Starting phenix.real_space_refine on Sun Apr 14 02:23:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/04_2024/6lrs_0960.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/04_2024/6lrs_0960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/04_2024/6lrs_0960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/04_2024/6lrs_0960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/04_2024/6lrs_0960.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/04_2024/6lrs_0960.pdb" } resolution = 3.37 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= 0.000 sd= 0.009 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 112 5.16 5 C 19228 2.51 5 N 5272 2.21 5 O 5544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T ARG 8": "NH1" <-> "NH2" Residue "T ARG 67": "NH1" <-> "NH2" Residue "T ARG 77": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 214": "NH1" <-> "NH2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G ARG 313": "NH1" <-> "NH2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H ARG 135": "NH1" <-> "NH2" Residue "H ARG 160": "NH1" <-> "NH2" Residue "H TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 188": "NH1" <-> "NH2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H ARG 286": "NH1" <-> "NH2" Residue "H ARG 296": "NH1" <-> "NH2" Residue "H ARG 313": "NH1" <-> "NH2" Residue "H PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 361": "NH1" <-> "NH2" Residue "S ARG 8": "NH1" <-> "NH2" Residue "S ARG 67": "NH1" <-> "NH2" Residue "S ARG 77": "NH1" <-> "NH2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 188": "NH1" <-> "NH2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F ARG 160": "NH1" <-> "NH2" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 188": "NH1" <-> "NH2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F ARG 216": "NH1" <-> "NH2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F ARG 296": "NH1" <-> "NH2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 361": "NH1" <-> "NH2" Residue "R ARG 8": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 77": "NH1" <-> "NH2" Residue "R ARG 86": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D ARG 296": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 361": "NH1" <-> "NH2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 67": "NH1" <-> "NH2" Residue "Q ARG 77": "NH1" <-> "NH2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 361": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30156 Number of models: 1 Model: "" Number of chains: 12 Chain: "T" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 877 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "G" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 392} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 877 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "E" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 392} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 877 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "C" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 392} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 877 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 392} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 15.85, per 1000 atoms: 0.53 Number of scatterers: 30156 At special positions: 0 Unit cell: (140.4, 140.4, 113.36, 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 112 16.00 O 5544 8.00 N 5272 7.00 C 19228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS G 248 " - pdb=" SG CYS H 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 173 " - pdb=" SG CYS H 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 248 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 173 " - pdb=" SG CYS F 193 " distance=2.05 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 173 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 193 " distance=2.05 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: 11.19 Conformation dependent library (CDL) restraints added in 5.6 seconds 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7000 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 38 sheets defined 37.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'T' and resid 20 through 33 removed outlier: 3.593A pdb=" N VAL T 28 " --> pdb=" O ILE T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 68 Processing helix chain 'T' and resid 69 through 74 Processing helix chain 'G' and resid 50 through 62 removed outlier: 3.682A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G 62 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 75 removed outlier: 3.785A pdb=" N LEU G 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 109 No H-bonds generated for 'chain 'G' and resid 107 through 109' Processing helix chain 'G' and resid 116 through 121 Processing helix chain 'G' and resid 142 through 147 removed outlier: 3.577A pdb=" N LYS G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 160 Processing helix chain 'G' and resid 182 through 195 removed outlier: 3.538A pdb=" N TYR G 191 " --> pdb=" O GLY G 187 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 230 removed outlier: 3.563A pdb=" N LEU G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 261 removed outlier: 3.760A pdb=" N GLU G 256 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 287 Processing helix chain 'G' and resid 311 through 316 removed outlier: 3.765A pdb=" N LEU G 315 " --> pdb=" O HIS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 323 Processing helix chain 'G' and resid 336 through 344 removed outlier: 4.019A pdb=" N GLY G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE G 342 " --> pdb=" O GLY G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 352 removed outlier: 3.739A pdb=" N LEU G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 435 removed outlier: 3.582A pdb=" N ALA G 424 " --> pdb=" O ALA G 420 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU G 425 " --> pdb=" O ASN G 421 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS G 428 " --> pdb=" O ALA G 424 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY G 435 " --> pdb=" O ALA G 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 64 removed outlier: 3.604A pdb=" N SER H 62 " --> pdb=" O VAL H 58 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.619A pdb=" N LEU H 108 " --> pdb=" O PRO H 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE H 109 " --> pdb=" O LEU H 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 105 through 109' Processing helix chain 'H' and resid 116 through 121 removed outlier: 3.654A pdb=" N SER H 120 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 147 Processing helix chain 'H' and resid 157 through 164 Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.516A pdb=" N ALA H 189 " --> pdb=" O ASN H 185 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS H 193 " --> pdb=" O ALA H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 233 removed outlier: 3.555A pdb=" N LEU H 220 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA H 231 " --> pdb=" O THR H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.685A pdb=" N ALA H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 288 Processing helix chain 'H' and resid 298 through 302 removed outlier: 3.651A pdb=" N VAL H 301 " --> pdb=" O MET H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 321 removed outlier: 3.692A pdb=" N LEU H 315 " --> pdb=" O HIS H 311 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG H 320 " --> pdb=" O ALA H 316 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 352 removed outlier: 3.769A pdb=" N ILE H 342 " --> pdb=" O GLY H 338 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE H 346 " --> pdb=" O ILE H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 386 No H-bonds generated for 'chain 'H' and resid 384 through 386' Processing helix chain 'H' and resid 387 through 394 removed outlier: 3.707A pdb=" N LEU H 391 " --> pdb=" O HIS H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 420 Processing helix chain 'H' and resid 422 through 427 Processing helix chain 'H' and resid 427 through 433 Processing helix chain 'H' and resid 442 through 450 removed outlier: 4.002A pdb=" N ILE H 446 " --> pdb=" O GLY H 442 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 447 " --> pdb=" O ASN H 443 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU H 448 " --> pdb=" O ASP H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 460 removed outlier: 3.992A pdb=" N ALA H 459 " --> pdb=" O GLU H 455 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 33 removed outlier: 3.593A pdb=" N VAL S 28 " --> pdb=" O ILE S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 68 Processing helix chain 'S' and resid 69 through 74 Processing helix chain 'E' and resid 50 through 64 removed outlier: 3.685A pdb=" N ALA E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.809A pdb=" N LEU E 75 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 142 through 147 removed