 ASN cc_start: 0.9088 (m-40) cc_final: 0.8765 (m-40) REVERT: H 343 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7593 (tm-30) REVERT: H 359 VAL cc_start: 0.9384 (t) cc_final: 0.9053 (p) REVERT: H 450 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8706 (mmmt) REVERT: H 483 MET cc_start: 0.9535 (tmm) cc_final: 0.8887 (tmm) REVERT: H 484 TYR cc_start: 0.8983 (m-80) cc_final: 0.8719 (m-10) REVERT: H 510 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8045 (tm-30) REVERT: K 4 TYR cc_start: 0.9070 (t80) cc_final: 0.8864 (t80) outliers start: 273 outliers final: 189 residues processed: 1097 average time/residue: 0.4037 time to fit residues: 727.0565 Evaluate side-chains 1118 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 899 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP 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 103 GLU 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 270 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 84 LEU 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 194 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 263 LEU 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 323 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 362 ILE 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 444 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 LYS 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 47 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 ILE 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 195 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 286 MET 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 352 GLU 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 414 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 447 VAL 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 34 ASP Chi-restraints excluded: chain D residue 37 ILE 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 142 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 235 LEU 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 325 MET Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 102 ASN 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 163 ILE Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 201 LEU 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 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 ILE 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 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 162 ASP 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 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 352 GLU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 103 GLU 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 269 ASP 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 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 395 GLU 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 49 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 382 SER 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 P 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 1 MET Chi-restraints excluded: chain K residue 3 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 377 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 230 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN G 465 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN ** H 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32072 Z= 0.216 Angle : 0.745 17.318 43488 Z= 0.360 Chirality : 0.047 0.329 4968 Planarity : 0.004 0.043 5448 Dihedral : 12.365 85.629 5393 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.54 % Favored : 92.44 % Rotamer: Outliers : 8.47 % Allowed : 27.87 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.13), residues: 3968 helix: -1.10 (0.14), residues: 1250 sheet: -2.18 (0.24), residues: 428 loop : -1.65 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 92 PHE 0.022 0.001 PHE G 90 TYR 0.027 0.002 TYR I 4 ARG 0.009 0.000 ARG A 149 *********************** 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 1226 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 949 time to evaluate : 3.510 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 70 MET cc_start: 0.9162 (mpp) cc_final: 0.8746 (mtt) REVERT: A 105 ARG cc_start: 0.8856 (mtp-110) cc_final: 0.8285 (ttm-80) REVERT: A 224 ARG cc_start: 0.8392 (ttt-90) cc_final: 0.7901 (tpp80) REVERT: A 229 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8369 (mtpp) REVERT: A 230 ASN cc_start: 0.9019 (t0) cc_final: 0.8749 (t0) REVERT: A 274 ASP cc_start: 0.8802 (t0) cc_final: 0.8561 (t0) REVERT: A 277 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7548 (tm-30) REVERT: A 296 ASN cc_start: 0.8698 (p0) cc_final: 0.8133 (t0) REVERT: A 335 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8404 (tm-30) REVERT: A 404 ASP cc_start: 0.8532 (t70) cc_final: 0.8123 (t0) REVERT: A 409 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8425 (ttmm) REVERT: A 412 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7257 (ptt90) REVERT: A 478 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8356 (pt0) REVERT: A 491 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: A 500 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8879 (tm-30) REVERT: B 103 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: B 160 SER cc_start: 0.8901 (t) cc_final: 0.8327 (m) REVERT: B 179 MET cc_start: 0.6892 (pp-130) cc_final: 0.6586 (pp-130) REVERT: B 259 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8056 (ttm-80) REVERT: B 277 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8613 (tt0) REVERT: B 334 GLN cc_start: 0.8913 (mt0) cc_final: 0.8555 (mt0) REVERT: B 335 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 352 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8135 (pp20) REVERT: B 408 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8290 (pp) REVERT: B 409 LYS cc_start: 0.8183 (mttp) cc_final: 0.7657 (mmtt) REVERT: B 412 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7451 (ptt90) REVERT: B 483 MET cc_start: 0.9150 (tmm) cc_final: 0.8876 (tmm) REVERT: B 492 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8508 (ttmt) REVERT: B 510 GLU cc_start: 0.8264 (tt0) cc_final: 0.8014 (tt0) REVERT: C 