Starting phenix.real_space_refine on Thu Aug 8 21:42:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l70_23209/08_2024/7l70_23209_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l70_23209/08_2024/7l70_23209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l70_23209/08_2024/7l70_23209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l70_23209/08_2024/7l70_23209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l70_23209/08_2024/7l70_23209_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l70_23209/08_2024/7l70_23209_neut.cif" } resolution = 2.8 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= 0.003 sd= 0.073 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: 4 Type Number sf(0) Gaussians S 137 5.16 5 C 15414 2.51 5 N 4221 2.21 5 O 4415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ASP 329": "OD1" <-> "OD2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 301": "OD1" <-> "OD2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 295": "OE1" <-> "OE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ASP 362": "OD1" <-> "OD2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "E GLU 445": "OE1" <-> "OE2" Residue "E ASP 450": "OD1" <-> "OD2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 417": "NH1" <-> "NH2" Residue "F GLU 439": "OE1" <-> "OE2" Residue "F GLU 445": "OE1" <-> "OE2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "F GLU 495": "OE1" <-> "OE2" Residue "F GLU 503": "OE1" <-> "OE2" Residue "G TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G LEU 49": "CD1" <-> "CD2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 74": "NH1" <-> "NH2" Residue "G PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H ARG 108": "NH1" <-> "NH2" Residue "H ASP 121": "OD1" <-> "OD2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 161": "OD1" <-> "OD2" Residue "I PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 217": "OE1" <-> "OE2" Residue "I ARG 324": "NH1" <-> "NH2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J ASP 111": "OD1" <-> "OD2" Residue "J PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 201": "OD1" <-> "OD2" Residue "J TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 227": "OE1" <-> "OE2" Residue "J GLU 307": "OE1" <-> "OE2" Residue "J ARG 324": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24187 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3195 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 3195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3195 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2479 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2734 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 332} Chain: "F" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2693 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 328} Chain: "G" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1977 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1966 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1682 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 205} Unresolved chain links: 1 Chain breaks: 3 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1794 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 14.54, per 1000 atoms: 0.60 Number of scatterers: 24187 At special positions: 0 Unit cell: (134.435, 174.515, 125.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 137 16.00 O 4415 8.00 N 4221 7.00 C 15414 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=0, symmetry=0 Time building additional restraints: 10.72 Conformation dependent library (CDL) restraints added in 3.6 seconds 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5946 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 31 sheets defined 44.1% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.797A pdb=" N ASP A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.738A pdb=" N LEU A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.621A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.623A pdb=" N ILE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.657A pdb=" N CYS A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.959A pdb=" N SER A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.752A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.957A pdb=" N ASN A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.609A pdb=" N ALA A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.797A pdb=" N ASP B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.621A pdb=" N TYR B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.623A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.657A pdb=" N CYS B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.959A pdb=" N SER B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.753A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.957A pdb=" N ASN B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.608A pdb=" N ALA B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 25 removed outlier: 3.648A pdb=" N GLY C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 removed outlier: 3.545A pdb=" N ASP C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.917A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 98 removed outlier: 3.868A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 153 removed outlier: 3.515A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 removed outlier: 3.955A pdb=" N ALA C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.529A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.653A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 removed outlier: 3.975A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 304' Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.532A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.736A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.679A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 98 removed outlier: 3.624A pdb=" N MET D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 153 removed outlier: 4.355A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.892A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.571A pdb=" N LEU D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.769A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 removed outlier: 4.213A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.810A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.978A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 3.729A pdb=" N LEU E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 removed outlier: 3.544A pdb=" N ALA E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP E 305 " --> pdb=" O ARG