outlier: 3.575A pdb=" N LYS E 147 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.538A pdb=" N TYR E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU E 192 " --> pdb=" O ARG E 188 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 230 removed outlier: 3.562A pdb=" N LEU E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 261 removed outlier: 3.761A pdb=" N GLU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 311 through 316 removed outlier: 3.764A pdb=" N LEU E 315 " --> pdb=" O HIS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 323 Processing helix chain 'E' and resid 336 through 344 removed outlier: 4.019A pdb=" N GLY E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 352 removed outlier: 3.725A pdb=" N LEU E 350 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 3.553A pdb=" N ALA E 424 " --> pdb=" O ALA E 420 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU E 425 " --> pdb=" O ASN E 421 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.650A pdb=" N SER F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.605A pdb=" N LEU F 108 " --> pdb=" O PRO F 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 109 " --> pdb=" O LEU F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 109' Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.661A pdb=" N SER F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 157 through 164 Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.880A pdb=" N CYS F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 233 removed outlier: 3.549A pdb=" N LEU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 261 removed outlier: 3.688A pdb=" N ALA F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 288 Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.650A pdb=" N VAL F 301 " --> pdb=" O MET F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.692A pdb=" N LEU F 315 " --> pdb=" O HIS F 311 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 removed outlier: 3.770A pdb=" N ILE F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE F 346 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 387 through 394 removed outlier: 3.693A pdb=" N LEU F 391 " --> pdb=" O HIS F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 422 through 427 Processing helix chain 'F' and resid 427 through 433 Processing helix chain 'F' and resid 442 through 450 removed outlier: 3.989A pdb=" N ILE F 446 " --> pdb=" O GLY F 442 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F 447 " --> pdb=" O ASN F 443 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 460 removed outlier: 3.994A pdb=" N ALA F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 33 removed outlier: 3.593A pdb=" N VAL R 28 " --> pdb=" O ILE R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 68 Processing helix chain 'R' and resid 69 through 74 Processing helix chain 'C' and resid 50 through 64 removed outlier: 3.621A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.786A pdb=" N LEU C 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.573A pdb=" N LYS C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.539A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 192 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 230 removed outlier: 3.568A pdb=" N LEU C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.760A pdb=" N GLU C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.764A pdb=" N LEU C 315 " --> pdb=" O HIS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 323 Processing helix chain 'C' and resid 336 through 344 removed outlier: 4.028A pdb=" N GLY C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.722A pdb=" N LEU C 350 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 414 through 435 removed outlier: 3.552A pdb=" N ALA C 424 " --> pdb=" O ALA C 420 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU C 425 " --> pdb=" O ASN C 421 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.601A pdb=" N SER D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.622A pdb=" N LEU D 108 " --> pdb=" O PRO D 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 109' Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.651A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 157 through 164 Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.882A pdb=" N CYS D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 233 removed outlier: 3.556A pdb=" N LEU D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.693A pdb=" N ALA D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 288 Processing helix chain 'D' and resid 298 through 302 removed outlier: 3.660A pdb=" N VAL D 301 " --> pdb=" O MET D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.690A pdb=" N LEU D 315 " --> pdb=" O HIS D 311 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 removed outlier: 3.772A pdb=" N ILE D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE D 346 " --> pdb=" O ILE D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 387 through 394 removed outlier: 3.708A pdb=" N LEU D 391 " --> pdb=" O HIS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 427 through 433 Processing helix chain 'D' and resid 442 through 450 removed outlier: 4.003A pdb=" N ILE D 446 " --> pdb=" O GLY D 442 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 447 " --> pdb=" O ASN D 443 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 460 removed outlier: 3.995A pdb=" N ALA D 459 " --> pdb=" O GLU D 455 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 33 removed outlier: 3.592A pdb=" N VAL Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 68 Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'A' and resid 50 through 62 removed outlier: 3.682A pdb=" N ALA A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.809A pdb=" N LEU A 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.575A pdb=" N LYS A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.525A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.569A pdb=" N LEU A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.759A pdb=" N GLU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.765A pdb=" N LEU A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 323 Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.028A pdb=" N GLY A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.714A pdb=" N LEU A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 414 through 435 removed outlier: 3.551A pdb=" N ALA A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 64 removed outlier: 3.641A pdb=" N SER B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.624A pdb=" N LEU B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 109' Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.657A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.873A pdb=" N CYS B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.538A pdb=" N LEU B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.687A pdb=" N ALA B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 288 Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.660A pdb=" N VAL B 301 " --> pdb=" O MET B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.691A pdb=" N LEU B 315 " --> pdb=" O HIS B 311 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 352 removed outlier: 3.771A pdb=" N ILE B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 394 removed outlier: 3.691A pdb=" N LEU B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.987A pdb=" N ILE B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 460 removed outlier: 3.997A pdb=" N ALA B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'T' and resid 54 through 55 removed outlier: 3.743A pdb=" N PHE T 101 " --> pdb=" O VAL T 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'G' and resid 84 through 85 removed outlier: 6.536A pdb=" N LEU G 38 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE G 139 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA G 40 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N GLY G 309 " --> pdb=" O ARG G 132 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU G 134 " --> pdb=" O GLY G 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 170 through 173 removed outlier: 7.204A pdb=" N LEU G 170 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE G 403 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY G 172 " --> pdb=" O PHE G 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 241 through 242 removed outlier: 5.318A pdb=" N LEU G 241 " --> pdb=" O MET G 267 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP G 269 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE G 266 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS G 295 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N HIS G 268 " --> pdb=" O HIS G 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AA7, first strand: chain 'G' and resid 354 through 355 Processing sheet with id=AA8, first strand: chain 'H' and resid 84 through 90 removed outlier: 6.702A