25 ASN cc_start: 0.8544 (t0) cc_final: 0.8210 (t0) REVERT: C 36 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8688 (pp) REVERT: C 37 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8564 (pt) REVERT: C 75 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7847 (mm-30) REVERT: C 105 ARG cc_start: 0.8710 (mtm110) cc_final: 0.8279 (tmm-80) REVERT: C 163 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8495 (pt) REVERT: C 164 ASP cc_start: 0.6818 (m-30) cc_final: 0.5866 (m-30) REVERT: C 179 MET cc_start: 0.7422 (pp-130) cc_final: 0.7097 (pp-130) REVERT: C 182 ARG cc_start: 0.8077 (tpm170) cc_final: 0.7611 (tpp-160) REVERT: C 206 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.7887 (mmmm) REVERT: C 218 LEU cc_start: 0.9564 (pt) cc_final: 0.9064 (tt) REVERT: C 224 ARG cc_start: 0.9019 (ttt-90) cc_final: 0.8099 (ttt180) REVERT: C 238 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8616 (mmmm) REVERT: C 279 ASN cc_start: 0.9008 (t0) cc_final: 0.8590 (t0) REVERT: C 297 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9050 (tm) REVERT: C 352 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8458 (pp20) REVERT: C 468 CYS cc_start: 0.8486 (t) cc_final: 0.7982 (t) REVERT: C 478 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: C 483 MET cc_start: 0.9232 (tmm) cc_final: 0.8808 (tmm) REVERT: D 93 HIS cc_start: 0.8881 (p-80) cc_final: 0.8552 (p90) REVERT: D 102 ASN cc_start: 0.9257 (t0) cc_final: 0.8947 (t0) REVERT: D 103 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: D 105 ARG cc_start: 0.8803 (mtm110) cc_final: 0.8509 (ttp80) REVERT: D 199 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8874 (tm-30) REVERT: D 235 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8098 (pp) REVERT: D 399 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: D 483 MET cc_start: 0.9720 (tmm) cc_final: 0.9512 (tmm) REVERT: E 28 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8517 (p0) REVERT: E 30 LEU cc_start: 0.9409 (mm) cc_final: 0.8856 (mm) REVERT: E 105 ARG cc_start: 0.8880 (mtp-110) cc_final: 0.8307 (ttm-80) REVERT: E 149 ARG cc_start: 0.8334 (mpt180) cc_final: 0.8084 (mpp80) REVERT: E 150 MET cc_start: 0.7117 (tmt) cc_final: 0.6548 (tmt) REVERT: E 179 MET cc_start: 0.7720 (ttp) cc_final: 0.7403 (ppp) REVERT: E 199 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9077 (mt-10) REVERT: E 241 LYS cc_start: 0.9229 (mptt) cc_final: 0.8897 (mmtm) REVERT: E 279 ASN cc_start: 0.8518 (t0) cc_final: 0.7389 (t0) REVERT: E 335 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8457 (tm-30) REVERT: E 450 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8500 (ptmm) REVERT: E 461 ILE cc_start: 0.9114 (pp) cc_final: 0.8677 (mt) REVERT: E 466 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8157 (t-90) REVERT: E 483 MET cc_start: 0.9432 (tmm) cc_final: 0.8748 (tmm) REVERT: E 500 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8742 (tm-30) REVERT: F 16 ASP cc_start: 0.8599 (t0) cc_final: 0.8338 (t0) REVERT: F 51 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8363 (tm) REVERT: F 55 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8202 (tt) REVERT: F 78 MET cc_start: 0.9180 (tpp) cc_final: 0.8952 (tpp) REVERT: F 95 CYS cc_start: 0.7868 (p) cc_final: 0.7267 (p) REVERT: F 103 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: F 139 PHE cc_start: 0.8319 (p90) cc_final: 0.7616 (p90) REVERT: F 179 MET cc_start: 0.7811 (pp-130) cc_final: 0.7492 (pp-130) REVERT: F 199 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: F 224 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8038 (ttt-90) REVERT: F 352 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7750 (pp20) REVERT: F 362 ILE cc_start: 0.9438 (mt) cc_final: 0.9227 (mm) REVERT: F 409 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8066 (mmtt) REVERT: F 412 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7541 (ptt90) REVERT: F 487 GLU cc_start: 0.8922 (tt0) cc_final: 0.8636 (tt0) REVERT: G 75 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7750 (mm-30) REVERT: G 78 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8631 (tmm) REVERT: G 103 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8249 (mm-30) REVERT: G 105 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8372 (tmm-80) REVERT: G 106 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8513 (ttmt) REVERT: G 192 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8044 (mm) REVERT: G 195 LYS cc_start: 0.9239 (pmmt) cc_final: 0.8592 (mttt) REVERT: G 238 LYS cc_start: 0.9230 (mttm) cc_final: 0.8945 (mtpp) REVERT: G 420 MET cc_start: 0.4396 (OUTLIER) cc_final: 0.3398 (tpp) REVERT: G 478 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7639 (pp30) REVERT: H 33 ASN cc_start: 0.8028 (t0) cc_final: 0.7775 (t0) REVERT: H 93 HIS cc_start: 0.8832 (p-80) cc_final: 0.8470 (p90) REVERT: H 105 ARG cc_start: 0.8514 (ptt90) cc_final: 0.8303 (ttp80) REVERT: H 228 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8439 (tmtt) REVERT: H 231 ARG cc_start: 0.8461 (mmp80) cc_final: 0.8206 (mmp-170) REVERT: H 274 ASP cc_start: 0.8923 (t70) cc_final: 0.8372 (t70) REVERT: H 285 ASN cc_start: 0.9089 (m-40) cc_final: 0.8733 (m110) REVERT: H 343 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7553 (tm-30) REVERT: H 359 VAL cc_start: 0.9376 (t) cc_final: 0.9053 (p) REVERT: H 450 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8708 (mmmt) REVERT: H 483 MET cc_start: 0.9523 (tmm) cc_final: 0.8876 (tmm) REVERT: H 484 TYR cc_start: 0.8984 (m-80) cc_final: 0.8696 (m-10) REVERT: H 510 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8028 (tm-30) REVERT: K 4 TYR cc_start: 0.9074 (t80) cc_final: 0.8868 (t80) outliers start: 277 outliers final: 191 residues processed: 1085 average time/residue: 0.3806 time to fit residues: 677.7709 Evaluate side-chains 1117 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 894 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP 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 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 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL 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 153 ARG 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 