E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 325 removed outlier: 4.352A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'E' and resid 368 through 380 removed outlier: 4.134A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 removed outlier: 3.534A pdb=" N VAL E 394 " --> pdb=" O ALA E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 418 through 430 removed outlier: 4.687A pdb=" N GLN E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 423 " --> pdb=" O GLY E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.804A pdb=" N LYS E 442 " --> pdb=" O GLU E 439 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 439 through 443' Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.540A pdb=" N ASP E 462 " --> pdb=" O ASP E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 511 through 517 Processing helix chain 'F' and resid 204 through 217 Processing helix chain 'F' and resid 221 through 239 removed outlier: 3.594A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.380A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 313 through 323 removed outlier: 3.783A pdb=" N GLN F 317 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE F 319 " --> pdb=" O ALA F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 353 removed outlier: 3.740A pdb=" N GLY F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 378 removed outlier: 4.056A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 removed outlier: 3.577A pdb=" N VAL F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 493 through 497 removed outlier: 3.575A pdb=" N VAL F 497 " --> pdb=" O PRO F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 517 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.609A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 removed outlier: 3.636A pdb=" N GLY G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 77 removed outlier: 3.838A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 116 removed outlier: 4.646A pdb=" N ARG G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASN G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 143 Processing helix chain 'G' and resid 160 through 170 removed outlier: 3.565A pdb=" N HIS G 170 " --> pdb=" O LYS G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 183 removed outlier: 3.835A pdb=" N VAL G 183 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 221 Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.888A pdb=" N LYS G 234 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE G 235 " --> pdb=" O SER G 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 231 through 235' Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.699A pdb=" N LYS G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 295 through 304 Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'H' and resid 21 through 35 removed outlier: 3.813A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 60 Processing helix chain 'H' and resid 62 through 76 removed outlier: 3.695A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 106 removed outlier: 4.004A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.656A pdb=" N LEU H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 143 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 186 through 190 Processing helix chain 'H' and resid 212 through 222 Processing helix chain 'H' and resid 231 through 235 removed outlier: 3.834A pdb=" N LYS H 234 " --> pdb=" O GLU H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.580A pdb=" N LYS H 251 " --> pdb=" O PRO H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 294 through 304 removed outlier: 3.567A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 43 removed outlier: 3.617A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 Processing helix chain 'I' and resid 113 through 123 removed outlier: 4.153A pdb=" N VAL I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 209 through 218 Processing helix chain 'I' and resid 223 through 234 removed outlier: 4.770A pdb=" N ILE I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 4.020A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 28 removed outlier: 3.562A pdb=" N LEU J 28 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 44 removed outlier: 3.744A pdb=" N LEU J 40 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 removed outlier: 3.612A pdb=" N ILE J 93 " --> pdb=" O SER J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 124 removed outlier: 4.014A pdb=" N VAL J 117 " --> pdb=" O ALA J 113 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE J 121 " --> pdb=" O VAL J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 208 through 218 removed outlier: 4.084A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN J 218 " --> pdb=" O PHE J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 236 Processing helix chain 'J' and resid 315 through 334 Proline residue: J 327 - end of helix removed outlier: 3.906A pdb=" N SER J 331 " --> pdb=" O PRO J 327 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA J 332 " --> pdb=" O LYS J 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.484A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 149 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE A 184 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 249 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A 182 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 251 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL A 180 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 214 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 338 removed outlier: 3.537A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.262A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.278A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.891A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 430 through 431 removed outlier: 6.689A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 448 " --> pdb=" O GLU A 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.484A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 149 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS B 247 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE B 184 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 249 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR B 182 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE B 251 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL B 180 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN B 286 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET B 181 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE B 287 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 