pdb=" N TYR H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE H 88 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE H 99 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU H 38 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE H 139 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA H 40 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY H 309 " --> pdb=" O ARG H 132 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU H 134 " --> pdb=" O GLY H 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 170 through 174 removed outlier: 6.355A pdb=" N LEU H 171 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS H 202 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS H 173 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR H 201 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASN H 242 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N HIS H 239 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N MET H 267 " --> pdb=" O HIS H 239 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU H 241 " --> pdb=" O MET H 267 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP H 269 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE H 266 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS H 295 " --> pdb=" O ILE H 266 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N HIS H 268 " --> pdb=" O HIS H 295 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS H 328 " --> pdb=" O LEU H 292 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ILE H 294 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE H 327 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER H 380 " --> pdb=" O ILE H 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 54 through 55 removed outlier: 3.742A pdb=" N PHE S 101 " --> pdb=" O VAL S 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB3, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.538A pdb=" N LEU E 38 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE E 139 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA E 40 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N GLY E 309 " --> pdb=" O ARG E 132 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU E 134 " --> pdb=" O GLY E 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 170 through 173 removed outlier: 7.202A pdb=" N LEU E 170 " --> pdb=" O LEU E 401 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE E 403 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY E 172 " --> pdb=" O PHE E 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 241 through 242 removed outlier: 5.333A pdb=" N LEU E 241 " --> pdb=" O MET E 267 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP E 269 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE E 266 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N HIS E 295 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS E 268 " --> pdb=" O HIS E 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AB7, first strand: chain 'E' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 90 removed outlier: 6.702A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE F 88 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE F 99 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 90 removed outlier: 6.702A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE F 88 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE F 99 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU F 38 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE F 139 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA F 40 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.357A pdb=" N LEU F 171 " --> pdb=" O PHE F 200 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS F 202 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS F 173 " --> pdb=" O LYS F 202 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR F 201 " --> pdb=" O TYR F 240 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ASN F 242 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N HIS F 239 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N MET F 267 " --> pdb=" O HIS F 239 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU F 241 " --> pdb=" O MET F 267 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASP F 269 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE F 266 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS F 295 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N HIS F 268 " --> pdb=" O HIS F 295 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N HIS F 328 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ILE F 294 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE F 327 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER F 380 " --> pdb=" O ILE F 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 54 through 55 removed outlier: 3.743A pdb=" N PHE R 101 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.534A pdb=" N LEU C 38 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE C 139 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA C 40 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY C 309 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 134 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 170 through 173 removed outlier: 7.205A pdb=" N LEU C 170 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE C 403 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY C 172 " --> pdb=" O PHE C 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 241 through 242 removed outlier: 5.322A pdb=" N LEU C 241 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP C 269 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE C 266 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N HIS C 295 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N HIS C 268 " --> pdb=" O HIS C 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC8, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC9, first strand: chain 'D' and resid 84 through 90 removed outlier: 6.701A pdb=" N TYR D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE D 88 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE D 99 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU D 38 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE D 139 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA D 40 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N GLY D 309 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU D 134 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.350A pdb=" N LEU D 171 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS D 202 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS D 173 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR D 201 " --> pdb=" O TYR D 240 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASN D 242 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N HIS D 239 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N MET D 267 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU D 241 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASP D 269 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE D 266 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N HIS D 295 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS D 268 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N HIS D 328 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE D 294 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE D 327 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER D 380 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 54 through 55 removed outlier: 3.742A pdb=" N PHE Q 101 " --> pdb=" O VAL Q 87 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AD4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.537A pdb=" N LEU A 38 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A 139 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 40 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N GLY A 309 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 134 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 170 through 173 removed outlier: 7.222A pdb=" N LEU A 170 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE A 403 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLY A 172 " --> pdb=" O PHE A 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'A' and resid 241 through 242 removed outlier: 5.319A pdb=" N LEU A 241 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP A 269 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE A 266 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS A 295 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS A 268 " --> pdb=" O HIS A 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AD8, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AD9, first strand: chain 'B' and resid 84 through 90 removed outlier: 6.700A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 88 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 99 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 