286 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 361 VAL 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 384 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 LYS 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 47 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 162 ASP 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 195 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 284 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 352 GLU 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 414 MET Chi-restraints excluded: chain C residue 417 LEU 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 C residue 488 LEU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 37 ILE 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 66 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 158 ILE Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 235 LEU 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 314 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 102 ASN 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 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 287 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 ILE 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 103 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 162 ASP 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 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE 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 488 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 164 ASP 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 269 ASP Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 325 MET 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 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 78 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain P 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 3 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 225 optimal weight: 0.2980 chunk 113 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 257 optimal weight: 0.0060 chunk 186 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 296 optimal weight: 0.2980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 309 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN D 22 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN E 283 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN G 478 GLN H 25 ASN H 372 HIS ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32072 Z= 0.188 Angle : 0.749 19.027 43488 Z= 0.359 Chirality : 0.047 0.440 4968 Planarity : 0.004 0.042 5448 Dihedral : 11.893 84.921 5387 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 7.03 % Allowed : 30.07 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3968 helix: -0.97 (0.14), residues: 1238 sheet: -2.13 (0.25), residues: 394 loop : -1.60 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 92 PHE 0.027 0.001 PHE G 90 TYR 0.028 0.002 TYR C 110 ARG 0.008 0.000 ARG C 407 *********************** 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 1177 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 947 time to evaluate : 3.564 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 70 MET cc_start: 0.9204 (mpp) cc_final: 0.8920 (mtt) REVERT: A 78 MET cc_start: 0.9397 (tpp) cc_final: 0.9185 (tpp) REVERT: A 105 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.8349 (ttm-80) REVERT: A 224 ARG cc_start: 0.8371 (ttt-90) cc_final: 0.7942 (tpp80) REVERT: A 230 ASN cc_start: 0.8959 (t0) cc_final: 0.8720 (t0) REVERT: A 274 ASP cc_start: 0.8793 (t0) cc_final: 0.8552 (t0) REVERT: A 277 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 296 ASN cc_start: 0.8681 (p0) cc_final: 0.8140 (t0) REVERT: A 335 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8402 (tm-30) REVERT: A 404 ASP cc_start: 0.8519 (t70) cc_final: 0.8125 (t0) REVERT: A 409 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8471 (ttmm) REVERT: A 412 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7265 (ptt90) REVERT: A 478 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8384 (pt0) REVERT: B 160 SER cc_start: 0.8947 (t) cc_final: 0.8368 (m) REVERT: B 179 MET cc_start: 0.6777 (pp-130) cc_final: 0.6520 (pp-130) REVERT: B 259 ARG cc_start: 0.8656 (mtp-110) cc_final: 0.8308 (ttm-80) REVERT: B 277 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8494 (tt0) REVERT: B 309 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: B 334 GLN cc_start: 0.8889 (mt0) cc_final: 0.8493 (mt0) REVERT: B 335 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 352 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7983 (pp20) REVERT: B 395 GLU cc_start: 0.8529 (mp0) cc_final: 0.8154 (mp0) REVERT: B 408 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8344 (pp) REVERT: B 412 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7351 (ptt90) REVERT: B 492 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8289 (ttmt) REVERT: B 510 GLU cc_start: 0.8299 (tt0) cc_final: 0.8044 (tt0) REVERT: C 25 ASN cc_start: 0.8505 (t0) cc_final: 0.8156 (t0) REVERT: C 36 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8729 (pp) REVERT: C 37 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8443 (pt) REVERT: C 75 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7924 (mm-30) REVERT: C 105 ARG cc_start: 0.8694 (mtm110) cc_final: 0.8272 (tmm-80) REVERT: C 134 LYS cc_start: 0.9275 (ptmm) cc_final: 0.8905 (tptt) REVERT: C 163 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8498 (pt) REVERT: C 164 ASP cc_start: 0.6936 (m-30) cc_final: 0.5846 (m-30) REVERT: C 179 MET cc_start: 0.7466 (pp-130) cc_final: 0.7140 (pp-130) REVERT: C 182 ARG cc_start: 0.8035 (tpm170) cc_final: 0.7443 (tpp-160) REVERT: C 206 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8663 (mmmm) REVERT: C 218 LEU cc_start: 0.9543 (pt) cc_final: 0.9067 (tt) REVERT: C 224 ARG cc_start: 0.8978 (ttt-90) cc_final: 0.8563 (ttm-80) REVERT: C 238 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8570 (mmmm) REVERT: C 279 ASN cc_start: 0.8938 (t0) cc_final: 0.8508 (t0) REVERT: C 369 ASN cc_start: 0.8598 (p0) cc_final: 0.8302 (p0) REVERT: C 468 CYS cc_start: 0.8428 (t) cc_final: 0.7850 (t) REVERT: C 478 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: C 483 MET cc_start: 0.9244 (tmm) cc_final: 0.8777 (tmm) REVERT: D 93 HIS cc_start: 0.8869 (p-80) cc_final: 0.8515 (p90) REVERT: D 103 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8110 (tp30) REVERT: D 105 ARG cc_start: 0.8764 (mtm110) cc_final: 0.8273 (ptp-170) REVERT: D 111 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7574 (mm-30) REVERT: D 231 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7412 (mmm160) REVERT: D 235 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7938 (pp) REVERT: D 319 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6781 (t0) REVERT: D 343 GLN cc_start: 0.8477 (tm-30) cc_final: 0.7572 (tm-30) REVERT: D 377 LEU cc_start: 0.9411 (mt) cc_final: 0.9170 (mt) REVERT: D 399 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: D 400 TYR cc_start: 0.6547 (m-10) cc_final: 0.5989 (m-10) REVERT: E 28 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8446 (p0) REVERT: E 30 LEU cc_start: 0.9393 (mm) cc_final: 0.8845 (mm) REVERT: E 80 ILE cc_start: 0.9426 (mt) cc_final: 0.9156 (tt) REVERT: E 149 ARG cc_start: 0.8270 (mpt180) cc_final: 0.8021 (mpp80) REVERT: E 150 MET cc_start: 0.7100 (tmt) cc_final: 0.6537 (tmt) REVERT: E 179 MET cc_start: 0.7582 (ttp) cc_final: 0.7110 (ppp) REVERT: E 241 LYS cc_start: 0.9220 (mptt) cc_final: 0.8891 (mmtm) REVERT: E 279 ASN cc_start: 0.8425 (t0) cc_final: 0.7397 (t0) REVERT: E 335 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8413 (tm-30) REVERT: E 388 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8804 (m) REVERT: E 450 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8183 (ptmm) REVERT: E 461 ILE cc_start: 0.9098 (pp) cc_final: 0.8742 (mt) REVERT: E 466 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8142 (t-90) REVERT: E 483 MET cc_start: 0.9470 (tmm) cc_final: 0.8764 (tmm) REVERT: E 500 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8749 (tm-30) REVERT: F 51 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8338 (tm) REVERT: F 55 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7945 (tt) REVERT: F 70 MET cc_start: 0.9035 (mtm) cc_final: 0.8809 (mtm) REVERT: F 95 CYS cc_start: 0.7911 (p) cc_final: 0.7275 (p) REVERT: F 103 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: F 114 PHE cc_start: 0.9102 (m-10) cc_final: 0.8833 (m-80) REVERT: F 139 PHE cc_start: 0.8408 (p90) cc_final: 0.7720 (p90) REVERT: F 179 MET cc_start: 0.7687 (pp-130) cc_final: 0.7400 (pp-130) REVERT: F 199 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: F 224 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8133 (ttt-90) REVERT: F 228 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8495 (mmmm) REVERT: F 352 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7766 (pp20) REVERT: F 409 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8190 (mttt) REVERT: F 412 ARG cc_start: 0.8086 (ttp80) cc_final: 0.6936 (ptt90) REVERT: F 484 TYR cc_start: 0.8291 (m-80) cc_final: 0.7999 (m-80) REVERT: F 487 GLU cc_start: 0.8885 (tt0) cc_final: 0.8633 (tt0) REVERT: G 75 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: G 78 MET cc_start: 0.9067 (mmm) cc_final: 0.8614 (tmm) REVERT: G 82 MET cc_start: 0.9285 (mmm) cc_final: 0.8551 (tpp) REVERT: G 103 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: G 105 ARG cc_start: 0.8698 (mtm110) cc_final: 0.8364 (tmm-80) REVERT: G 106 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8454 (ttmt) REVERT: G 182 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7667 (mmm160) REVERT: G 195 LYS cc_start: 0.9200 (pmmt) cc_final: 0.8570 (mttt) REVERT: G 277 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7529 (tm-30) REVERT: G 420 MET cc_start: 0.4239 (OUTLIER) cc_final: 0.3382 (tpp) REVERT: G 478 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7787 (pp30) REVERT: H 93 HIS cc_start: 0.8849 (p-80) cc_final: 0.8449 (p90) REVERT: H 136 ARG cc_start: 0.7302 (ttt90) cc_final: 0.7052 (ttt90) REVERT: H 228 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8387 (tmtt) REVERT: H 231 ARG cc_start: 0.8448 (mmp80) cc_final: 0.8210 (mmp-170) REVERT: H 274 ASP cc_start: 0.8928 (t70) cc_final: 0.8323 (t70) REVERT: H 296 ASN cc_start: 0.8689 (m-40) cc_final: 0.8337 (p0) REVERT: H 309 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: H 343 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7525 (tm-30) REVERT: H 359 VAL cc_start: 0.9361 (t) cc_final: 0.9003 (p) REVERT: H 386 MET cc_start: 0.8858 (pmm) cc_final: 0.8455 (pmm) REVERT: H 480 ARG cc_start: 0.9184 (mtm-85) cc_final: 0.8844 (mtm180) REVERT: H 483 MET cc_start: 0.9502 (tmm) cc_final: 0.8938 (tmm) REVERT: O 1 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5250 (pmm) outliers start: 230 outliers final: 156 residues processed: 1066 average time/residue: 0.3963 time to fit residues: 688.4701 Evaluate side-chains 1092 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 906 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP 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 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 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 66 VAL 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 153 ARG Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 263 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 323 VAL 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 384 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 LYS 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 47 ASP 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 96 THR Chi-restraints excluded: chain C residue 162 ASP 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 206 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 306 THR 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 414 MET Chi-restraints excluded: chain C residue 417 LEU 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 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 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 306 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 127 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 287 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 450 LYS 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 19 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 55 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 153 ARG Chi-restraints excluded: chain F residue 162 ASP 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 222 ILE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE 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 444 SER Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 164 ASP 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 269 ASP Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 325 MET 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 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 78 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 211 ILE Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain P 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 1 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.0970 chunk 361 optimal weight: 4.9990 chunk 330 optimal weight: 0.0870 chunk 352 optimal weight: 0.0970 chunk 211 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 318 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 chunk 350 optimal weight: 8.9990 overall best weight: 1.0558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32072 Z= 0.236 Angle : 0.771 18.888 43488 Z= 0.372 Chirality : 0.048 0.463 4968 Planarity : 0.004 0.139 5448 Dihedral : 11.771 85.391 5381 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 6.54 % Allowed : 31.14 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3968 helix: -0.91 (0.14), residues: 1242 sheet: -2.20 (0.24), residues: 416 loop : -1.57 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 93 PHE 0.018 0.001 PHE G 90 TYR 0.034 0.002 TYR H 484 ARG 0.027 0.001 ARG D 407 *********************** 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 1141 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 927 time to evaluate : 3.179 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 70 MET cc_start: 0.9208 (mpp) cc_final: 0.8998 (mtm) REVERT: A 78 MET cc_start: 0.9445 (tpp) cc_final: 0.9238 (tpp) REVERT: A 105 ARG cc_start: 0.8856 (mtp-110) cc_final: 0.8378 (ttm-80) REVERT: A 224 ARG cc_start: 0.8308 (ttt-90) cc_final: 0.8004 (tpp80) REVERT: A 242 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7748 (mmtt) REVERT: A 274 ASP cc_start: 0.8800 (t0) cc_final: 0.8566 (t0) REVERT: A 277 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 296 ASN cc_start: 0.8650 (p0) cc_final: 0.8142 (t0) REVERT: A 335 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 404 ASP cc_start: 0.8516 (t70) cc_final: 0.8157 (t0) REVERT: A 409 LYS cc_start: 0.9249 (ttmm) cc_final: 0.8466 (ttmm) REVERT: A 412 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7313 (ptt90) REVERT: A 478 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8434 (pt0) REVERT: B 95 CYS cc_start: 0.7972 (p) cc_final: 0.7330 (p) REVERT: B 160 SER cc_start: 0.8958 (t) cc_final: 0.8390 (m) REVERT: B 179 MET cc_start: 0.6771 (pp-130) cc_final: 0.6552 (pp-130) REVERT: B 259 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.8254 (ttm-80) REVERT: B 277 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8516 (tt0) REVERT: B 334 GLN cc_start: 0.8854 (mt0) cc_final: 0.8395 (mt0) REVERT: B 335 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 352 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8213 (pp20) REVERT: B 385 MET cc_start: 0.8762 (ttm) cc_final: 0.8295 (ttp) REVERT: B 395 GLU cc_start: 0.8569 (mp0) cc_final: 0.8218 (mp0) REVERT: B 412 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7206 (ptt90) REVERT: B 492 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8461 (ttmt) REVERT: B 510 GLU cc_start: 0.8331 (tt0) cc_final: 0.8067 (tt0) REVERT: C 25 ASN cc_start: 0.8583 (t0) cc_final: 0.8106 (t0) REVERT: C 36 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8739 (pp) REVERT: C 37 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8510 (pt) REVERT: C 75 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7962 (mm-30) REVERT: C 105 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8298 (tmm-80) REVERT: C 134 LYS cc_start: 0.9268 (ptmm) cc_final: 0.8888 (tptt) REVERT: C 163 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8519 (pt) REVERT: C 164 ASP cc_start: 0.6991 (m-30) cc_final: 0.6166 (m-30) REVERT: C 174 PHE cc_start: 0.7897 (m-80) cc_final: 0.7346 (m-80) REVERT: C 179 MET cc_start: 0.7486 (pp-130) cc_final: 0.7133 (pp-130) REVERT: C 182 ARG cc_start: 0.8035 (tpm170) cc_final: 0.7438 (tpp-160) REVERT: C 206 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8675 (mmmm) REVERT: C 218 LEU cc_start: 0.9566 (pt) cc_final: 0.9118 (tt) REVERT: C 224 ARG cc_start: 0.8986 (ttt-90) cc_final: 0.8579 (ttm-80) REVERT: C 231 ARG cc_start: 0.8468 (mmt-90) cc_final: 0.8219 (mmt-90) REVERT: C 238 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8622 (mmmm) REVERT: C 279 ASN cc_start: 0.8917 (t0) cc_final: 0.8484 (t0) REVERT: C 352 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8390 (pp20) REVERT: C 369 ASN cc_start: 0.8601 (p0) cc_final: 0.8301 (p0) REVERT: C 468 CYS cc_start: 0.8479 (t) cc_final: 0.7974 (t) REVERT: C 478 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: C 483 MET cc_start: 0.9231 (tmm) cc_final: 0.8813 (tmm) REVERT: D 65 LEU cc_start: 0.9541 (mm) cc_final: 0.9250 (mm) REVERT: D 93 HIS cc_start: 0.8896 (p-80) cc_final: 0.8534 (p90) REVERT: D 105 ARG cc_start: 0.8787 (mtm110) cc_final: 0.8125 (mmt90) REVERT: D 111 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7734 (mm-30) REVERT: D 231 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7467 (mmm160) REVERT: D 343 GLN cc_start: 0.8614 (tm-30) cc_final: 0.7660 (tm-30) REVERT: D 399 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: D 483 MET cc_start: 0.9663 (tmm) cc_final: 0.9451 (tmm) REVERT: E 28 ASP cc_start: 0.9221 (OUTLIER) cc_final: 0.8480 (p0) REVERT: E 30 LEU cc_start: 0.9408 (mm) cc_final: 0.8839 (mm) REVERT: E 105 ARG cc_start: 0.8837 (mtp-110) cc_final: 0.8296 (ttm-80) REVERT: E 149 ARG cc_start: 0.8345 (mpt180) cc_final: 0.8097 (mpp80) REVERT: E 150 MET cc_start: 0.7081 (tmt) cc_final: 0.6512 (tmt) REVERT: E 179 MET cc_start: 0.7520 (ttp) cc_final: 0.7261 (ppp) REVERT: E 241 LYS cc_start: 0.9204 (mptt) cc_final: 0.8877 (mmtm) REVERT: E 279 ASN cc_start: 0.8521 (t0) cc_final: 0.7403 (t0) REVERT: E 335 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8451 (tm-30) REVERT: E 450 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8478 (ptmm) REVERT: E 466 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8127 (t-90) REVERT: E 483 MET cc_start: 0.9469 (tmm) cc_final: 0.8768 (tmm) REVERT: E 500 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8717 (tm-30) REVERT: F 16 ASP cc_start: 0.8586 (t0) cc_final: 0.8369 (t0) REVERT: F 51 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8380 (tm) REVERT: F 55 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8409 (tt) REVERT: F 95 CYS cc_start: 0.7945 (p) cc_final: 0.7307 (p) REVERT: F 103 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: F 139 PHE cc_start: 0.8380 (p90) cc_final: 0.7701 (p90) REVERT: F 179 MET cc_start: 0.7709 (pp-130) cc_final: 0.7438 (pp-130) REVERT: F 199 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8331 (pm20) REVERT: F 224 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8196 (ttm-80) REVERT: F 228 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8497 (mmmm) REVERT: F 352 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7887 (pp20) REVERT: F 409 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8096 (mmtt) REVERT: F 412 ARG cc_start: 0.8122 (ttp80) cc_final: 0.6936 (ptt90) REVERT: F 487 GLU cc_start: 0.8876 (tt0) cc_final: 0.8608 (tt0) REVERT: G 75 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: G 78 MET cc_start: 0.9099 (mmm) cc_final: 0.8606 (tmm) REVERT: G 82 MET cc_start: 0.9280 (mmm) cc_final: 0.8559 (tpp) REVERT: G 103 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8253 (mm-30) REVERT: G 105 ARG cc_start: 0.8707 (mtm110) cc_final: 0.8378 (tmm-80) REVERT: G 106 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8485 (ttmt) REVERT: G 182 ARG cc_start: 0.8405 (mmm160) cc_final: 0.7826 (mmm160) REVERT: G 192 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7990 (mm) REVERT: G 195 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8608 (mttt) REVERT: G 232 ASP cc_start: 0.8438 (t70) cc_final: 0.8116 (t0) REVERT: G 238 LYS cc_start: 0.9234 (mttm) cc_final: 0.8981 (mmmm) REVERT: G 277 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7592 (tm-30) REVERT: G 420 MET cc_start: 0.4270 (OUTLIER) cc_final: 0.3388 (tpp) REVERT: G 478 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7575 (pp30) REVERT: G 498 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8094 (tm-30) REVERT: H 93 HIS cc_start: 0.8858 (p-80) cc_final: 0.8486 (p90) REVERT: H 131 PHE cc_start: 0.8980 (m-80) cc_final: 0.8347 (m-80) REVERT: H 228 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8423 (tmtt) REVERT: H 231 ARG cc_start: 0.8463 (mmp80) cc_final: 0.8214 (mmp-170) REVERT: H 274 ASP cc_start: 0.8930 (t70) cc_final: 0.8387 (t70) REVERT: H 296 ASN cc_start: 0.8685 (m-40) cc_final: 0.8292 (p0) REVERT: H 309 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: H 343 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7627 (tm-30) REVERT: H 359 VAL cc_start: 0.9368 (t) cc_final: 0.9014 (p) REVERT: H 386 MET cc_start: 0.8934 (pmm) cc_final: 0.8404 (pmm) REVERT: H 483 MET cc_start: 0.9452 (tmm) cc_final: 0.8917 (tmm) REVERT: N 7 SER cc_start: 0.9308 (p) cc_final: 0.8978 (p) REVERT: O 1 MET cc_start: 0.5612 (OUTLIER) cc_final: 0.5158 (pmm) outliers start: 214 outliers final: 172 residues processed: 1038 average time/residue: 0.4060 time to fit residues: 688.3575 Evaluate side-chains 1098 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 899 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP 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 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 66 VAL 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 153 ARG Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 263 LEU 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 315 ASP 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 384 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 LYS 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 47 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 162 ASP 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 206 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 235 LEU 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 352 GLU 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 414 MET 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 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 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 306 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 102 ASN 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 227 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 450 LYS 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 19 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 55 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 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 162 ASP 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 222 ILE Chi-restraints excluded: chain F residue 235 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 370 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 164 ASP 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 195 LYS Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 325 MET 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 362 ILE 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 28 ASP 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 78 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 221 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain P 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 1 MET Chi-restraints excluded: chain K residue 3 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 2.9990 chunk 372 optimal weight: 0.5980 chunk 227 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 chunk 390 optimal weight: 0.3980 chunk 359 optimal weight: 0.3980 chunk 310 optimal weight: 0.9990 chunk 32 optimal weight: 0.0020 chunk 240 optimal weight: 0.5980 chunk 190 optimal weight: 0.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** 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 ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN G 478 GLN H 303 ASN ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32072 Z= 0.191 Angle : 0.780 17.948 43488 Z= 0.372 Chirality : 0.048 0.471 4968 Planarity : 0.004 0.079 5448 Dihedral : 11.565 86.926 5381 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 5.87 % Allowed : 32.06 % Favored : 62.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3968 helix: -0.95 (0.14), residues: 1244 sheet: -2.17 (0.24), residues: 402 loop : -1.61 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 92 PHE 0.018 0.001 PHE G 90 TYR 0.041 0.002 TYR H 484 ARG 0.018 0.001 ARG D 407 ********************** 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 1129 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 937 time to evaluate : 3.347 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: A 70 MET cc_start: 0.9206 (mpp) cc_final: 0.8927 (mtm) REVERT: A 78 MET cc_start: 0.9361 (tpp) cc_final: 0.9157 (tpp) REVERT: A 105 ARG cc_start: 0.8862 (mtp-110) cc_final: 0.8396 (ttm-80) REVERT: A 224 ARG cc_start: 0.8263 (ttt-90) cc_final: 0.8056 (tpp80) REVERT: A 242 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7736 (mmtt) REVERT: A 274 ASP cc_start: 0.8757 (t0) cc_final: 0.8514 (t0) REVERT: A 277 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7299 (tm-30) REVERT: A 279 ASN cc_start: 0.8306 (t0) cc_final: 0.7833 (t0) REVERT: A 296 ASN cc_start: 0.8648 (p0) cc_final: 0.8181 (t0) REVERT: A 335 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8414 (tm-30) REVERT: A 404 ASP cc_start: 0.8426 (t70) cc_final: 0.8076 (t0) REVERT: A 409 LYS cc_start: 0.9222 (ttmm) cc_final: 0.8780 (ttmm) REVERT: A 466 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7992 (t-90) REVERT: A 478 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: B 95 CYS cc_start: 0.7883 (p) cc_final: 0.7452 (p) REVERT: B 160 SER cc_start: 0.8897 (t) cc_final: 0.8336 (m) REVERT: B 231 ARG cc_start: 0.8887 (mmt-90) cc_final: 0.8638 (mmt-90) REVERT: B 259 ARG cc_start: 0.8561 (mtp-110) cc_final: 0.8202 (ttm-80) REVERT: B 277 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8437 (tt0) REVERT: B 312 ASN cc_start: 0.9202 (m-40) cc_final: 0.8608 (t0) REVERT: B 334 GLN cc_start: 0.8863 (mt0) cc_final: 0.8437 (mt0) REVERT: B 335 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 352 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8024 (pp20) REVERT: B 385 MET cc_start: 0.8680 (ttm) cc_final: 0.8204 (ttp) REVERT: B 395 GLU cc_start: 0.8530 (mp0) cc_final: 0.8192 (mp0) REVERT: B 487 GLU cc_start: 0.8767 (tt0) cc_final: 0.8558 (tt0) REVERT: B 492 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8442 (ttmt) REVERT: B 510 GLU cc_start: 0.8312 (tt0) cc_final: 0.8049 (tt0) REVERT: C 25 ASN cc_start: 0.8504 (t0) cc_final: 0.8026 (t0) REVERT: C 36 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8751 (pp) REVERT: C 37 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8406 (pt) REVERT: C 75 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7971 (mm-30) REVERT: C 105 ARG cc_start: 0.8629 (mtm110) cc_final: 0.8293 (tmm-80) REVERT: C 134 LYS cc_start: 0.9281 (ptmm) cc_final: 0.8916 (tptt) REVERT: C 163 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8500 (pt) REVERT: C 164 ASP cc_start: 0.7003 (m-30) cc_final: 0.6220 (m-30) REVERT: C 179 MET cc_start: 0.7412 (pp-130) cc_final: 0.7068 (pp-130) REVERT: C 182 ARG cc_start: 0.8044 (tpm170) cc_final: 0.7494 (tpp-160) REVERT: C 195 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8259 (tttt) REVERT: C 206 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8598 (mmmm) REVERT: C 218 LEU cc_start: 0.9568 (pt) cc_final: 0.9146 (tt) REVERT: C 224 ARG cc_start: 0.8964 (ttt-90) cc_final: 0.8574 (ttm-80) REVERT: C 231 ARG cc_start: 0.8477 (mmt-90) cc_final: 0.8247 (mmt-90) REVERT: C 238 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8594 (mmmm) REVERT: C 279 ASN cc_start: 0.8760 (t0) cc_final: 0.8286 (t0) REVERT: C 296 ASN cc_start: 0.8601 (p0) cc_final: 0.8263 (p0) REVERT: C 309 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: C 352 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8376 (pp20) REVERT: C 369 ASN cc_start: 0.8576 (p0) cc_final: 0.8288 (p0) REVERT: C 468 CYS cc_start: 0.8432 (t) cc_final: 0.7861 (t) REVERT: C 478 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: C 483 MET cc_start: 0.9250 (tmm) cc_final: 0.8799 (tmm) REVERT: D 93 HIS cc_start: 0.8918 (p-80) cc_final: 0.8516 (p90) REVERT: D 102 ASN cc_start: 0.9238 (t0) cc_final: 0.8942 (t0) REVERT: D 103 GLU cc_start: 0.8502 (tp30) cc_final: 0.8189 (mm-30) REVERT: D 111 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7771 (mm-30) REVERT: D 199 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8880 (tm-30) REVERT: D 231 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7619 (mmm160) REVERT: D 235 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7928 (pp) REVERT: D 399 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: E 16 ASP cc_start: 0.8984 (t70) cc_final: 0.8590 (t0) REVERT: E 28 ASP cc_start: 0.9213 (OUTLIER) cc_final: 0.8443 (p0) REVERT: E 30 LEU cc_start: 0.9383 (mm) cc_final: 0.8864 (mm) REVERT: E 105 ARG cc_start: 0.8775 (mtp-110) cc_final: 0.8186 (ttm-80) REVERT: E 149 ARG cc_start: 0.8276 (mpt180) cc_final: 0.8029 (mpp80) REVERT: E 150 MET cc_start: 0.7053 (tmt) cc_final: 0.6492 (tmt) REVERT: E 179 MET cc_start: 0.7511 (ttp) cc_final: 0.7208 (ppp) REVERT: E 241 LYS cc_start: 0.9197 (mptt) cc_final: 0.8873 (mmtm) REVERT: E 279 ASN cc_start: 0.8422 (t0) cc_final: 0.7474 (t0) REVERT: E 335 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8756 (tm-30) REVERT: E 375 LYS cc_start: 0.9484 (mtmm) cc_final: 0.9251 (ttmt) REVERT: E 385 MET cc_start: 0.8932 (ttp) cc_final: 0.8644 (ttp) REVERT: E 461 ILE cc_start: 0.9104 (pp) cc_final: 0.8653 (mp) REVERT: E 466 HIS cc_start: 0.8765 (OUTLIER) cc_final: 0.8108 (t-90) REVERT: E 483 MET cc_start: 0.9443 (tmm) cc_final: 0.8712 (tmm) REVERT: F 16 ASP cc_start: 0.8643 (t0) cc_final: 0.8416 (t0) REVERT: F 51 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8378 (tm) REVERT: F 55 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8391 (tt) REVERT: F 95 CYS cc_start: 0.7926 (p) cc_final: 0.7261 (p) REVERT: F 103 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: F 114 PHE cc_start: 0.9039 (m-10) cc_final: 0.8489 (m-10) REVERT: F 139 PHE cc_start: 0.8428 (p90) cc_final: 0.7801 (p90) REVERT: F 179 MET cc_start: 0.7613 (pp-130) cc_final: 0.7350 (pp-130) REVERT: F 199 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: F 224 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8183 (ttm-80) REVERT: F 228 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8558 (mmmm) REVERT: F 312 ASN cc_start: 0.9350 (m-40) cc_final: 0.8841 (t0) REVERT: F 352 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7721 (pp20) REVERT: F 409 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8225 (mttt) REVERT: F 412 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7501 (ptt90) REVERT: F 449 ASP cc_start: 0.8100 (p0) cc_final: 0.7790 (p0) REVERT: F 483 MET cc_start: 0.9039 (tmm) cc_final: 0.8764 (tmm) REVERT: G 75 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: G 78 MET cc_start: 0.9038 (mmm) cc_final: 0.8583 (tmm) REVERT: G 82 MET cc_start: 0.9266 (mmm) cc_final: 0.8566 (tpp) REVERT: G 103 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8293 (mm-30) REVERT: G 105 ARG cc_start: 0.8608 (mtm110) cc_final: 0.8310 (tmm-80) REVERT: G 106 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8423 (ttmt) REVERT: G 182 ARG cc_start: 0.8422 (mmm160) cc_final: 0.7877 (mmm160) REVERT: G 195 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8570 (mttt) REVERT: G 232 ASP cc_start: 0.8442 (t70) cc_final: 0.8084 (t0) REVERT: G 277 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7496 (tm-30) REVERT: G 337 LEU cc_start: 0.9222 (mp) cc_final: 0.8906 (tp) REVERT: G 420 MET cc_start: 0.4157 (OUTLIER) cc_final: 0.3378 (tpp) REVERT: G 478 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7454 (pp30) REVERT: G 498 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8066 (tm-30) REVERT: H 93 HIS cc_start: 0.8808 (p-80) cc_final: 0.8418 (p90) REVERT: H 111 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7707 (mm-30) REVERT: H 131 PHE cc_start: 0.8942 (m-80) cc_final: 0.8415 (m-80) REVERT: H 136 ARG cc_start: 0.7298 (ttt90) cc_final: 0.7034 (ttt90) REVERT: H 274 ASP cc_start: 0.8859 (t70) cc_final: 0.8189 (t70) REVERT: H 296 ASN cc_start: 0.8592 (m-40) cc_final: 0.8253 (p0) REVERT: H 309 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: H 343 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7420 (tm-30) REVERT: H 359 VAL cc_start: 0.9350 (t) cc_final: 0.8983 (p) REVERT: H 386 MET cc_start: 0.8980 (pmm) cc_final: 0.8654 (pmm) REVERT: H 470 ASP cc_start: 0.8767 (t0) cc_final: 0.8300 (m-30) REVERT: H 483 MET cc_start: 0.9235 (tmm) cc_final: 0.8770 (tmm) REVERT: H 484 TYR cc_start: 0.8341 (m-10) cc_final: 0.7836 (m-10) REVERT: N 7 SER cc_start: 0.9242 (p) cc_final: 0.8797 (p) REVERT: O 1 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.5123 (pmm) outliers start: 192 outliers final: 145 residues processed: 1033 average time/residue: 0.3991 time to fit residues: 674.5389 Evaluate side-chains 1098 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 924 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP 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 130 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 66 VAL 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 153 ARG Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 263 LEU 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 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 384 VAL Chi-restraints excluded: chain B residue 492 LYS 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 78 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 162 ASP 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 195 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 235 LEU 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 309 GLN Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 352 GLU 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 414 MET 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 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 158 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 73 VAL 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 227 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 55 LEU 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 121 LEU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 162 ASP 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 296 ASN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 325 MET 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 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 37 ILE Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain P 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 1 MET Chi-restraints excluded: chain K residue 3 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.8980 chunk 331 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 311 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 319 optimal weight: 0.6980 chunk 39 optimal weight: 0.0000 chunk 57 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 465 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 25 ASN H 33 ASN ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113082 restraints weight = 52577.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117424 restraints weight = 26595.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120339 restraints weight = 16586.012| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32072 Z= 0.212 Angle : 0.791 17.697 43488 Z= 0.377 Chirality : 0.048 0.438 4968 Planarity : 0.004 0.055 5448 Dihedral : 11.405 88.209 5380 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.99 % Allowed : 32.21 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.13), residues: 3968 helix: -0.87 (0.14), residues: 1232 sheet: -2.17 (0.24), residues: 402 loop : -1.54 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 92 PHE 0.020 0.001 PHE B 357 TYR 0.032 0.002 TYR F 110 ARG 0.017 0.001 ARG D 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10141.00 seconds wall clock time: 183 minutes 58.40 seconds (11038.40 seconds total)