214 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS J 196 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE J 158 " --> pdb=" O HIS J 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 338 removed outlier: 3.538A pdb=" N ILE B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.263A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.277A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 401 through 402 removed outlier: 6.891A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 430 through 431 removed outlier: 6.690A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 448 " --> pdb=" O GLU B 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.487A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 231 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU C 163 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 190 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.508A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.466A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR F 336 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLY F 404 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.853A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.237A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.445A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY G 196 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AC7, first strand: chain 'H' and resid 177 through 178 removed outlier: 7.218A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 286 " --> pdb=" O GLY H 289 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AC9, first strand: chain 'I' and resid 51 through 53 removed outlier: 3.872A pdb=" N ALA I 202 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU I 128 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N HIS I 303 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET I 130 " --> pdb=" O HIS I 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AD2, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AD3, first strand: chain 'J' and resid 101 through 103 Processing sheet with id=AD4, first strand: chain 'J' and resid 132 through 134 973 hydrogen bonds defined for protein. 2724 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: 8.44 Time building geometry restraints manager: 11.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3950 1.31 - 1.44: 6229 1.44 - 1.56: 14247 1.56 - 1.69: 2 1.69 - 1.81: 208 Bond restraints: 24636 Sorted by residual: bond pdb=" CA SER H 62 " pdb=" C SER H 62 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.23e-02 6.61e+03 1.59e+01 bond pdb=" CA ARG G 46 " pdb=" C ARG G 46 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.32e-02 5.74e+03 1.56e+01 bond pdb=" C LEU H 56 " pdb=" O LEU H 56 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.40e+01 bond pdb=" C ASP H 60 " pdb=" O ASP H 60 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.14e-02 7.69e+03 1.34e+01 bond pdb=" C SER H 62 " pdb=" O SER H 62 " ideal model delta sigma weight residual 1.234 1.188 0.046 1.26e-02 6.30e+03 1.32e+01 ... (remaining 24631 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.65: 713 106.65 - 113.48: 13919 113.48 - 120.30: 8657 120.30 - 127.13: 9871 127.13 - 133.96: 271 Bond angle restraints: 33431 Sorted by residual: angle pdb=" C ASP G 19 " pdb=" N MET G 20 " pdb=" CA MET G 20 " ideal model delta sigma weight residual 120.90 130.06 -9.16 1.41e+00 5.03e-01 4.22e+01 angle pdb=" N PRO G 18 " pdb=" CA PRO G 18 " pdb=" C PRO G 18 " ideal model delta sigma weight residual 113.53 122.30 -8.77 1.39e+00 5.18e-01 3.98e+01 angle pdb=" CA GLU A 104 " pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " ideal model delta sigma weight residual 114.10 126.66 -12.56 2.00e+00 2.50e-01 3.95e+01 angle pdb=" CA GLU B 104 " pdb=" CB GLU B 104 " pdb=" CG GLU B 104 " ideal model delta sigma weight residual 114.10 126.64 -12.54 2.00e+00 2.50e-01 3.93e+01 angle pdb=" N ASP G 60 " pdb=" CA ASP G 60 " pdb=" C ASP G 60 " ideal model delta sigma weight residual 107.62 119.31 -11.69 1.97e+00 2.58e-01 3.52e+01 ... (remaining 33426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 14145 24.05 - 48.10: 628 48.10 - 72.14: 131 72.14 - 96.19: 25 96.19 - 120.24: 2 Dihedral angle restraints: 14931 sinusoidal: 5787 harmonic: 9144 Sorted by residual: dihedral pdb=" CA PHE A 57 " pdb=" C PHE A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual 180.00 59.76 120.24 0 5.00e+00 4.00e-02 5.78e+02 dihedral pdb=" CA PHE B 57 " pdb=" C PHE B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta harmonic sigma weight residual 180.00 59.89 120.11 0 5.00e+00 4.00e-02 5.77e+02 dihedral pdb=" CA GLU C 281 " pdb=" C GLU C 281 " pdb=" N GLU C 282 " pdb=" CA GLU C 282 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 14928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.556: 3963 0.556 - 1.112: 4 1.112 - 1.668: 0 1.668 - 2.224: 0 2.224 - 2.780: 1 Chirality restraints: 3968 Sorted by residual: chirality pdb=" CG LEU G 49 " pdb=" CB LEU G 49 " pdb=" CD1 LEU G 49 " pdb=" CD2 LEU G 49 " both_signs ideal model delta sigma weight residual False -2.59 0.19 -2.78 2.00e-01 2.50e+01 1.93e+02 chirality pdb=" CG LEU A 70 " pdb=" CB LEU A 70 " pdb=" CD1 LEU A 70 " pdb=" CD2 LEU A 70 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CG LEU B 70 " pdb=" CB LEU B 70 " pdb=" CD1 LEU B 70 " pdb=" CD2 LEU B 70 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.31e+01 ... (remaining 3965 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 13 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLN G 13 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN G 13 " 0.023 2.00e-02 2.50e+03 pdb=" N MET G 14 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 384 " 0.019 2.00e-02 2.50e+03 2.13e-02 6.79e+00 pdb=" CG HIS B 384 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS B 384 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 384 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS B 384 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 384 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 384 " -0.019 2.00e-02 2.50e+03 2.12e-02 6.77e+00 pdb=" CG HIS A 384 " 0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS A 384 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 384 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 384 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 384 " -0.006 2.00e-02 2.50e+03 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 65 2.44 - 3.05: 15438 3.05 - 3.67: 35504 3.67 - 4.28: 52752 4.28 - 4.90: 90401 Nonbonded interactions: 194160 Sorted by model distance: nonbonded pdb=" O ASN G 48 " pdb=" OG SER G 51 " model vdw 1.824 3.040 nonbonded pdb=" OG1 THR D 76 " pdb=" OG1 THR D 238 " model vdw 1.958 3.040 nonbonded pdb=" OG SER B 130 " pdb=" O GLN B 267 " model vdw 2.030 3.040 nonbonded pdb=" OG SER A 130 " pdb=" O GLN A 267 " model vdw 2.030 3.040 nonbonded pdb=" O LYS J 328 " pdb=" OG SER J 331 " model vdw 2.052 3.040 ... (remaining 194155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 279 or (resid 280 through 283 and (name N or nam \ e CA or name C or name O or name CB )) or resid 284 through 351)) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 172 through 517) selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 9 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 14 or (resid 15 through 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 74 or (resi \ d 75 through 76 and (name N or name CA or name C or name O or name CB )) or resi \ d 77 or resid 91 through 305)) selection = (chain 'H' and (resid 9 through 58 or (resid 59 through 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 305)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB )) or resid 58 through 60 or resid 85 through 106 or (resi \ d 107 and (name N or name CA or name C or name O or name CB )) or resid 108 thro \ ugh 135 or (resid 157 and (name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 158 through \ 236 or resid 298 through 334)) } 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 individual isotropic 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: 4.940 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: 1.120 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 67.960 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 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:14.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.003 0.073 24636 Z= 0.201 Angle : 0.583 12.562 33431 Z= 0.336 Chirality : 0.071 2.780 3968 Planarity : 0.003 0.065 4248 Dihedral : 14.391 120.238 8985 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 2.66 % Allowed : 13.31 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.14 (0.14), residues: 3080 helix: -0.15 (0.15), residues: 1187 sheet: -2.05 (0.23), residues: 425 loop : -2.31 (0.14), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 51 HIS 0.024 0.001 HIS B 384 PHE 0.017 0.001 PHE A 57 TYR 0.007 0.001 TYR J 210 ARG 0.008 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 381 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7197 (t-100) cc_final: 0.6366 (t60) REVERT: A 173 LYS cc_start: 0.6795 (mptt) cc_final: 0.6566 (mptt) REVERT: B 109 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 370 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7883 (m) REVERT: B 371 ASN cc_start: 0.7987 (m-40) cc_final: 0.7498 (p0) REVERT: C 203 MET cc_start: 0.8027 (ttt) cc_final: 0.7787 (ttm) REVERT: E 235 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7534 (tp-100) REVERT: E 249 SER cc_start: 0.8243 (t) cc_final: 0.7730 (m) REVERT: E 467 ARG cc_start: 0.7643 (mpt180) cc_final: 0.7174 (mmm160) REVERT: F 495 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7237 (pt0) REVERT: G 45 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7321 (tm) REVERT: G 54 GLU cc_start: 0.5415 (tp30) cc_final: 0.4940 (tp30) REVERT: H 139 GLU cc_start: 0.7952 (tt0) cc_final: 0.7494 (tm-30) REVERT: I 100 ASP cc_start: 0.7979 (m-30) cc_final: 0.7701 (m-30) REVERT: I 320 MET cc_start: 0.8380 (mmt) cc_final: 0.8174 (pp-130) REVERT: J 50 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7588 (mt-10) outliers start: 70 outliers final: 23 residues processed: 444 average time/residue: 1.3111 time to fit residues: 668.2130 Evaluate side-chains 230 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain J residue 158 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 5.9990 chunk 233 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN B 44 GLN B 337 HIS B 376 ASN B 410 GLN C 80 ASN C 130 GLN C 158 HIS C 160 HIS C 252 HIS D 80 ASN D 158 HIS D 160 HIS D 331 ASN E 213 GLN ** E 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS E 431 ASN E 448 GLN F 185 GLN F 213 GLN F 448 GLN ** F 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 GLN G 222 GLN G 243 GLN H 43 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 222 GLN H 243 GLN J 41 ASN J 236 GLN J 303 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 24636 Z= 0.427 Angle : 0.711 9.820 33431 Z= 0.359 Chirality : 0.048 0.173 3968 Planarity : 0.005 0.098 4248 Dihedral : 6.386 124.517 3415 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.94 % Favored : 94.94 % Rotamer: Outliers : 4.90 % Allowed : 16.58 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.01 (0.15), residues: 3080 helix: 0.63 (0.15), residues: 1197 sheet: -1.62 (0.23), residues: 413 loop : -1.47 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.008 0.001 HIS J 196 PHE 0.026 0.002 PHE C 177 TYR 0.032 0.002 TYR A 128 ARG 0.011 0.001 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 215 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7573 (t-100) cc_final: 0.6612 (t60) REVERT: B 109 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.7800 (p) REVERT: B 370 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7873 (m) REVERT: B 371 ASN cc_start: 0.8006 (m-40) cc_final: 0.7259 (p0) REVERT: D 213 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6069 (tm-30) REVERT: E 210 LEU cc_start: 0.8079 (tp) cc_final: 0.7430 (tp) REVERT: E 214 TYR cc_start: 0.7933 (m-10) cc_final: 0.7419 (m-10) REVERT: E 235 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7976 (mm-40) REVERT: E 249 SER cc_start: 0.8279 (t) cc_final: 0.7919 (m) REVERT: E 467 ARG cc_start: 0.7868 (mpt180) cc_final: 0.7341 (mmm160) REVERT: F 235 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6808 (tm-30) REVERT: G 164 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7534 (tpt) REVERT: H 139 GLU cc_start: 0.7957 (tt0) cc_final: 0.7604 (tm-30) REVERT: I 100 ASP cc_start: 0.8356 (m-30) cc_final: 0.7949 (m-30) REVERT: I 320 MET cc_start: 0.8280 (mmt) cc_final: 0.7998 (pp-130) REVERT: J 49 GLU cc_start: 0.7934 (pm20) cc_final: 0.7316 (pm20) REVERT: J 50 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7630 (mt-10) REVERT: J 316 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7750 (tt) outliers start: 129 outliers final: 55 residues processed: 329 average time/residue: 1.1442 time to fit residues: 444.1767 Evaluate side-chains 247 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 186 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 316 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 232 optimal weight: 0.0060 chunk 190 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 277 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN A 376 ASN B 359 ASN D 331 ASN ** E 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN F 223 ASN F 455 ASN G 244 GLN H 43 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24636 Z= 0.188 Angle : 0.548 7.905 33431 Z= 0.278 Chirality : 0.043 0.148 3968 Planarity : 0.004 0.120 4248 Dihedral : 5.272 79.929 3398 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 4.64 % Allowed : 17.19 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -0.36 (0.15), residues: 3080 helix: 1.21 (0.16), residues: 1184 sheet: -1.25 (0.24), residues: 415 loop : -1.13 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 37 HIS 0.005 0.001 HIS C 261 PHE 0.017 0.001 PHE D 272 TYR 0.024 0.001 TYR A 128 ARG 0.007 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 216 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7582 (t-100) cc_final: 0.6672 (t60) REVERT: A 130 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7323 (t) REVERT: A 181 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8037 (ttp) REVERT: A 187 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8148 (pt0) REVERT: B 109 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.7827 (p) REVERT: B 130 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8215 (t) REVERT: B 370 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7864 (m) REVERT: B 371 ASN cc_start: 0.8074 (m-40) cc_final: 0.7372 (p0) REVERT: D 58 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7373 (mtp) REVERT: D 64 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: D 213 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.5986 (tm-30) REVERT: D 305 LYS cc_start: 0.8753 (mmpt) cc_final: 0.8481 (mmtp) REVERT: E 171 LYS cc_start: 0.7762 (pmtt) cc_final: 0.7528 (ptmm) REVERT: E 210 LEU cc_start: 0.8019 (tp) cc_final: 0.7551 (tp) REVERT: E 214 TYR cc_start: 0.7853 (m-10) cc_final: 0.7555 (m-10) REVERT: E 235 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7894 (mm-40) REVERT: E 467 ARG cc_start: 0.7825 (mpt180) cc_final: 0.7298 (mmm160) REVERT: F 207 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7558 (mpt) REVERT: F 235 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: H 49 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7116 (mt) REVERT: H 53 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7879 (mp) REVERT: H 139 GLU cc_start: 0.7911 (tt0) cc_final: 0.7605 (tm-30) REVERT: I 320 MET cc_start: 0.8303 (mmt) cc_final: 0.8021 (pp-130) REVERT: I 321 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8312 (mm-30) REVERT: J 44 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: J 49 GLU cc_start: 0.7960 (pm20) cc_final: 0.7288 (pm20) REVERT: J 50 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7627 (mt-10) REVERT: J 111 ASP cc_start: 0.7206 (p0) cc_final: 0.6995 (p0) outliers start: 122 outliers final: 49 residues processed: 320 average time/residue: 1.1035 time to fit residues: 417.2729 Evaluate side-chains 253 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 190 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 80 optimal weight: 0.0370 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 376 ASN A 384 HIS B 255 GLN B 359 ASN ** E 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN F 455 ASN H 43 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24636 Z= 0.324 Angle : 0.610 8.755 33431 Z= 0.309 Chirality : 0.045 0.200 3968 Planarity : 0.005 0.107 4248 Dihedral : 5.247 76.373 3396 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 5.06 % Allowed : 17.57 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -0.23 (0.15), residues: 3080 helix: 1.21 (0.16), residues: 1190 sheet: -1.20 (0.24), residues: 408 loop : -0.95 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.005 0.001 HIS J 196 PHE 0.025 0.002 PHE G 100 TYR 0.023 0.002 TYR I 92 ARG 0.008 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 197 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7621 (t-100) cc_final: 0.6748 (t60) REVERT: A 128 TYR cc_start: 0.6761 (m-80) cc_final: 0.6487 (m-80) REVERT: A 130 SER cc_start: 0.7826 (OUTLIER) cc_final: 0.7520 (t) REVERT: A 181 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8211 (ttp) REVERT: A 187 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8145 (pt0) REVERT: B 109 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.7932 (p) REVERT: B 130 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8297 (t) REVERT: B 152 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8159 (m-10) REVERT: B 418 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7034 (tp30) REVERT: C 68 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7200 (mpp) REVERT: D 58 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7502 (mtp) REVERT: D 213 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6127 (tm-30) REVERT: D 305 LYS cc_start: 0.8703 (mmpt) cc_final: 0.8422 (mmtp) REVERT: E 171 LYS cc_start: 0.7797 (pmtt) cc_final: 0.7492 (ptmm) REVERT: E 210 LEU cc_start: 0.8061 (tp) cc_final: 0.7759 (tp) REVERT: E 214 TYR cc_start: 0.7968 (m-10) cc_final: 0.7696 (m-10) REVERT: E 235 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8004 (mm-40) REVERT: E 467 ARG cc_start: 0.7844 (mpt180) cc_final: 0.7371 (mmm160) REVERT: F 207 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7621 (mpt) REVERT: F 230 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7395 (mp) REVERT: F 235 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: G 164 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7555 (tpt) REVERT: H 53 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7863 (mp) REVERT: H 139 GLU cc_start: 0.7954 (tt0) cc_final: 0.7672 (tm-30) REVERT: I 100 ASP cc_start: 0.8313 (m-30) cc_final: 0.7907 (m-30) REVERT: I 320 MET cc_start: 0.8302 (mmt) cc_final: 0.7974 (pp-130) REVERT: J 50 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7882 (mp0) REVERT: J 179 GLU cc_start: 0.7549 (pm20) cc_final: 0.7239 (pp20) REVERT: J 306 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6865 (mmtm) outliers start: 133 outliers final: 64 residues processed: 312 average time/residue: 1.1168 time to fit residues: 411.7679 Evaluate side-chains 262 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 182 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 306 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 254 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 359 ASN A 376 ASN B 359 ASN D 331 ASN E 238 GLN E 254 ASN ** E 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E 479 HIS ** F 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 479 HIS H 43 GLN H 214 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 24636 Z= 0.434 Angle : 0.664 9.013 33431 Z= 0.336 Chirality : 0.048 0.174 3968 Planarity : 0.005 0.100 4248 Dihedral : 5.348 73.669 3387 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.77 % Rotamer: Outliers : 5.93 % Allowed : 17.49 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -0.32 (0.15), residues: 3080 helix: 1.04 (0.15), residues: 1192 sheet: -1.20 (0.24), residues: 407 loop : -0.91 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.006 0.001 HIS D 160 PHE 0.027 0.002 PHE G 100 TYR 0.025 0.002 TYR I 92 ARG 0.009 0.001 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 184 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7704 (t-100) cc_final: 0.6911 (t60) REVERT: A 130 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7510 (t) REVERT: A 181 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8278 (ttp) REVERT: A 187 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: B 109 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7928 (p) REVERT: B 130 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8307 (t) REVERT: B 152 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8124 (m-10) REVERT: B 418 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7151 (tp30) REVERT: C 203 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7917 (ttm) REVERT: D 58 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7513 (mtp) REVERT: D 64 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: D 213 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6125 (tm-30) REVERT: E 171 LYS cc_start: 0.7843 (pmtt) cc_final: 0.7484 (ptmm) REVERT: E 235 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8041 (mm-40) REVERT: E 292 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7672 (mtp85) REVERT: E 467 ARG cc_start: 0.7893 (mpt180) cc_final: 0.7410 (mmm160) REVERT: F 235 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: F 415 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7002 (tpp) REVERT: G 164 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7348 (tpt) REVERT: H 53 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7851 (mp) REVERT: H 139 GLU cc_start: 0.7946 (tt0) cc_final: 0.7699 (tm-30) REVERT: I 100 ASP cc_start: 0.8396 (m-30) cc_final: 0.8182 (m-30) REVERT: I 320 MET cc_start: 0.8343 (mmt) cc_final: 0.7974 (pp-130) REVERT: J 35 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5810 (tm) REVERT: J 44 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: J 50 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7922 (mp0) REVERT: J 179 GLU cc_start: 0.7688 (pm20) cc_final: 0.7319 (pp20) REVERT: J 306 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6941 (mmtm) REVERT: J 326 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7320 (p) outliers start: 156 outliers final: 85 residues processed: 320 average time/residue: 1.1299 time to fit residues: 425.5866 Evaluate side-chains 279 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 174 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 306 LYS Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 137 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 0.3980 chunk 156 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN D 162 ASN D 331 ASN E 281 ASN E 431 ASN F 254 ASN F 430 HIS ** F 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN H 43 GLN I 323 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24636 Z= 0.213 Angle : 0.571 8.617 33431 Z= 0.289 Chirality : 0.044 0.194 3968 Planarity : 0.004 0.092 4248 Dihedral : 4.979 68.881 3387 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 4.64 % Allowed : 18.94 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: 0.04 (0.16), residues: 3080 helix: 1.30 (0.16), residues: 1202 sheet: -1.01 (0.25), residues: 407 loop : -0.69 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 37 HIS 0.004 0.001 HIS C 261 PHE 0.025 0.001 PHE G 100 TYR 0.027 0.001 TYR I 92 ARG 0.009 0.000 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 189 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7680 (t-100) cc_final: 0.6890 (t60) REVERT: A 130 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7382 (t) REVERT: A 175 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: A 187 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: B 130 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8257 (t) REVERT: B 152 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8141 (m-10) REVERT: B 209 THR cc_start: 0.7134 (OUTLIER) cc_final: 0.6908 (p) REVERT: C 68 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7232 (mtp) REVERT: D 58 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7549 (mtp) REVERT: D 64 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: D 213 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.5852 (tm-30) REVERT: E 171 LYS cc_start: 0.7765 (pmtt) cc_final: 0.7481 (ptmm) REVERT: E 179 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7306 (mp) REVERT: E 192 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8930 (tt) REVERT: E 210 LEU cc_start: 0.8096 (tp) cc_final: 0.7885 (tp) REVERT: E 235 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8016 (mm-40) REVERT: E 467 ARG cc_start: 0.7895 (mpt180) cc_final: 0.7410 (mmm160) REVERT: F 235 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6781 (tm-30) REVERT: G 70 GLU cc_start: 0.8233 (mp0) cc_final: 0.7994 (mp0) REVERT: G 164 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7536 (tpt) REVERT: H 53 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7847 (mp) REVERT: H 139 GLU cc_start: 0.7886 (tt0) cc_final: 0.7654 (tm-30) REVERT: I 100 ASP cc_start: 0.8314 (m-30) cc_final: 0.8073 (m-30) REVERT: I 320 MET cc_start: 0.8276 (mmt) cc_final: 0.7951 (pp-130) REVERT: J 35 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5841 (tm) REVERT: J 50 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7909 (mp0) REVERT: J 111 ASP cc_start: 0.7452 (p0) cc_final: 0.7168 (p0) REVERT: J 179 GLU cc_start: 0.7666 (pm20) cc_final: 0.7322 (pp20) REVERT: J 326 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7596 (p) REVERT: J 331 SER cc_start: 0.8853 (p) cc_final: 0.8324 (t) outliers start: 122 outliers final: 61 residues processed: 297 average time/residue: 1.1674 time to fit residues: 406.5793 Evaluate side-chains 251 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 173 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 169 optimal weight: 0.0980 chunk 217 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 250 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 296 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 359 ASN B 302 ASN B 359 ASN D 331 ASN E 431 ASN G 244 GLN H 43 GLN H 128 HIS J 218 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24636 Z= 0.172 Angle : 0.549 9.645 33431 Z= 0.276 Chirality : 0.043 0.196 3968 Planarity : 0.004 0.076 4248 Dihedral : 4.641 65.178 3384 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 4.37 % Allowed : 19.58 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: 0.32 (0.16), residues: 3080 helix: 1.52 (0.16), residues: 1203 sheet: -0.82 (0.25), residues: 413 loop : -0.53 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 37 HIS 0.004 0.001 HIS C 261 PHE 0.024 0.001 PHE G 100 TYR 0.028 0.001 TYR I 92 ARG 0.012 0.000 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 186 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7679 (t-100) cc_final: 0.6919 (t60) REVERT: A 128 TYR cc_start: 0.6426 (m-80) cc_final: 0.6170 (m-80) REVERT: A 175 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: B 152 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8128 (m-10) REVERT: B 231 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: C 68 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7127 (mpp) REVERT: C 166 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7484 (ttp) REVERT: C 340 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7107 (mtm) REVERT: D 64 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: D 213 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.5736 (tm-30) REVERT: E 171 LYS cc_start: 0.7724 (pmtt) cc_final: 0.7499 (ptmm) REVERT: E 192 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8907 (tt) REVERT: E 235 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7991 (mm-40) REVERT: E 467 ARG cc_start: 0.7877 (mpt180) cc_final: 0.7356 (mmm160) REVERT: F 230 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7325 (mp) REVERT: G 164 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7627 (tpt) REVERT: H 53 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7845 (mp) REVERT: H 139 GLU cc_start: 0.7861 (tt0) cc_final: 0.7617 (tm-30) REVERT: I 100 ASP cc_start: 0.8255 (m-30) cc_final: 0.7888 (m-30) REVERT: I 320 MET cc_start: 0.8288 (mmt) cc_final: 0.8006 (pp-130) REVERT: J 35 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5832 (tm) REVERT: J 50 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7900 (mp0) REVERT: J 111 ASP cc_start: 0.7434 (p0) cc_final: 0.7105 (p0) REVERT: J 179 GLU cc_start: 0.7655 (pm20) cc_final: 0.7422 (pp20) REVERT: J 326 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7620 (p) REVERT: J 331 SER cc_start: 0.8909 (p) cc_final: 0.8429 (t) outliers start: 115 outliers final: 54 residues processed: 286 average time/residue: 1.1799 time to fit residues: 396.8020 Evaluate side-chains 242 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 174 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 359 ASN D 331 ASN E 431 ASN ** F 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN H 43 GLN I 323 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24636 Z= 0.253 Angle : 0.586 9.459 33431 Z= 0.295 Chirality : 0.044 0.181 3968 Planarity : 0.004 0.075 4248 Dihedral : 4.653 66.218 3383 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.03 % Rotamer: Outliers : 4.49 % Allowed : 19.62 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: 0.35 (0.16), residues: 3080 helix: 1.51 (0.16), residues: 1203 sheet: -0.77 (0.26), residues: 410 loop : -0.50 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 111 HIS 0.004 0.001 HIS C 160 PHE 0.023 0.001 PHE G 100 TYR 0.027 0.001 TYR I 92 ARG 0.010 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 178 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7753 (t-100) cc_final: 0.6918 (t60) REVERT: A 130 SER cc_start: 0.7810 (OUTLIER) cc_final: 0.7479 (t) REVERT: A 175 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: A 228 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6771 (tt) REVERT: B 152 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8158 (m-10) REVERT: C 203 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7415 (tpp) REVERT: C 340 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7248 (mtm) REVERT: D 64 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: D 213 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.5790 (tm-30) REVERT: D 305 LYS cc_start: 0.8530 (mmpt) cc_final: 0.8253 (mttm) REVERT: E 171 LYS cc_start: 0.7713 (pmtt) cc_final: 0.7460 (ptmm) REVERT: E 192 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8910 (tt) REVERT: E 235 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8030 (mm-40) REVERT: E 467 ARG cc_start: 0.7888 (mpt180) cc_final: 0.7412 (mmm160) REVERT: H 53 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7870 (mp) REVERT: H 139 GLU cc_start: 0.7871 (tt0) cc_final: 0.7621 (tm-30) REVERT: I 100 ASP cc_start: 0.8288 (m-30) cc_final: 0.7895 (m-30) REVERT: J 35 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5852 (tm) REVERT: J 50 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7914 (mp0) REVERT: J 111 ASP cc_start: 0.7411 (p0) cc_final: 0.7066 (p0) REVERT: J 179 GLU cc_start: 0.7700 (pm20) cc_final: 0.7408 (pp20) REVERT: J 326 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7598 (p) REVERT: J 331 SER cc_start: 0.8962 (p) cc_final: 0.8493 (t) outliers start: 118 outliers final: 76 residues processed: 285 average time/residue: 1.1307 time to fit residues: 384.9919 Evaluate side-chains 258 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 170 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 495 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 261 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 359 ASN B 359 ASN D 331 ASN E 431 ASN ** F 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN H 43 GLN I 323 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24636 Z= 0.315 Angle : 0.617 10.210 33431 Z= 0.310 Chirality : 0.046 0.179 3968 Planarity : 0.004 0.076 4248 Dihedral : 4.791 64.567 3383 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 4.41 % Allowed : 19.58 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: 0.24 (0.16), residues: 3080 helix: 1.42 (0.15), residues: 1202 sheet: -0.78 (0.26), residues: 406 loop : -0.57 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.005 0.001 HIS C 160 PHE 0.024 0.002 PHE G 100 TYR 0.035 0.002 TYR F 173 ARG 0.010 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 174 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7767 (t-100) cc_final: 0.6991 (t60) REVERT: A 130 SER cc_start: 0.7844 (OUTLIER) cc_final: 0.7490 (t) REVERT: A 175 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: A 228 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6925 (tt) REVERT: B 152 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8183 (m-10) REVERT: C 340 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7226 (mtm) REVERT: D 64 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: D 213 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.5821 (tm-30) REVERT: D 305 LYS cc_start: 0.8556 (mmpt) cc_final: 0.8278 (mttm) REVERT: D 327 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.6391 (m-40) REVERT: E 192 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8828 (tt) REVERT: E 196 MET cc_start: 0.7693 (mtm) cc_final: 0.7389 (ptp) REVERT: E 235 GLN cc_start: 0.8464 (mm-40) cc_final: 0.7994 (mm-40) REVERT: E 292 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7768 (mtm-85) REVERT: E 467 ARG cc_start: 0.7896 (mpt180) cc_final: 0.7458 (mmm160) REVERT: H 53 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7851 (mp) REVERT: H 139 GLU cc_start: 0.7901 (tt0) cc_final: 0.7648 (tm-30) REVERT: I 100 ASP cc_start: 0.8316 (m-30) cc_final: 0.8083 (m-30) REVERT: J 50 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7912 (mp0) REVERT: J 111 ASP cc_start: 0.7437 (p0) cc_final: 0.7207 (p0) REVERT: J 179 GLU cc_start: 0.7725 (pm20) cc_final: 0.7413 (pp20) REVERT: J 326 VAL cc_start: 0.7929 (OUTLIER) cc_final: 0.7669 (p) REVERT: J 331 SER cc_start: 0.8990 (p) cc_final: 0.8517 (t) outliers start: 116 outliers final: 75 residues processed: 277 average time/residue: 1.2071 time to fit residues: 391.4204 Evaluate side-chains 255 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 168 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 5.9990 chunk 292 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 359 ASN B 359 ASN E 431 ASN ** F 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24636 Z= 0.197 Angle : 0.583 10.933 33431 Z= 0.291 Chirality : 0.044 0.190 3968 Planarity : 0.004 0.074 4248 Dihedral : 4.593 61.636 3382 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 3.19 % Allowed : 20.91 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: 0.41 (0.16), residues: 3080 helix: 1.54 (0.16), residues: 1203 sheet: -0.68 (0.26), residues: 410 loop : -0.46 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 37 HIS 0.004 0.001 HIS C 261 PHE 0.023 0.001 PHE G 100 TYR 0.025 0.001 TYR I 92 ARG 0.011 0.000 ARG H 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 180 time to evaluate : 2.572 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: A 97 TRP cc_start: 0.7769 (t-100) cc_final: 0.6953 (t60) REVERT: A 130 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7459 (t) REVERT: A 175 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: B 152 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8123 (m-10) REVERT: C 340 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7140 (mtm) REVERT: D 64 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: D 213 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.5770 (tm-30) REVERT: D 305 LYS cc_start: 0.8554 (mmpt) cc_final: 0.8284 (mttm) REVERT: D 327 ASN cc_start: 0.6528 (OUTLIER) cc_final: 0.6282 (m-40) REVERT: E 171 LYS cc_start: 0.7862 (pmtt) cc_final: 0.7634 (ptmm) REVERT: E 192 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8827 (tt) REVERT: E 196 MET cc_start: 0.7678 (mtm) cc_final: 0.7353 (ptp) REVERT: E 235 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8006 (mm-40) REVERT: E 467 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7456 (mmm160) REVERT: G 14 MET cc_start: 0.7303 (tpp) cc_final: 0.6997 (ttm) REVERT: H 53 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7872 (mp) REVERT: H 139 GLU cc_start: 0.7851 (tt0) cc_final: 0.7611 (tm-30) REVERT: I 100 ASP cc_start: 0.8267 (m-30) cc_final: 0.7902 (m-30) REVERT: I 169 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5594 (t80) REVERT: J 50 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7925 (mp0) REVERT: J 111 ASP cc_start: 0.7372 (p0) cc_final: 0.7154 (p0) REVERT: J 179 GLU cc_start: 0.7685 (pm20) cc_final: 0.7376 (pp20) REVERT: J 326 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7623 (p) REVERT: J 331 SER cc_start: 0.8984 (p) cc_final: 0.8525 (t) outliers start: 84 outliers final: 62 residues processed: 259 average time/residue: 1.3376 time to fit residues: 411.4188 Evaluate side-chains 245 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 172 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 495 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.487 > 50: distance: 97 - 100: 8.279 distance: 100 - 101: 24.999 distance: 101 - 102: 21.100 distance: 102 - 103: 18.319 distance: 102 - 104: 28.674 distance: 104 - 105: 12.549 distance: 105 - 106: 21.347 distance: 105 - 108: 30.015 distance: 106 - 107: 26.847 distance: 106 - 109: 17.214 distance: 109 - 110: 15.748 distance: 110 - 111: 11.663 distance: 110 - 113: 12.392 distance: 111 - 112: 9.046 distance: 111 - 118: 7.502 distance: 113 - 114: 9.377 distance: 114 - 115: 19.568 distance: 115 - 116: 12.043 distance: 115 - 117: 13.947 distance: 118 - 119: 14.627 distance: 119 - 120: 10.363 distance: 120 - 121: 11.178 distance: 120 - 126: 7.575 distance: 122 - 123: 5.208 distance: 122 - 124: 10.683 distance: 123 - 125: 12.434 distance: 126 - 127: 12.493 distance: 127 - 128: 12.727 distance: 127 - 130: 19.985 distance: 128 - 129: 11.999 distance: 128 - 136: 13.760 distance: 130 - 131: 19.699 distance: 131 - 132: 11.291 distance: 131 - 133: 9.244 distance: 132 - 134: 14.445 distance: 133 - 135: 7.241 distance: 136 - 137: 8.151 distance: 137 - 138: 19.232 distance: 137 - 140: 12.455 distance: 138 - 139: 7.642 distance: 138 - 145: 29.391 distance: 140 - 141: 17.311 distance: 141 - 142: 20.903 distance: 142 - 143: 12.396 distance: 142 - 144: 25.650 distance: 145 - 146: 6.648 distance: 146 - 147: 13.483 distance: 146 - 149: 24.066 distance: 147 - 148: 6.048 distance: 147 - 151: 12.433 distance: 149 - 150: 20.773 distance: 151 - 152: 10.457 distance: 152 - 153: 5.253 distance: 152 - 155: 4.467 distance: 153 - 154: 9.280 distance: 153 - 159: 12.781 distance: 155 - 156: 7.232 distance: 156 - 157: 17.580 distance: 156 - 158: 15.234 distance: 159 - 160: 18.054 distance: 160 - 161: 14.212 distance: 160 - 163: 16.165 distance: 161 - 162: 22.287 distance: 161 - 167: 10.455 distance: 163 - 164: 22.179 distance: 164 - 165: 27.314 distance: 164 - 166: 30.320 distance: 167 - 168: 17.185 distance: 168 - 169: 12.458 distance: 168 - 171: 11.370 distance: 169 - 170: 18.798 distance: 169 - 173: 7.813 distance: 171 - 172: 18.582