84 through 90 removed outlier: 6.700A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 88 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 99 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 38 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE B 139 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 40 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.358A pdb=" N LEU B 171 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS B 202 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS B 173 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR B 201 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN B 242 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N HIS B 239 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N MET B 267 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU B 241 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASP B 269 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE B 266 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS B 295 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS B 268 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS B 328 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE B 294 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B 327 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER B 380 " --> pdb=" O ILE B 327 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.52 Time building geometry restraints manager: 12.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9960 1.34 - 1.46: 7295 1.46 - 1.58: 13485 1.58 - 1.70: 0 1.70 - 1.83: 164 Bond restraints: 30904 Sorted by residual: bond pdb=" CB THR H 280 " pdb=" CG2 THR H 280 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.28e+00 bond pdb=" CB THR F 280 " pdb=" CG2 THR F 280 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.28e+00 bond pdb=" CB THR D 280 " pdb=" CG2 THR D 280 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.28e+00 bond pdb=" CB THR B 280 " pdb=" CG2 THR B 280 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.21e+00 bond pdb=" C HIS C 410 " pdb=" N PRO C 411 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.82e+00 ... (remaining 30899 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.32: 520 104.32 - 111.84: 13523 111.84 - 119.37: 11950 119.37 - 126.89: 15497 126.89 - 134.42: 510 Bond angle restraints: 42000 Sorted by residual: angle pdb=" C TYR T 36 " pdb=" N ILE T 37 " pdb=" CA ILE T 37 " ideal model delta sigma weight residual 123.25 131.48 -8.23 1.10e+00 8.26e-01 5.60e+01 angle pdb=" C TYR Q 36 " pdb=" N ILE Q 37 " pdb=" CA ILE Q 37 " ideal model delta sigma weight residual 123.25 131.48 -8.23 1.10e+00 8.26e-01 5.59e+01 angle pdb=" C TYR S 36 " pdb=" N ILE S 37 " pdb=" CA ILE S 37 " ideal model delta sigma weight residual 123.25 131.42 -8.17 1.10e+00 8.26e-01 5.52e+01 angle pdb=" C TYR R 36 " pdb=" N ILE R 37 " pdb=" CA ILE R 37 " ideal model delta sigma weight residual 123.25 131.42 -8.17 1.10e+00 8.26e-01 5.51e+01 angle pdb=" N VAL E 158 " pdb=" CA VAL E 158 " pdb=" C VAL E 158 " ideal model delta sigma weight residual 112.96 108.20 4.76 1.00e+00 1.00e+00 2.26e+01 ... (remaining 41995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 17306 15.71 - 31.42: 738 31.42 - 47.13: 160 47.13 - 62.84: 24 62.84 - 78.55: 20 Dihedral angle restraints: 18248 sinusoidal: 7272 harmonic: 10976 Sorted by residual: dihedral pdb=" CA PRO C 177 " pdb=" C PRO C 177 " pdb=" N LYS C 178 " pdb=" CA LYS C 178 " ideal model delta harmonic sigma weight residual -180.00 -128.51 -51.49 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA PRO G 177 " pdb=" C PRO G 177 " pdb=" N LYS G 178 " pdb=" CA LYS G 178 " ideal model delta harmonic sigma weight residual -180.00 -128.56 -51.44 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA PRO E 177 " pdb=" C PRO E 177 " pdb=" N LYS E 178 " pdb=" CA LYS E 178 " ideal model delta harmonic sigma weight residual -180.00 -128.57 -51.43 0 5.00e+00 4.00e-02 1.06e+02 ... (remaining 18245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3038 0.054 - 0.108: 1192 0.108 - 0.162: 308 0.162 - 0.216: 38 0.216 - 0.270: 12 Chirality restraints: 4588 Sorted by residual: chirality pdb=" CG LEU C 134 " pdb=" CB LEU C 134 " pdb=" CD1 LEU C 134 " pdb=" CD2 LEU C 134 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU A 134 " pdb=" CB LEU A 134 " pdb=" CD1 LEU A 134 " pdb=" CD2 LEU A 134 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE C 266 " pdb=" CA ILE C 266 " pdb=" CG1 ILE C 266 " pdb=" CG2 ILE C 266 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4585 not shown) Planarity restraints: 5468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 36 " -0.059 2.00e-02 2.50e+03 3.11e-02 1.93e+01 pdb=" CG TYR R 36 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR R 36 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR R 36 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR R 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR R 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 36 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR R 36 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 36 " -0.059 2.00e-02 2.50e+03 3.10e-02 1.93e+01 pdb=" CG TYR S 36 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR S 36 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR S 36 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR S 36 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR S 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR S 36 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR S 36 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 36 " 0.059 2.00e-02 2.50e+03 3.10e-02 1.92e+01 pdb=" CG TYR T 36 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR T 36 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR T 36 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR T 36 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR T 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR T 36 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR T 36 " 0.027 2.00e-02 2.50e+03 ... (remaining 5465 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7411 2.79 - 3.32: 27813 3.32 - 3.84: 53731 3.84 - 4.37: 67628 4.37 - 4.90: 108305 Nonbonded interactions: 264888 Sorted by model distance: nonbonded pdb=" OD1 ASN G 206 " pdb=" OG SER H 120 " model vdw 2.260 2.440 nonbonded pdb=" OD1 ASN A 206 " pdb=" OG SER B 120 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR A 191 " pdb=" OE1 GLU A 232 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR H 419 " pdb=" OE1 GLU H 455 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASN C 206 " pdb=" OG SER D 120 " model vdw 2.266 2.440 ... (remaining 264883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 23 through 435) selection = chain 'C' selection = (chain 'D' and resid 23 through 435) selection = chain 'E' selection = (chain 'F' and resid 23 through 435) selection = chain 'G' selection = (chain 'H' and resid 23 through 435) } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.940 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: 5.080 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 78.480 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 : 0.006 0.089 30904 Z= 0.414 Angle : 1.035 9.417 42000 Z= 0.583 Chirality : 0.060 0.270 4588 Planarity : 0.007 0.054 5468 Dihedral : 10.049 75.320 11224 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.38 % Allowed : 2.01 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -5.21 (0.10), residues: 3808 helix: -4.49 (0.06), residues: 1376 sheet: -3.47 (0.17), residues: 500 loop : -2.56 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 53 HIS 0.023 0.004 HIS E 295 PHE 0.045 0.005 PHE S 90 TYR 0.059 0.004 TYR R 36 ARG 0.010 0.001 ARG E 286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 905 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 23 GLN cc_start: 0.7713 (mt0) cc_final: 0.7444 (mt0) REVERT: G 97 GLN cc_start: 0.7976 (tt0) cc_final: 0.7755 (tt0) REVERT: G 116 ASN cc_start: 0.8271 (t0) cc_final: 0.7549 (t0) REVERT: G 129 LYS cc_start: 0.7719 (mtpp) cc_final: 0.7228 (mtmm) REVERT: G 156 ILE cc_start: 0.6691 (mt) cc_final: 0.6464 (mt) REVERT: G 214 ARG cc_start: 0.7756 (mmt180) cc_final: 0.7399 (mmt180) REVERT: G 253 LYS cc_start: 0.8001 (mttt) cc_final: 0.7797 (ttmm) REVERT: H 104 TYR cc_start: 0.8636 (m-80) cc_final: 0.8431 (m-80) REVERT: H 161 ASP cc_start: 0.7279 (m-30) cc_final: 0.6955 (m-30) REVERT: H 195 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7045 (ttt180) REVERT: H 295 HIS cc_start: 0.7250 (t-90) cc_final: 0.6868 (t70) REVERT: H 302 ILE cc_start: 0.7936 (mt) cc_final: 0.7732 (mt) REVERT: E 97 GLN cc_start: 0.7968 (tt0) cc_final: 0.7745 (tt0) REVERT: E 116 ASN cc_start: 0.8274 (t0) cc_final: 0.7543 (t0) REVERT: E 129 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7279 (mtmm) REVERT: E 156 ILE cc_start: 0.6690 (mt) cc_final: 0.6455 (mt) REVERT: E 214 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7424 (mmt180) REVERT: E 253 LYS cc_start: 0.8003 (mttt) cc_final: 0.7799 (ttmm) REVERT: E 267 MET cc_start: 0.7646 (ttp) cc_final: 0.7314 (ttp) REVERT: F 84 ARG cc_start: 0.7847 (ptp90) cc_final: 0.7589 (ptp-170) REVERT: F 161 ASP cc_start: 0.7328 (m-30) cc_final: 0.7100 (m-30) REVERT: F 195 ARG cc_start: 0.7382 (ttp80) cc_final: 0.7081 (ttt180) REVERT: F 220 LEU cc_start: 0.8662 (mt) cc_final: 0.8438 (mt) REVERT: F 295 HIS cc_start: 0.7246 (t-90) cc_final: 0.6895 (t70) REVERT: R 92 ASN cc_start: 0.5903 (m-40) cc_final: 0.5319 (p0) REVERT: C 116 ASN cc_start: 0.8268 (t0) cc_final: 0.7545 (t0) REVERT: C 129 LYS cc_start: 0.7718 (mtpp) cc_final: 0.7224 (mtmm) REVERT: C 156 ILE cc_start: 0.6694 (mt) cc_final: 0.6460 (mt) REVERT: C 214 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7405 (mmt180) REVERT: C 253 LYS cc_start: 0.7998 (mttt) cc_final: 0.7792 (ttmm) REVERT: D 84 ARG cc_start: 0.7853 (ptp90) cc_final: 0.7651 (ptp-170) REVERT: D 104 TYR cc_start: 0.8623 (m-80) cc_final: 0.8419 (m-80) REVERT: D 161 ASP cc_start: 0.7280 (m-30) cc_final: 0.6945 (m-30) REVERT: D 195 ARG cc_start: 0.7383 (ttp80) cc_final: 0.7087 (ttt180) REVERT: D 220 LEU cc_start: 0.8635 (mt) cc_final: 0.8416 (mt) REVERT: D 295 HIS cc_start: 0.7231 (t-90) cc_final: 0.6838 (t70) REVERT: Q 58 LEU cc_start: 0.6679 (mt) cc_final: 0.6479 (tt) REVERT: Q 88 VAL cc_start: 0.7058 (t) cc_final: 0.6751 (t) REVERT: A 97 GLN cc_start: 0.7973 (tt0) cc_final: 0.7750 (tt0) REVERT: A 116 ASN cc_start: 0.8268 (t0) cc_final: 0.7551 (t0) REVERT: A 129 LYS cc_start: 0.7708 (mtpp) cc_final: 0.7210 (mtmm) REVERT: A 156 ILE cc_start: 0.6690 (mt) cc_final: 0.6457 (mt) REVERT: A 214 ARG cc_start: 0.7695 (mmt180) cc_final: 0.7316 (mmt180) REVERT: A 253 LYS cc_start: 0.8000 (mttt) cc_final: 0.7786 (ttmm) REVERT: B 84 ARG cc_start: 0.7858 (ptp90) cc_final: 0.7658 (ptp-170) REVERT: B 104 TYR cc_start: 0.8613 (m-80) cc_final: 0.8405 (m-80) REVERT: B 195 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7054 (ttt180) REVERT: B 220 LEU cc_start: 0.8660 (mt) cc_final: 0.8433 (mt) REVERT: B 295 HIS cc_start: 0.7235 (t-90) cc_final: 0.6848 (t70) outliers start: 12 outliers final: 4 residues processed: 909 average time/residue: 0.5000 time to fit residues: 683.1171 Evaluate side-chains 554 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 550 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain A residue 378 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.7980 chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 341 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 387 HIS ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 ASN H 305 GLN H 308 HIS ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 HIS H 430 GLN S 27 GLN ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 ASN S 97 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN E 387 HIS ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN F 308 HIS ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 HIS F 430 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 308 HIS ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS D 430 GLN ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN Q 97 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 308 HIS ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS B 430 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 30904 Z= 0.461 Angle : 0.797 15.585 42000 Z= 0.419 Chirality : 0.050 0.169 4588 Planarity : 0.006 0.057 5468 Dihedral : 6.878 42.238 4216 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.23 % Allowed : 9.52 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.11), residues: 3808 helix: -3.11 (0.10), residues: 1420 sheet: -3.39 (0.17), residues: 460 loop : -2.15 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 284 HIS 0.009 0.002 HIS C 239 PHE 0.024 0.003 PHE C 200 TYR 0.042 0.002 TYR S 36 ARG 0.011 0.001 ARG H 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 555 time to evaluate : 3.501 Fit side-chains revert: symmetry clash REVERT: T 65 THR cc_start: 0.7171 (t) cc_final: 0.6836 (m) REVERT: G 129 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7606 (mtmm) REVERT: G 353 ASN cc_start: 0.8151 (t0) cc_final: 0.7911 (t0) REVERT: H 192 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: H 195 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7555 (ptm160) REVERT: H 198 LEU cc_start: 0.8231 (mt) cc_final: 0.8001 (mt) REVERT: H 288 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8630 (m-40) REVERT: H 302 ILE cc_start: 0.8120 (mt) cc_final: 0.7642 (mt) REVERT: H 349 LEU cc_start: 0.8489 (mt) cc_final: 0.8277 (mt) REVERT: S 65 THR cc_start: 0.7194 (t) cc_final: 0.6888 (m) REVERT: E 129 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7661 (mtmm) REVERT: E 353 ASN cc_start: 0.8163 (t0) cc_final: 0.7921 (t0) REVERT: F 195 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7481 (ptm160) REVERT: F 198 LEU cc_start: 0.8213 (mt) cc_final: 0.7983 (mt) REVERT: F 288 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8641 (m-40) REVERT: F 349 LEU cc_start: 0.8511 (mt) cc_final: 0.8298 (mt) REVERT: R 65 THR cc_start: 0.7159 (t) cc_final: 0.6833 (m) REVERT: R 92 ASN cc_start: 0.5878 (m-40) cc_final: 0.5288 (p0) REVERT: C 129 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7604 (mtmm) REVERT: C 353 ASN cc_start: 0.8153 (t0) cc_final: 0.7913 (t0) REVERT: D 192 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: D 195 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7480 (ptm160) REVERT: D 198 LEU cc_start: 0.8220 (mt) cc_final: 0.7983 (mt) REVERT: D 349 LEU cc_start: 0.8506 (mt) cc_final: 0.8295 (mt) REVERT: A 129 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7603 (mtmm) REVERT: A 202 LYS cc_start: 0.7704 (ttpm) cc_final: 0.7483 (ttpp) REVERT: A 353 ASN cc_start: 0.8151 (t0) cc_final: 0.7917 (t0) REVERT: B 195 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7569 (ttt-90) REVERT: B 198 LEU cc_start: 0.8195 (mt) cc_final: 0.7963 (mt) REVERT: B 349 LEU cc_start: 0.8498 (mt) cc_final: 0.8241 (mt) outliers start: 70 outliers final: 40 residues processed: 584 average time/residue: 0.4696 time to fit residues: 426.0942 Evaluate side-chains 510 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 466 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 288 ASN Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 217 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 284 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 342 optimal weight: 0.9990 chunk 369 optimal weight: 8.9990 chunk 304 optimal weight: 0.7980 chunk 339 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 74 GLN T 97 GLN ** T 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 230 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 HIS H 410 HIS S 74 GLN ** S 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 230 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 ASN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS F 410 HIS R 74 GLN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 230 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 410 HIS Q 74 GLN ** Q 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 230 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS B 410 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30904 Z= 0.195 Angle : 0.626 14.776 42000 Z= 0.323 Chirality : 0.044 0.142 4588 Planarity : 0.004 0.049 5468 Dihedral : 6.174 40.655 4216 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.97 % Allowed : 12.64 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.12), residues: 3808 helix: -2.20 (0.12), residues: 1396 sheet: -3.08 (0.18), residues: 472 loop : -1.94 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 71 HIS 0.007 0.001 HIS C 239 PHE 0.027 0.002 PHE B 128 TYR 0.033 0.002 TYR S 36 ARG 0.007 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 553 time to evaluate : 3.271 Fit side-chains revert: symmetry clash REVERT: T 65 THR cc_start: 0.7179 (t) cc_final: 0.6928 (m) REVERT: G 129 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7312 (mtmm) REVERT: G 202 LYS cc_start: 0.7349 (ttpm) cc_final: 0.6907 (ttpt) REVERT: H 195 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7522 (ttp-110) REVERT: H 283 ARG cc_start: 0.7511 (mmm160) cc_final: 0.7130 (mmm-85) REVERT: H 302 ILE cc_start: 0.8031 (mt) cc_final: 0.7588 (mt) REVERT: S 65 THR cc_start: 0.7191 (t) cc_final: 0.6911 (m) REVERT: E 129 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7355 (mtmm) REVERT: E 202 LYS cc_start: 0.7481 (ttpm) cc_final: 0.7012 (ttpt) REVERT: E 428 CYS cc_start: 0.4727 (m) cc_final: 0.3873 (t) REVERT: F 195 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7434 (ptm160) REVERT: F 283 ARG cc_start: 0.7517 (mmm160) cc_final: 0.7135 (mmm-85) REVERT: F 344 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7657 (mmm) REVERT: R 65 THR cc_start: 0.7194 (t) cc_final: 0.6882 (m) REVERT: R 92 ASN cc_start: 0.6025 (m-40) cc_final: 0.5429 (p0) REVERT: C 129 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7316 (mtmm) REVERT: C 202 LYS cc_start: 0.7370 (ttpm) cc_final: 0.6900 (ttpt) REVERT: C 339 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: C 428 CYS cc_start: 0.4746 (m) cc_final: 0.3893 (t) REVERT: D 52 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7572 (mp0) REVERT: D 195 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7413 (ttp-110) REVERT: D 283 ARG cc_start: 0.7558 (mmm160) cc_final: 0.7163 (mmm-85) REVERT: D 344 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7656 (mmm) REVERT: A 129 LYS cc_start: 0.7857 (mtpp) cc_final: 0.7301 (mtmm) REVERT: A 202 LYS cc_start: 0.7355 (ttpm) cc_final: 0.6883 (ttpt) REVERT: A 339 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: A 428 CYS cc_start: 0.4730 (m) cc_final: 0.3880 (t) REVERT: B 195 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7323 (ptm160) REVERT: B 283 ARG cc_start: 0.7503 (mmm160) cc_final: 0.7119 (mmm-85) REVERT: B 349 LEU cc_start: 0.8392 (mt) cc_final: 0.8188 (mt) outliers start: 62 outliers final: 40 residues processed: 586 average time/residue: 0.4416 time to fit residues: 409.1743 Evaluate side-chains 489 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 445 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 343 optimal weight: 0.6980 chunk 363 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 97 optimal weight: 0.0030 overall best weight: 2.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 ASN G 150 GLN G 154 HIS ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 ASN G 357 GLN H 97 GLN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 150 GLN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 ASN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 HIS ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN E 150 GLN E 154 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 ASN ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 ASN F 97 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 HIS ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN C 116 ASN C 150 GLN C 154 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 150 GLN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 150 GLN A 154 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 150 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30904 Z= 0.359 Angle : 0.676 13.397 42000 Z= 0.351 Chirality : 0.047 0.177 4588 Planarity : 0.005 0.036 5468 Dihedral : 6.103 39.577 4216 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.54 % Allowed : 14.04 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.12), residues: 3808 helix: -1.83 (0.13), residues: 1408 sheet: -2.88 (0.19), residues: 448 loop : -1.81 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 53 HIS 0.010 0.001 HIS C 239 PHE 0.029 0.002 PHE B 128 TYR 0.039 0.002 TYR S 36 ARG 0.006 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 488 time to evaluate : 3.563 Fit side-chains revert: symmetry clash REVERT: T 65 THR cc_start: 0.7233 (t) cc_final: 0.6966 (m) REVERT: G 129 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7611 (mtmm) REVERT: G 176 LYS cc_start: 0.5150 (tttp) cc_final: 0.4941 (tttp) REVERT: G 202 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7031 (ttpt) REVERT: G 428 CYS cc_start: 0.4738 (m) cc_final: 0.3982 (t) REVERT: H 192 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: H 302 ILE cc_start: 0.8481 (mt) cc_final: 0.7928 (mt) REVERT: S 65 THR cc_start: 0.7193 (t) cc_final: 0.6922 (m) REVERT: E 129 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7666 (mtmm) REVERT: E 176 LYS cc_start: 0.5148 (tttp) cc_final: 0.4935 (tttp) REVERT: E 202 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7026 (ttpt) REVERT: E 428 CYS cc_start: 0.4617 (m) cc_final: 0.4105 (t) REVERT: F 288 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8666 (m-40) REVERT: F 302 ILE cc_start: 0.7978 (mt) cc_final: 0.7757 (mt) REVERT: R 1 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.5056 (mmm) REVERT: R 65 THR cc_start: 0.7150 (t) cc_final: 0.6874 (m) REVERT: R 92 ASN cc_start: 0.6024 (m-40) cc_final: 0.5303 (p0) REVERT: R 100 SER cc_start: 0.7562 (t) cc_final: 0.7309 (m) REVERT: C 129 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7611 (mtmm) REVERT: C 202 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6889 (ttpt) REVERT: C 205 GLU cc_start: 0.6125 (mt-10) cc_final: 0.5900 (mt-10) REVERT: C 428 CYS cc_start: 0.4752 (m) cc_final: 0.4025 (t) REVERT: A 129 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7601 (mtmm) REVERT: A 202 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6954 (ttpt) REVERT: A 428 CYS cc_start: 0.4736 (m) cc_final: 0.4020 (t) REVERT: B 302 ILE cc_start: 0.7964 (mt) cc_final: 0.7748 (mt) REVERT: B 349 LEU cc_start: 0.8362 (mt) cc_final: 0.8082 (mt) outliers start: 111 outliers final: 73 residues processed: 549 average time/residue: 0.4647 time to fit residues: 414.6816 Evaluate side-chains 527 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 447 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 202 LYS Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 HIS H 410 HIS ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 410 HIS A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS B 410 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30904 Z= 0.213 Angle : 0.602 13.999 42000 Z= 0.309 Chirality : 0.044 0.168 4588 Planarity : 0.004 0.034 5468 Dihedral : 5.807 39.355 4216 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.12 % Allowed : 14.52 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.67 (0.13), residues: 3808 helix: -1.45 (0.13), residues: 1400 sheet: -2.70 (0.20), residues: 444 loop : -1.72 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 369 HIS 0.007 0.001 HIS A 239 PHE 0.017 0.002 PHE B 346 TYR 0.033 0.002 TYR S 36 ARG 0.004 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 502 time to evaluate : 3.445 Fit side-chains revert: symmetry clash REVERT: T 43 ASN cc_start: 0.7219 (t0) cc_final: 0.6780 (t0) REVERT: T 65 THR cc_start: 0.7074 (t) cc_final: 0.6784 (m) REVERT: G 129 LYS cc_start: 0.8010 (mtpp) cc_final: 0.7469 (mtmm) REVERT: G 428 CYS cc_start: 0.4852 (m) cc_final: 0.4085 (t) REVERT: H 192 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: H 213 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: H 283 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7236 (mmm-85) REVERT: H 302 ILE cc_start: 0.8169 (mt) cc_final: 0.7784 (mt) REVERT: S 43 ASN cc_start: 0.7314 (t0) cc_final: 0.6898 (t0) REVERT: S 65 THR cc_start: 0.7064 (t) cc_final: 0.6803 (m) REVERT: E 129 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7539 (mttp) REVERT: E 202 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6900 (ttpt) REVERT: E 428 CYS cc_start: 0.4526 (m) cc_final: 0.4064 (t) REVERT: F 213 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: F 283 ARG cc_start: 0.7594 (mmm160) cc_final: 0.7155 (mmm-85) REVERT: F 302 ILE cc_start: 0.7904 (mt) cc_final: 0.7585 (mt) REVERT: R 43 ASN cc_start: 0.7210 (t0) cc_final: 0.6762 (t0) REVERT: R 65 THR cc_start: 0.7034 (t) cc_final: 0.6740 (m) REVERT: R 92 ASN cc_start: 0.5807 (m-40) cc_final: 0.5512 (p0) REVERT: R 100 SER cc_start: 0.7591 (t) cc_final: 0.7344 (m) REVERT: C 129 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7474 (mtmm) REVERT: C 202 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.7009 (ttpt) REVERT: C 266 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7371 (tt) REVERT: C 428 CYS cc_start: 0.4605 (m) cc_final: 0.4136 (t) REVERT: D 52 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7580 (mp0) REVERT: D 213 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: D 283 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7276 (mmm-85) REVERT: A 129 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7437 (mtmm) REVERT: A 202 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.7057 (ttpt) REVERT: A 266 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7373 (tt) REVERT: A 428 CYS cc_start: 0.4605 (m) cc_final: 0.4111 (t) REVERT: B 213 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: B 283 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7312 (mmm-85) REVERT: B 302 ILE cc_start: 0.7920 (mt) cc_final: 0.7596 (mt) REVERT: B 349 LEU cc_start: 0.8241 (mt) cc_final: 0.8019 (mt) outliers start: 98 outliers final: 59 residues processed: 554 average time/residue: 0.4110 time to fit residues: 368.4715 Evaluate side-chains 543 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 474 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 213 GLN Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 363 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 GLN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 230 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 402 GLN H 116 ASN H 124 ASN ** H 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 HIS S 34 GLN ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 