Starting phenix.real_space_refine (version: dev) on Mon Feb 27 13:36:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/02_2023/6lrs_0960.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/02_2023/6lrs_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_0960/02_2023/6lrs_0960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/02_2023/6lrs_0960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/02_2023/6lrs_0960.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lrs_0960/02_2023/6lrs_0960.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 16.31, per 1000 atoms: 0.54 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: 11.53 Conformation dependent library (CDL) restraints added in 3.9 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: 1.81 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: 12.34 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 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. 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.010 Check model and map are aligned: 0.440 Process input model: 73.610 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.260 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 % 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 *********************** 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 : 3.397 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 outliers start: 12 outliers final: 4 residues processed: 909 average time/residue: 0.4979 time to fit residues: 681.2512 Evaluate side-chains 541 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 537 time to evaluate : 3.341 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3091 time to fit residues: 7.3236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 341 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 ASN ** G 124 ASN ** 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 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 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 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** 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 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 116 ASN ** 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 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 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3086 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= 0.486 Angle : 0.820 16.923 42000 Z= 0.427 Chirality : 0.051 0.188 4588 Planarity : 0.006 0.061 5468 Dihedral : 6.832 41.897 4212 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 2.42 % 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: -4.10 (0.11), residues: 3808 helix: -3.09 (0.10), residues: 1420 sheet: -3.43 (0.17), residues: 460 loop : -2.14 (0.13), residues: 1928 *********************** 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 634 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 558 time to evaluate : 3.539 Fit side-chains revert: symmetry clash outliers start: 76 outliers final: 43 residues processed: 592 average time/residue: 0.4688 time to fit residues: 432.5407 Evaluate side-chains 494 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 451 time to evaluate : 3.225 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2918 time to fit residues: 27.9228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 284 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 chunk 342 optimal weight: 0.9980 chunk 369 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** G 353 ASN ** G 357 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 305 GLN ** 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 97 GLN ** 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 353 ASN E 357 GLN ** 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 ** R 104 HIS ** 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 353 ASN ** 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 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 ** A 357 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 30904 Z= 0.198 Angle : 0.624 12.749 42000 Z= 0.322 Chirality : 0.045 0.134 4588 Planarity : 0.004 0.049 5468 Dihedral : 6.083 40.679 4212 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.32 (0.12), residues: 3808 helix: -2.15 (0.12), residues: 1384 sheet: -3.10 (0.18), residues: 472 loop : -1.93 (0.13), residues: 1952 *********************** 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 609 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 549 time to evaluate : 3.565 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 29 residues processed: 586 average time/residue: 0.4384 time to fit residues: 412.5425 Evaluate side-chains 474 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 445 time to evaluate : 3.581 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3034 time to fit residues: 20.7722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 177 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 343 optimal weight: 0.9990 chunk 363 optimal weight: 9.9990 chunk 179 optimal weight: 0.6980 chunk 325 optimal weight: 9.9990 chunk 97 optimal weight: 0.0060 overall best weight: 2.5402 ------------------------------------------------------------------------------- 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 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 GLN G 402 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 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 HIS H 410 HIS ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** 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 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS F 410 HIS ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 384 HIS D 410 HIS ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 402 GLN 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 384 HIS B 410 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 30904 Z= 0.322 Angle : 0.661 15.754 42000 Z= 0.339 Chirality : 0.047 0.220 4588 Planarity : 0.005 0.038 5468 Dihedral : 5.956 39.898 4212 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 2.07 % 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: -2.96 (0.12), residues: 3808 helix: -1.75 (0.13), residues: 1372 sheet: -2.92 (0.19), residues: 496 loop : -1.78 (0.13), residues: 1940 *********************** 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 567 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 502 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 28 residues processed: 537 average time/residue: 0.4299 time to fit residues: 369.9204 Evaluate side-chains 486 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 458 time to evaluate : 3.275 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2894 time to fit residues: 19.5477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 149 optimal weight: 0.0670 chunk 310 optimal weight: 0.0070 chunk 251 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 326 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 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 ** 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 ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS F 410 HIS ** R 27 GLN ** 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** 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 ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 30904 Z= 0.187 Angle : 0.590 15.180 42000 Z= 0.302 Chirality : 0.044 0.166 4588 Planarity : 0.004 0.036 5468 Dihedral : 5.635 39.286 4212 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 1.94 % 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: -2.55 (0.13), residues: 3808 helix: -1.37 (0.13), residues: 1392 sheet: -2.66 (0.20), residues: 504 loop : -1.56 (0.14), residues: 1912 *********************** 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 562 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 501 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 30 residues processed: 538 average time/residue: 0.4092 time to fit residues: 359.4999 Evaluate side-chains 486 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 456 time to evaluate : 3.102 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2924 time to fit residues: 21.1696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 20.0000 chunk 327 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 363 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 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** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 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 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 HIS ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 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** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 30904 Z= 0.328 Angle : 0.659 15.756 42000 Z= 0.335 Chirality : 0.047 0.164 4588 Planarity : 0.004 0.035 5468 Dihedral : 5.724 38.594 4212 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.49 (0.13), residues: 3808 helix: -1.24 (0.13), residues: 1388 sheet: -2.64 (0.20), residues: 488 loop : -1.61 (0.13), residues: 1932 *********************** 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 550 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 487 time to evaluate : 3.666 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 38 residues processed: 524 average time/residue: 0.4163 time to fit residues: 356.8408 Evaluate side-chains 495 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 457 time to evaluate : 3.710 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2875 time to fit residues: 25.2693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 362 optimal weight: 0.9990 chunk 226 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 402 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 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 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 402 GLN D 410 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** 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 384 HIS B 402 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 30904 Z= 0.194 Angle : 0.585 15.275 42000 Z= 0.297 Chirality : 0.044 0.161 4588 Planarity : 0.004 0.035 5468 Dihedral : 5.464 38.805 4212 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.17 (0.13), residues: 3808 helix: -0.89 (0.14), residues: 1380 sheet: -2.41 (0.21), residues: 488 loop : -1.51 (0.14), residues: 1940 *********************** 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 527 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 483 time to evaluate : 3.373 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 512 average time/residue: 0.4149 time to fit residues: 350.4541 Evaluate side-chains 475 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 453 time to evaluate : 3.410 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2851 time to fit residues: 16.5814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 216 optimal weight: 0.0030 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 230 optimal weight: 0.0050 chunk 246 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 284 optimal weight: 9.9990 overall best weight: 0.7606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 GLN G 230 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 387 HIS ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN E 97 GLN E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 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 384 HIS ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** 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** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 230 GLN D 387 HIS D 410 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 230 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 230 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 30904 Z= 0.182 Angle : 0.583 16.134 42000 Z= 0.294 Chirality : 0.043 0.148 4588 Planarity : 0.004 0.036 5468 Dihedral : 5.276 38.132 4212 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 1.46 % 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: -1.95 (0.13), residues: 3808 helix: -0.65 (0.14), residues: 1408 sheet: -2.19 (0.22), residues: 448 loop : -1.49 (0.14), residues: 1952 *********************** 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 539 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 493 time to evaluate : 3.623 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 26 residues processed: 522 average time/residue: 0.4088 time to fit residues: 351.9153 Evaluate side-chains 469 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 443 time to evaluate : 3.182 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3116 time to fit residues: 19.5025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 10.0000 chunk 347 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 265 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 chunk 319 optimal weight: 0.9980 chunk 336 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 34 GLN ** 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** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 387 HIS ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 387 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 230 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 387 HIS ** Q 27 GLN ** 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 328 HIS ** 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 387 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 30904 Z= 0.247 Angle : 0.609 15.319 42000 Z= 0.307 Chirality : 0.045 0.148 4588 Planarity : 0.004 0.036 5468 Dihedral : 5.334 36.909 4212 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 1.08 % 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: -1.89 (0.13), residues: 3808 helix: -0.49 (0.14), residues: 1388 sheet: -2.24 (0.21), residues: 476 loop : -1.52 (0.14), residues: 1944 *********************** 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 487 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 453 time to evaluate : 3.320 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 472 average time/residue: 0.4340 time to fit residues: 335.6887 Evaluate side-chains 461 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 443 time to evaluate : 3.465 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2931 time to fit residues: 14.9629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 4.9990 chunk 357 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 374 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 230 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 239 HIS ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN H 124 ASN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 239 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** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 GLN ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 30904 Z= 0.266 Angle : 0.620 16.323 42000 Z= 0.312 Chirality : 0.045 0.218 4588 Planarity : 0.004 0.036 5468 Dihedral : 5.379 37.133 4212 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.73 % 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: -1.86 (0.13), residues: 3808 helix: -0.41 (0.14), residues: 1376 sheet: -2.13 (0.21), residues: 484 loop : -1.57 (0.13), residues: 1948 ********************** 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 469 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 446 time to evaluate : 3.321 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 460 average time/residue: 0.4377 time to fit residues: 331.7248 Evaluate side-chains 437 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 430 time to evaluate : 3.517 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3142 time to fit residues: 9.1493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 0.6980 chunk 317 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 306 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 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** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 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 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** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 384 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.180032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.148030 restraints weight = 32637.528| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.74 r_work: 0.3382 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4739 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= 0.213 Angle : 0.594 15.317 42000 Z= 0.299 Chirality : 0.044 0.164 4588 Planarity : 0.004 0.036 5468 Dihedral : 5.269 37.190 4212 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.76 % 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: -1.74 (0.13), residues: 3808 helix: -0.33 (0.14), residues: 1388 sheet: -1.91 (0.22), residues: 436 loop : -1.56 (0.13), residues: 1984 =============================================================================== Job complete usr+sys time: 7313.65 seconds wall clock time: 134 minutes 36.49 seconds (8076.49 seconds total)