230 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 GLN C 150 GLN C 230 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 124 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 230 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 124 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 30904 Z= 0.457 Angle : 0.730 12.219 42000 Z= 0.375 Chirality : 0.049 0.173 4588 Planarity : 0.005 0.037 5468 Dihedral : 6.143 38.855 4216 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.66 % Allowed : 15.29 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.73 (0.13), residues: 3808 helix: -1.50 (0.13), residues: 1376 sheet: -2.85 (0.20), residues: 464 loop : -1.71 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 53 HIS 0.009 0.002 HIS C 239 PHE 0.023 0.003 PHE D 346 TYR 0.040 0.003 TYR S 36 ARG 0.007 0.001 ARG H 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 465 time to evaluate : 3.645 Fit side-chains revert: symmetry clash REVERT: T 43 ASN cc_start: 0.7240 (t0) cc_final: 0.6923 (t0) REVERT: T 65 THR cc_start: 0.7127 (t) cc_final: 0.6814 (m) REVERT: G 129 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7743 (mttp) REVERT: G 428 CYS cc_start: 0.4616 (m) cc_final: 0.4152 (t) REVERT: H 192 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: H 213 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: H 302 ILE cc_start: 0.7981 (mt) cc_final: 0.7532 (mt) REVERT: S 65 THR cc_start: 0.7175 (t) cc_final: 0.6896 (m) REVERT: E 129 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7699 (mttp) REVERT: E 428 CYS cc_start: 0.4601 (m) cc_final: 0.4116 (t) REVERT: F 213 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: F 220 LEU cc_start: 0.8585 (mt) cc_final: 0.8380 (mt) REVERT: R 1 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.5085 (mmm) REVERT: R 43 ASN cc_start: 0.7229 (t0) cc_final: 0.6926 (t0) REVERT: R 65 THR cc_start: 0.7032 (t) cc_final: 0.6712 (m) REVERT: C 129 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7693 (mttp) REVERT: C 428 CYS cc_start: 0.4620 (m) cc_final: 0.4132 (t) REVERT: D 213 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7471 (pt0) REVERT: D 220 LEU cc_start: 0.8561 (mt) cc_final: 0.8348 (mt) REVERT: D 344 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7829 (mmp) REVERT: Q 52 TYR cc_start: 0.8977 (m-80) cc_final: 0.8603 (m-80) REVERT: A 129 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7702 (mttp) REVERT: A 428 CYS cc_start: 0.4607 (m) cc_final: 0.4131 (t) REVERT: B 132 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7574 (ttm170) REVERT: B 213 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: B 220 LEU cc_start: 0.8584 (mt) cc_final: 0.8378 (mt) outliers start: 115 outliers final: 73 residues processed: 538 average time/residue: 0.4345 time to fit residues: 376.5851 Evaluate side-chains 511 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 431 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 213 GLN Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 265 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 306 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 362 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 34 GLN G 97 GLN G 150 GLN G 230 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN H 124 ASN H 384 HIS H 410 HIS E 97 GLN E 150 GLN E 230 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 HIS ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN F 384 HIS ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 230 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 124 ASN ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 410 HIS A 97 GLN A 150 GLN A 230 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN B 116 ASN B 124 ASN B 384 HIS B 410 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30904 Z= 0.210 Angle : 0.598 13.361 42000 Z= 0.304 Chirality : 0.044 0.165 4588 Planarity : 0.004 0.041 5468 Dihedral : 5.668 39.679 4216 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.61 % Allowed : 16.88 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.29 (0.13), residues: 3808 helix: -1.03 (0.14), residues: 1372 sheet: -2.35 (0.21), residues: 456 loop : -1.62 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 67 HIS 0.008 0.001 HIS E 239 PHE 0.017 0.002 PHE D 346 TYR 0.030 0.002 TYR S 36 ARG 0.004 0.000 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 474 time to evaluate : 3.463 Fit side-chains revert: symmetry clash REVERT: T 43 ASN cc_start: 0.7042 (t0) cc_final: 0.6733 (t0) REVERT: T 65 THR cc_start: 0.7043 (t) cc_final: 0.6705 (m) REVERT: G 129 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7537 (mttp) REVERT: G 428 CYS cc_start: 0.4861 (m) cc_final: 0.4208 (t) REVERT: H 192 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: H 213 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: H 283 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7178 (mmm-85) REVERT: H 302 ILE cc_start: 0.7827 (mt) cc_final: 0.7381 (mt) REVERT: S 43 ASN cc_start: 0.7116 (t0) cc_final: 0.6691 (t0) REVERT: S 65 THR cc_start: 0.6804 (t) cc_final: 0.6537 (m) REVERT: E 129 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7553 (mttp) REVERT: E 428 CYS cc_start: 0.4557 (m) cc_final: 0.4203 (t) REVERT: F 213 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7508 (pt0) REVERT: F 283 ARG cc_start: 0.7597 (mmm160) cc_final: 0.7218 (mmm-85) REVERT: R 43 ASN cc_start: 0.7083 (t0) cc_final: 0.6768 (t0) REVERT: R 65 THR cc_start: 0.6941 (t) cc_final: 0.6608 (m) REVERT: C 129 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7536 (mttp) REVERT: C 428 CYS cc_start: 0.4562 (m) cc_final: 0.4223 (t) REVERT: D 213 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: D 283 ARG cc_start: 0.7608 (mmm160) cc_final: 0.7237 (mmm-85) REVERT: Q 43 ASN cc_start: 0.6979 (t0) cc_final: 0.6533 (t0) REVERT: A 129 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7404 (mtmm) REVERT: A 428 CYS cc_start: 0.4554 (m) cc_final: 0.4224 (t) REVERT: B 213 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: B 283 ARG cc_start: 0.7601 (mmm160) cc_final: 0.7239 (mmm-85) outliers start: 82 outliers final: 53 residues processed: 526 average time/residue: 0.4570 time to fit residues: 382.4673 Evaluate side-chains 481 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 423 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 213 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 384 HIS H 410 HIS ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 410 HIS Q 34 GLN ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 230 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS B 410 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 30904 Z= 0.417 Angle : 0.700 12.381 42000 Z= 0.356 Chirality : 0.048 0.168 4588 Planarity : 0.005 0.036 5468 Dihedral : 5.949 38.535 4216 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.76 % Allowed : 15.99 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.47 (0.13), residues: 3808 helix: -1.09 (0.14), residues: 1372 sheet: -2.53 (0.20), residues: 476 loop : -1.76 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 56 HIS 0.008 0.001 HIS A 239 PHE 0.019 0.002 PHE D 346 TYR 0.040 0.002 TYR S 36 ARG 0.005 0.001 ARG H 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 444 time to evaluate : 3.451 Fit side-chains revert: symmetry clash REVERT: T 9 ARG cc_start: 0.6115 (mtt180) cc_final: 0.5644 (mmm-85) REVERT: T 43 ASN cc_start: 0.7262 (t0) cc_final: 0.6934 (t0) REVERT: T 65 THR cc_start: 0.7120 (t) cc_final: 0.6785 (m) REVERT: G 129 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7661 (mttp) REVERT: G 428 CYS cc_start: 0.4774 (m) cc_final: 0.4295 (t) REVERT: H 192 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: H 213 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7471 (pt0) REVERT: S 9 ARG cc_start: 0.6183 (mtt180) cc_final: 0.5630 (mmm-85) REVERT: S 43 ASN cc_start: 0.7322 (t0) cc_final: 0.6903 (t0) REVERT: S 65 THR cc_start: 0.7119 (t) cc_final: 0.6789 (m) REVERT: E 129 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7673 (mttp) REVERT: E 428 CYS cc_start: 0.4663 (m) cc_final: 0.4248 (t) REVERT: F 213 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: F 220 LEU cc_start: 0.8547 (mt) cc_final: 0.8313 (mt) REVERT: R 9 ARG cc_start: 0.6110 (mtt180) cc_final: 0.5631 (mmm-85) REVERT: R 43 ASN cc_start: 0.7255 (t0) cc_final: 0.6924 (t0) REVERT: R 65 THR cc_start: 0.7173 (t) cc_final: 0.6823 (m) REVERT: C 129 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7670 (mttp) REVERT: C 428 CYS cc_start: 0.4671 (m) cc_final: 0.4276 (t) REVERT: D 213 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: Q 9 ARG cc_start: 0.6226 (mtt180) cc_final: 0.5749 (mmm-85) REVERT: Q 43 ASN cc_start: 0.7136 (t0) cc_final: 0.6750 (t0) REVERT: A 129 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7677 (mttp) REVERT: A 428 CYS cc_start: 0.4683 (m) cc_final: 0.4279 (t) REVERT: B 213 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7484 (pt0) outliers start: 118 outliers final: 93 residues processed: 520 average time/residue: 0.4498 time to fit residues: 376.5979 Evaluate side-chains 525 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 427 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 213 GLN Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 8.9990 chunk 347 optimal weight: 0.9990 chunk 316 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 319 optimal weight: 0.7980 chunk 336 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 384 HIS ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 239 HIS ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 384 HIS D 410 HIS Q 104 HIS A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN B 384 HIS B 410 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30904 Z= 0.249 Angle : 0.625 13.763 42000 Z= 0.317 Chirality : 0.045 0.166 4588 Planarity : 0.004 0.042 5468 Dihedral : 5.723 38.736 4216 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.03 % Allowed : 17.17 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3808 helix: -0.83 (0.14), residues: 1368 sheet: -2.26 (0.22), residues: 456 loop : -1.66 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 56 HIS 0.008 0.001 HIS A 239 PHE 0.019 0.002 PHE D 109 TYR 0.034 0.002 TYR S 36 ARG 0.006 0.000 ARG Q 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 444 time to evaluate : 3.504 Fit side-chains revert: symmetry clash REVERT: T 9 ARG cc_start: 0.6257 (mtt180) cc_final: 0.5681 (mmm-85) REVERT: T 43 ASN cc_start: 0.7111 (t0) cc_final: 0.6783 (t0) REVERT: T 65 THR cc_start: 0.7095 (t) cc_final: 0.6741 (m) REVERT: G 129 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7545 (mttp) REVERT: G 428 CYS cc_start: 0.4641 (m) cc_final: 0.4215 (t) REVERT: H 192 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: H 213 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7533 (pt0) REVERT: H 283 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7300 (mmm-85) REVERT: H 302 ILE cc_start: 0.7835 (mt) cc_final: 0.7441 (mt) REVERT: S 9 ARG cc_start: 0.6266 (mtt180) cc_final: 0.5664 (mmm-85) REVERT: S 43 ASN cc_start: 0.7055 (t0) cc_final: 0.6666 (t0) REVERT: S 65 THR cc_start: 0.7072 (t) cc_final: 0.6746 (m) REVERT: E 129 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7567 (mttp) REVERT: E 428 CYS cc_start: 0.4616 (m) cc_final: 0.4269 (t) REVERT: F 213 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: F 283 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7216 (mmm-85) REVERT: R 1 MET cc_start: 0.5393 (OUTLIER) cc_final: 0.5034 (mmm) REVERT: R 9 ARG cc_start: 0.6265 (mtt180) cc_final: 0.5706 (mmm-85) REVERT: R 43 ASN cc_start: 0.7054 (t0) cc_final: 0.6730 (t0) REVERT: R 65 THR cc_start: 0.7140 (t) cc_final: 0.6787 (m) REVERT: R 92 ASN cc_start: 0.5805 (m-40) cc_final: 0.5390 (p0) REVERT: C 129 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7549 (mttp) REVERT: C 428 CYS cc_start: 0.4632 (m) cc_final: 0.4288 (t) REVERT: D 213 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: D 283 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7231 (mmm-85) REVERT: Q 9 ARG cc_start: 0.6266 (mtt180) cc_final: 0.5679 (mmm-85) REVERT: Q 43 ASN cc_start: 0.6956 (t0) cc_final: 0.6584 (t0) REVERT: A 129 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7595 (mttp) REVERT: A 428 CYS cc_start: 0.4647 (m) cc_final: 0.4294 (t) REVERT: B 213 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: B 283 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7230 (mmm-85) outliers start: 95 outliers final: 74 residues processed: 507 average time/residue: 0.4360 time to fit residues: 357.1469 Evaluate side-chains 514 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 434 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 213 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 2.9990 chunk 357 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 374 optimal weight: 0.4980 chunk 344 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 230 GLN H 384 HIS ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 230 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 HIS C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 230 GLN D 384 HIS D 410 HIS A 150 GLN A 239 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 230 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS B 410 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30904 Z= 0.224 Angle : 0.607 13.191 42000 Z= 0.308 Chirality : 0.044 0.159 4588 Planarity : 0.004 0.042 5468 Dihedral : 5.553 38.485 4216 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.83 % Allowed : 17.55 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.00 (0.13), residues: 3808 helix: -0.63 (0.14), residues: 1372 sheet: -2.18 (0.22), residues: 448 loop : -1.59 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 56 HIS 0.009 0.001 HIS E 239 PHE 0.018 0.002 PHE D 346 TYR 0.032 0.002 TYR S 36 ARG 0.007 0.000 ARG E 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 447 time to evaluate : 3.678 Fit side-chains revert: symmetry clash REVERT: T 9 ARG cc_start: 0.6377 (mtt180) cc_final: 0.5750 (mmm-85) REVERT: T 43 ASN cc_start: 0.7015 (t0) cc_final: 0.6707 (t0) REVERT: T 65 THR cc_start: 0.7161 (t) cc_final: 0.6767 (m) REVERT: G 129 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7530 (mttp) REVERT: G 428 CYS cc_start: 0.4628 (m) cc_final: 0.4245 (t) REVERT: H 192 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: H 213 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7508 (pt0) REVERT: H 283 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7278 (mmm-85) REVERT: H 302 ILE cc_start: 0.7800 (mt) cc_final: 0.7428 (mt) REVERT: S 9 ARG cc_start: 0.6349 (mtt180) cc_final: 0.5796 (mmm-85) REVERT: S 43 ASN cc_start: 0.7061 (t0) cc_final: 0.6689 (t0) REVERT: S 65 THR cc_start: 0.7130 (t) cc_final: 0.6781 (m) REVERT: E 129 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7529 (mttp) REVERT: E 428 CYS cc_start: 0.4601 (m) cc_final: 0.4288 (t) REVERT: F 213 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7586 (pt0) REVERT: F 283 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7252 (mmm-85) REVERT: R 1 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.5025 (mmm) REVERT: R 9 ARG cc_start: 0.6147 (mtt180) cc_final: 0.5586 (mmm-85) REVERT: R 43 ASN cc_start: 0.7005 (t0) cc_final: 0.6723 (t0) REVERT: R 65 THR cc_start: 0.7194 (t) cc_final: 0.6861 (m) REVERT: C 129 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7530 (mttp) REVERT: C 428 CYS cc_start: 0.4606 (m) cc_final: 0.4360 (t) REVERT: D 213 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: D 283 ARG cc_start: 0.7735 (mmm160) cc_final: 0.7239 (mmm-85) REVERT: Q 9 ARG cc_start: 0.6319 (mtt180) cc_final: 0.5829 (mmm-85) REVERT: Q 43 ASN cc_start: 0.6903 (t0) cc_final: 0.6573 (t0) REVERT: A 129 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7448 (mttp) REVERT: A 428 CYS cc_start: 0.4631 (m) cc_final: 0.4318 (t) REVERT: B 213 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: B 283 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7243 (mmm-85) outliers start: 89 outliers final: 67 residues processed: 506 average time/residue: 0.4585 time to fit residues: 371.8529 Evaluate side-chains 503 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 430 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 213 GLN Chi-restraints excluded: chain H residue 230 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 230 GLN Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 6.9990 chunk 317 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 0.0370 chunk 298 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 306 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 104 HIS G 150 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 230 GLN H 384 HIS H 410 HIS ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 230 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 HIS C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 230 GLN D 384 HIS A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 230 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.177815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.147126 restraints weight = 32612.748| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.64 r_work: 0.3375 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30904 Z= 0.231 Angle : 0.604 13.158 42000 Z= 0.306 Chirality : 0.044 0.160 4588 Planarity : 0.004 0.043 5468 Dihedral : 5.501 38.200 4216 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.06 % Allowed : 17.32 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.93 (0.13), residues: 3808 helix: -0.52 (0.14), residues: 1372 sheet: -2.19 (0.22), residues: 476 loop : -1.55 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 56 HIS 0.009 0.001 HIS A 239 PHE 0.018 0.002 PHE D 346 TYR 0.032 0.002 TYR S 36 ARG 0.003 0.000 ARG B 195 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: