Starting phenix.real_space_refine on Thu Apr 11 11:49:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m18_30040/04_2024/6m18_30040_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m18_30040/04_2024/6m18_30040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m18_30040/04_2024/6m18_30040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m18_30040/04_2024/6m18_30040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m18_30040/04_2024/6m18_30040_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m18_30040/04_2024/6m18_30040_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4 5.49 5 S 128 5.16 5 C 14618 2.51 5 N 3562 2.21 5 O 4220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B ARG 518": "NH1" <-> "NH2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B ARG 678": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 768": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C GLU 568": "OE1" <-> "OE2" Residue "C ARG 607": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 671": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 768": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22534 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4794 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 573} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4794 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 573} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'3PH': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'3PH': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 11.75, per 1000 atoms: 0.52 Number of scatterers: 22534 At special positions: 0 Unit cell: (111.961, 138.049, 184.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 4 15.00 O 4220 8.00 N 3562 7.00 C 14618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 383 " distance=2.05 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.05 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=1.85 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.02 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 383 " distance=2.05 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=1.85 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 701 " - " ASN A 158 " " NAG A 702 " - " ASN A 182 " " NAG A 703 " - " ASN A 354 " " NAG A 704 " - " ASN A 368 " " NAG B 901 " - " ASN B 322 " " NAG C 701 " - " ASN C 158 " " NAG C 702 " - " ASN C 182 " " NAG C 703 " - " ASN C 354 " " NAG C 704 " - " ASN C 368 " " NAG D 901 " - " ASN D 322 " " NAG E 1 " - " ASN A 258 " " NAG F 1 " - " ASN B 53 " " NAG G 1 " - " ASN B 90 " " NAG H 1 " - " ASN B 103 " " NAG I 1 " - " ASN B 432 " " NAG J 1 " - " ASN B 546 " " NAG K 1 " - " ASN B 690 " " NAG L 1 " - " ASN C 258 " " NAG M 1 " - " ASN D 53 " " NAG N 1 " - " ASN D 90 " " NAG O 1 " - " ASN D 103 " " NAG P 1 " - " ASN D 432 " " NAG Q 1 " - " ASN D 546 " " NAG R 1 " - " ASN D 690 " Time building additional restraints: 9.85 Conformation dependent library (CDL) restraints added in 4.5 seconds 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 6 sheets defined 57.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 21 through 24 No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 39 through 49 removed outlier: 3.683A pdb=" N THR A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.561A pdb=" N GLN A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 82 through 96 removed outlier: 3.548A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 113 through 141 removed outlier: 3.683A pdb=" N TYR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.514A pdb=" N TRP A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 211 removed outlier: 3.767A pdb=" N CYS A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 243 Proline residue: A 230 - end of helix removed outlier: 3.621A pdb=" N ILE A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 267 through 278 removed outlier: 3.817A pdb=" N VAL A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 4.382A pdb=" N TYR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 348 removed outlier: 3.736A pdb=" N VAL A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.775A pdb=" N CYS A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 No H-bonds generated for 'chain 'A' and resid 397 through 400' Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.882A pdb=" N THR A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 440 removed outlier: 4.224A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 445 No H-bonds generated for 'chain 'A' and resid 442 through 445' Processing helix chain 'A' and resid 455 through 474 removed outlier: 3.661A pdb=" N THR A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 506 removed outlier: 3.503A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.643A pdb=" N CYS A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 522 removed outlier: 3.520A pdb=" N LYS A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 535 Processing helix chain 'A' and resid 537 through 552 removed outlier: 3.564A pdb=" N LEU A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 607 removed outlier: 3.780A pdb=" N TYR A 583 " --> pdb=" O ASN A 580 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 587 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 590 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 591 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL A 592 " --> pdb=" O VAL A 589 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.161A pdb=" N THR A 596 " --> pdb=" O PRO A 593 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 597 " --> pdb=" O SER A 594 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.720A pdb=" N ILE A 602 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 604 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 605 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 607 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 52 removed outlier: 3.526A pdb=" N THR B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 82 removed outlier: 3.991A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET B 82 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 101 removed outlier: 3.525A pdb=" N GLN B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 107 removed outlier: 3.939A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 112 through 129 removed outlier: 3.570A pdb=" N ASN B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 3.604A pdb=" N MET B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 193 removed outlier: 3.625A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.674A pdb=" N GLU B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 removed outlier: 4.705A pdb=" N ASP B 206 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR B 207 " --> pdb=" O TRP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 248 removed outlier: 3.629A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.580A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.616A pdb=" N TYR B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER B 280 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.591A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 366 through 382 removed outlier: 3.647A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 400 through 411 removed outlier: 3.924A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 4.105A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 445 removed outlier: 3.530A pdb=" N LYS B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 465 Processing helix chain 'B' and resid 470 through 483 removed outlier: 4.094A pdb=" N TRP B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N MET B 474 " --> pdb=" O ASP B 471 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 475 " --> pdb=" O GLN B 472 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 476 " --> pdb=" O TRP B 473 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP B 477 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP B 478 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 479 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 480 " --> pdb=" O TRP B 477 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 481 " --> pdb=" O TRP B 478 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 482 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 483 " --> pdb=" O MET B 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 470 through 483' Processing helix chain 'B' and resid 504 through 507 No H-bonds generated for 'chain 'B' and resid 504 through 507' Processing helix chain 'B' and resid 513 through 532 removed outlier: 3.826A pdb=" N THR B 517 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 521 " --> pdb=" O ARG B 518 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 522 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 525 " --> pdb=" O GLN B 522 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 526 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 527 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 529 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS B 530 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 531 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 532 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.890A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.715A pdb=" N GLU B 571 " --> pdb=" O THR B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 589 through 598 removed outlier: 3.706A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 627 No H-bonds generated for 'chain 'B' and resid 624 through 627' Processing helix chain 'B' and resid 637 through 657 Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' Processing helix chain 'B' and resid 697 through 706 removed outlier: 3.621A pdb=" N LYS B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.542A pdb=" N ALA B 714 " --> pdb=" O ARG B 710 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 763 removed outlier: 3.809A pdb=" N THR B 763 " --> pdb=" O ILE B 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 39 through 49 removed outlier: 3.683A pdb=" N THR C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.561A pdb=" N GLN C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 82 through 96 removed outlier: 3.548A pdb=" N ILE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 93 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 104 No H-bonds generated for 'chain 'C' and resid 101 through 104' Processing helix chain 'C' and resid 113 through 141 removed outlier: 3.683A pdb=" N TYR C 128 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.514A pdb=" N TRP C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 211 removed outlier: 3.767A pdb=" N CYS C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 243 Proline residue: C 230 - end of helix removed outlier: 3.621A pdb=" N ILE C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 259 through 262 Processing helix chain 'C' and resid 267 through 278 removed outlier: 3.817A pdb=" N VAL C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 292 removed outlier: 4.382A pdb=" N TYR C 292 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 348 removed outlier: 3.736A pdb=" N VAL C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 339 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.775A pdb=" N CYS C 367 " --> pdb=" O MET C 363 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 400 No H-bonds generated for 'chain 'C' and resid 397 through 400' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.882A pdb=" N THR C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 440 removed outlier: 4.224A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 445 No H-bonds generated for 'chain 'C' and resid 442 through 445' Processing helix chain 'C' and resid 455 through 474 removed outlier: 3.661A pdb=" N THR C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE C 473 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 506 removed outlier: 3.503A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Proline residue: C 493 - end of helix removed outlier: 3.643A pdb=" N CYS C 500 " --> pdb=" O ILE C 496 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 522 removed outlier: 3.520A pdb=" N LYS C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 535 Processing helix chain 'C' and resid 537 through 552 removed outlier: 3.564A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 546 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 607 removed outlier: 3.780A pdb=" N TYR C 583 " --> pdb=" O ASN C 580 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 587 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 589 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 590 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY C 591 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL C 592 " --> pdb=" O VAL C 589 " (cutoff:3.500A) Proline residue: C 593 - end of helix removed outlier: 4.161A pdb=" N THR C 596 " --> pdb=" O PRO C 593 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 597 " --> pdb=" O SER C 594 " (cutoff:3.500A) Proline residue: C 598 - end of helix removed outlier: 3.720A pdb=" N ILE C 602 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS C 604 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 605 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 607 " --> pdb=" O LYS C 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 52 removed outlier: 3.526A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 82 removed outlier: 3.991A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.525A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 107 removed outlier: 3.939A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 107' Processing helix chain 'D' and resid 112 through 129 removed outlier: 3.570A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.604A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 193 removed outlier: 3.625A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.674A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 207 removed outlier: 4.705A pdb=" N ASP D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR D 207 " --> pdb=" O TRP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 248 removed outlier: 3.629A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.580A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 282 removed outlier: 3.616A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 281 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 299 No H-bonds generated for 'chain 'D' and resid 296 through 299' Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.591A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 366 through 382 removed outlier: 3.647A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 392 No H-bonds generated for 'chain 'D' and resid 390 through 392' Processing helix chain 'D' and resid 400 through 411 removed outlier: 3.924A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.105A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 removed outlier: 3.530A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 470 through 483 removed outlier: 4.094A pdb=" N TRP D 473 " --> pdb=" O LYS D 470 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N MET D 474 " --> pdb=" O ASP D 471 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 475 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 476 " --> pdb=" O TRP D 473 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP D 477 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP D 478 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 479 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 480 " --> pdb=" O TRP D 477 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS D 481 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 482 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 483 " --> pdb=" O MET D 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 470 through 483' Processing helix chain 'D' and resid 504 through 507 No H-bonds generated for 'chain 'D' and resid 504 through 507' Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.826A pdb=" N THR D 517 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR D 521 " --> pdb=" O ARG D 518 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 522 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 525 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN D 526 " --> pdb=" O PHE D 523 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 527 " --> pdb=" O GLN D 524 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 529 " --> pdb=" O GLN D 526 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS D 530 " --> pdb=" O GLU D 527 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN D 531 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 532 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 541 No H-bonds generated for 'chain 'D' and resid 539 through 541' Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.890A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 571 removed outlier: 3.715A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 589 through 598 removed outlier: 3.706A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 627 No H-bonds generated for 'chain 'D' and resid 624 through 627' Processing helix chain 'D' and resid 637 through 657 Processing helix chain 'D' and resid 667 through 669 No H-bonds generated for 'chain 'D' and resid 667 through 669' Processing helix chain 'D' and resid 697 through 706 removed outlier: 3.621A pdb=" N LYS D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 removed outlier: 3.542A pdb=" N ALA D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 715 " --> pdb=" O ILE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 763 removed outlier: 3.809A pdb=" N THR D 763 " --> pdb=" O ILE D 759 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 131 through 133 Processing sheet with id= B, first strand: chain 'B' and resid 347 through 350 Processing sheet with id= C, first strand: chain 'B' and resid 618 through 621 Processing sheet with id= D, first strand: chain 'D' and resid 131 through 133 Processing sheet with id= E, first strand: chain 'D' and resid 347 through 350 Processing sheet with id= F, first strand: chain 'D' and resid 618 through 621 780 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 10.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 6602 1.34 - 1.47: 6442 1.47 - 1.61: 9848 1.61 - 1.74: 2 1.74 - 1.88: 210 Bond restraints: 23104 Sorted by residual: bond pdb=" C31 3PH C 705 " pdb=" O31 3PH C 705 " ideal model delta sigma weight residual 1.325 1.456 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C31 3PH A 705 " pdb=" O31 3PH A 705 " ideal model delta sigma weight residual 1.325 1.456 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C21 3PH C 705 " pdb=" O21 3PH C 705 " ideal model delta sigma weight residual 1.328 1.454 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 3PH A 705 " pdb=" O21 3PH A 705 " ideal model delta sigma weight residual 1.328 1.454 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 3PH C 706 " pdb=" O21 3PH C 706 " ideal model delta sigma weight residual 1.328 1.453 -0.125 2.00e-02 2.50e+03 3.92e+01 ... (remaining 23099 not shown) Histogram of bond angle deviations from ideal: 98.74 - 106.67: 766 106.67 - 114.60: 13398 114.60 - 122.52: 14624 122.52 - 130.45: 2452 130.45 - 138.37: 162 Bond angle restraints: 31402 Sorted by residual: angle pdb=" N LEU A 485 " pdb=" CA LEU A 485 " pdb=" C LEU A 485 " ideal model delta sigma weight residual 111.28 121.05 -9.77 1.09e+00 8.42e-01 8.03e+01 angle pdb=" N LEU C 485 " pdb=" CA LEU C 485 " pdb=" C LEU C 485 " ideal model delta sigma weight residual 111.28 121.05 -9.77 1.09e+00 8.42e-01 8.03e+01 angle pdb=" C CYS D 133 " pdb=" N ASN D 134 " pdb=" CA ASN D 134 " ideal model delta sigma weight residual 120.49 132.77 -12.28 1.42e+00 4.96e-01 7.48e+01 angle pdb=" C CYS B 133 " pdb=" N ASN B 134 " pdb=" CA ASN B 134 " ideal model delta sigma weight residual 120.49 132.77 -12.28 1.42e+00 4.96e-01 7.48e+01 angle pdb=" C ILE C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.24 112.45 6.79 1.04e+00 9.25e-01 4.27e+01 ... (remaining 31397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12536 17.97 - 35.93: 1160 35.93 - 53.90: 310 53.90 - 71.86: 66 71.86 - 89.83: 22 Dihedral angle restraints: 14094 sinusoidal: 6192 harmonic: 7902 Sorted by residual: dihedral pdb=" CB CYS B 344 " pdb=" SG CYS B 344 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -5.98 -80.02 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -5.98 -80.02 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CA GLU B 145 " pdb=" C GLU B 145 " pdb=" N PRO B 146 " pdb=" CA PRO B 146 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 14091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3480 0.189 - 0.378: 38 0.378 - 0.567: 8 0.567 - 0.756: 0 0.756 - 0.945: 2 Chirality restraints: 3528 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-02 2.50e+03 2.23e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-02 2.50e+03 2.23e+03 chirality pdb=" CA TRP A 195 " pdb=" N TRP A 195 " pdb=" C TRP A 195 " pdb=" CB TRP A 195 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 ... (remaining 3525 not shown) Planarity restraints: 3940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 492 " -0.069 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO A 493 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 492 " 0.069 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO C 493 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO C 493 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 493 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 217 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C GLU C 217 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU C 217 " -0.017 2.00e-02 2.50e+03 pdb=" N THR C 218 " -0.016 2.00e-02 2.50e+03 ... (remaining 3937 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 256 2.63 - 3.20: 19098 3.20 - 3.76: 33513 3.76 - 4.33: 49463 4.33 - 4.90: 78989 Nonbonded interactions: 181319 Sorted by model distance: nonbonded pdb=" N GLU D 171 " pdb=" OE1 GLU D 171 " model vdw 2.060 2.520 nonbonded pdb=" N GLU B 171 " pdb=" OE1 GLU B 171 " model vdw 2.060 2.520 nonbonded pdb=" O ASN D 330 " pdb=" OG SER D 331 " model vdw 2.150 2.440 nonbonded pdb=" O ASN B 330 " pdb=" OG SER B 331 " model vdw 2.150 2.440 nonbonded pdb=" O CYS C 62 " pdb=" CA GLY C 67 " model vdw 2.257 3.440 ... (remaining 181314 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.010 Extract box with map and model: 6.640 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 59.820 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.007 0.131 23104 Z= 0.471 Angle : 1.038 13.374 31402 Z= 0.601 Chirality : 0.069 0.945 3528 Planarity : 0.007 0.100 3916 Dihedral : 15.273 89.829 8984 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 1.11 % Allowed : 7.70 % Favored : 91.19 % Rotamer: Outliers : 3.28 % Allowed : 6.73 % Favored : 89.99 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.88 (0.11), residues: 2700 helix: -4.22 (0.06), residues: 1608 sheet: 0.33 (0.67), residues: 44 loop : -3.27 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 56 HIS 0.007 0.001 HIS B 241 PHE 0.036 0.002 PHE B 400 TYR 0.022 0.002 TYR C 560 ARG 0.005 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 342 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7770 (mm) REVERT: B 62 MET cc_start: 0.7843 (ptt) cc_final: 0.7553 (ptp) REVERT: B 152 MET cc_start: 0.9242 (mmm) cc_final: 0.8931 (mmm) REVERT: B 249 MET cc_start: 0.8905 (mtm) cc_final: 0.8564 (mtp) REVERT: B 334 THR cc_start: 0.8933 (t) cc_final: 0.8661 (m) REVERT: B 383 MET cc_start: 0.8954 (mtp) cc_final: 0.8738 (mtm) REVERT: B 474 MET cc_start: 0.9146 (mmm) cc_final: 0.8876 (mmp) REVERT: B 625 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8639 (mtpt) REVERT: C 494 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7771 (mm) REVERT: D 62 MET cc_start: 0.7845 (ptt) cc_final: 0.7554 (ptp) REVERT: D 152 MET cc_start: 0.9244 (mmm) cc_final: 0.8933 (mmm) REVERT: D 249 MET cc_start: 0.8904 (mtm) cc_final: 0.8564 (mtp) REVERT: D 334 THR cc_start: 0.8932 (t) cc_final: 0.8661 (m) REVERT: D 383 MET cc_start: 0.8958 (mtp) cc_final: 0.8741 (mtm) REVERT: D 474 MET cc_start: 0.9148 (mmm) cc_final: 0.8877 (mmp) REVERT: D 625 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8640 (mtpt) outliers start: 78 outliers final: 6 residues processed: 404 average time/residue: 1.2221 time to fit residues: 569.4976 Evaluate side-chains 188 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 680 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 94 GLN ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 293 ASN A 297 ASN A 310 ASN A 365 GLN A 574 GLN B 33 ASN B 42 GLN B 64 ASN B 98 GLN B 101 GLN B 194 ASN B 373 HIS B 493 HIS B 505 HIS B 586 ASN B 599 ASN B 718 ASN C 40 GLN C 94 GLN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN C 293 ASN C 297 ASN C 310 ASN C 365 GLN C 574 GLN D 33 ASN D 42 GLN D 64 ASN D 98 GLN D 101 GLN D 194 ASN D 373 HIS D 493 HIS D 505 HIS D 586 ASN D 599 ASN D 718 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23104 Z= 0.192 Angle : 0.674 9.332 31402 Z= 0.341 Chirality : 0.046 0.493 3528 Planarity : 0.005 0.070 3916 Dihedral : 9.529 59.992 3904 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.67 % Favored : 93.19 % Rotamer: Outliers : 1.85 % Allowed : 13.37 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.14), residues: 2700 helix: -2.05 (0.11), residues: 1604 sheet: 0.29 (0.75), residues: 42 loop : -2.87 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 196 HIS 0.005 0.001 HIS D 241 PHE 0.026 0.001 PHE A 546 TYR 0.016 0.001 TYR C 209 ARG 0.006 0.000 ARG D 678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 194 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7496 (tmm) cc_final: 0.7160 (ttt) REVERT: A 524 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.4240 (p-80) REVERT: B 34 HIS cc_start: 0.8507 (t-170) cc_final: 0.8157 (t70) REVERT: B 152 MET cc_start: 0.9185 (mmm) cc_final: 0.8942 (mmm) REVERT: B 249 MET cc_start: 0.8885 (mtm) cc_final: 0.8603 (mtp) REVERT: B 359 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8216 (tt) REVERT: C 210 MET cc_start: 0.7493 (tmm) cc_final: 0.7161 (ttt) REVERT: C 524 HIS cc_start: 0.5778 (OUTLIER) cc_final: 0.4241 (p-80) REVERT: D 34 HIS cc_start: 0.8503 (t-170) cc_final: 0.8152 (t70) REVERT: D 152 MET cc_start: 0.9185 (mmm) cc_final: 0.8945 (mmm) REVERT: D 249 MET cc_start: 0.8885 (mtm) cc_final: 0.8606 (mtp) REVERT: D 359 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8214 (tt) outliers start: 44 outliers final: 18 residues processed: 224 average time/residue: 1.2353 time to fit residues: 322.5471 Evaluate side-chains 176 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 559 ARG Chi-restraints excluded: chain D residue 689 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 243 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 241 optimal weight: 0.0980 chunk 83 optimal weight: 0.2980 chunk 195 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 574 GLN B 58 ASN B 340 GLN B 718 ASN C 108 HIS ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN C 574 GLN D 58 ASN D 340 GLN D 718 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23104 Z= 0.162 Angle : 0.601 9.616 31402 Z= 0.300 Chirality : 0.043 0.438 3528 Planarity : 0.004 0.061 3916 Dihedral : 8.372 59.141 3894 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.07 % Favored : 93.78 % Rotamer: Outliers : 2.10 % Allowed : 13.62 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 2700 helix: -0.72 (0.13), residues: 1604 sheet: 0.05 (0.68), residues: 42 loop : -2.59 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 241 PHE 0.020 0.001 PHE C 529 TYR 0.017 0.001 TYR A 578 ARG 0.002 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 178 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6965 (mpt) REVERT: A 210 MET cc_start: 0.7560 (tmm) cc_final: 0.7085 (ttt) REVERT: A 524 HIS cc_start: 0.5661 (OUTLIER) cc_final: 0.4276 (p-80) REVERT: B 152 MET cc_start: 0.9116 (mmm) cc_final: 0.8876 (mmm) REVERT: B 171 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5797 (mp0) REVERT: B 249 MET cc_start: 0.8852 (mtm) cc_final: 0.8565 (mtp) REVERT: B 332 MET cc_start: 0.8242 (tpt) cc_final: 0.7831 (tpt) REVERT: B 334 THR cc_start: 0.8911 (t) cc_final: 0.8580 (m) REVERT: B 359 LEU cc_start: 0.8443 (tp) cc_final: 0.8217 (tt) REVERT: B 474 MET cc_start: 0.9159 (mmp) cc_final: 0.8895 (mmm) REVERT: B 475 LYS cc_start: 0.9002 (tttt) cc_final: 0.8778 (tttm) REVERT: C 124 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6963 (mpt) REVERT: C 210 MET cc_start: 0.7561 (tmm) cc_final: 0.7087 (ttt) REVERT: C 524 HIS cc_start: 0.5659 (OUTLIER) cc_final: 0.4276 (p-80) REVERT: D 152 MET cc_start: 0.9118 (mmm) cc_final: 0.8876 (mmm) REVERT: D 171 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5798 (mp0) REVERT: D 249 MET cc_start: 0.8849 (mtm) cc_final: 0.8563 (mtp) REVERT: D 332 MET cc_start: 0.8241 (tpt) cc_final: 0.7829 (tpt) REVERT: D 334 THR cc_start: 0.8911 (t) cc_final: 0.8580 (m) REVERT: D 359 LEU cc_start: 0.8442 (tp) cc_final: 0.8216 (tt) REVERT: D 474 MET cc_start: 0.9161 (mmp) cc_final: 0.8896 (mmm) REVERT: D 475 LYS cc_start: 0.9004 (tttt) cc_final: 0.8779 (tttm) outliers start: 50 outliers final: 18 residues processed: 214 average time/residue: 1.1845 time to fit residues: 297.6659 Evaluate side-chains 186 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 559 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 116 optimal weight: 0.2980 chunk 163 optimal weight: 30.0000 chunk 244 optimal weight: 3.9990 chunk 259 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN B 277 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN D 58 ASN D 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23104 Z= 0.174 Angle : 0.564 7.145 31402 Z= 0.284 Chirality : 0.043 0.411 3528 Planarity : 0.004 0.051 3916 Dihedral : 7.766 57.615 3894 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer: Outliers : 2.02 % Allowed : 14.47 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2700 helix: -0.16 (0.13), residues: 1606 sheet: 0.09 (0.68), residues: 42 loop : -2.36 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 196 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.001 PHE C 529 TYR 0.017 0.001 TYR A 578 ARG 0.002 0.000 ARG D 710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 172 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6899 (mpt) REVERT: A 524 HIS cc_start: 0.5611 (OUTLIER) cc_final: 0.4040 (p-80) REVERT: B 60 GLN cc_start: 0.8342 (pm20) cc_final: 0.8090 (pm20) REVERT: B 249 MET cc_start: 0.8864 (mtm) cc_final: 0.8597 (mtp) REVERT: B 332 MET cc_start: 0.8083 (tpt) cc_final: 0.7784 (tpt) REVERT: B 359 LEU cc_start: 0.8451 (tp) cc_final: 0.8214 (tt) REVERT: B 408 MET cc_start: 0.9101 (mmt) cc_final: 0.8616 (mmt) REVERT: B 475 LYS cc_start: 0.9084 (tttt) cc_final: 0.8844 (tttm) REVERT: B 625 LYS cc_start: 0.8979 (mttt) cc_final: 0.8777 (mtpm) REVERT: C 124 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6899 (mpt) REVERT: C 524 HIS cc_start: 0.5607 (OUTLIER) cc_final: 0.4037 (p-80) REVERT: D 60 GLN cc_start: 0.8340 (pm20) cc_final: 0.8087 (pm20) REVERT: D 249 MET cc_start: 0.8864 (mtm) cc_final: 0.8597 (mtp) REVERT: D 332 MET cc_start: 0.8082 (tpt) cc_final: 0.7784 (tpt) REVERT: D 359 LEU cc_start: 0.8446 (tp) cc_final: 0.8208 (tt) REVERT: D 408 MET cc_start: 0.9100 (mmt) cc_final: 0.8615 (mmt) REVERT: D 475 LYS cc_start: 0.9085 (tttt) cc_final: 0.8844 (tttm) REVERT: D 625 LYS cc_start: 0.8982 (mttt) cc_final: 0.8777 (mtpm) outliers start: 48 outliers final: 16 residues processed: 204 average time/residue: 1.2431 time to fit residues: 296.5047 Evaluate side-chains 168 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 559 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN B 58 ASN B 149 ASN B 718 ASN C 340 ASN C 574 GLN D 34 HIS D 149 ASN D 718 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23104 Z= 0.268 Angle : 0.610 9.172 31402 Z= 0.308 Chirality : 0.045 0.391 3528 Planarity : 0.004 0.047 3916 Dihedral : 7.774 59.660 3894 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 2.48 % Allowed : 15.48 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2700 helix: 0.09 (0.13), residues: 1616 sheet: 0.10 (0.72), residues: 42 loop : -2.16 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.008 0.001 HIS D 34 PHE 0.026 0.001 PHE C 546 TYR 0.016 0.002 TYR B 381 ARG 0.004 0.000 ARG D 710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 162 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6972 (mpt) REVERT: A 156 ASN cc_start: 0.6474 (OUTLIER) cc_final: 0.5788 (p0) REVERT: A 210 MET cc_start: 0.7526 (tmm) cc_final: 0.7144 (ttt) REVERT: A 464 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7994 (tm) REVERT: A 524 HIS cc_start: 0.5865 (OUTLIER) cc_final: 0.4231 (p-80) REVERT: B 60 GLN cc_start: 0.8361 (pm20) cc_final: 0.8088 (pm20) REVERT: B 62 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7825 (ptm) REVERT: B 249 MET cc_start: 0.8870 (mtm) cc_final: 0.8611 (mtp) REVERT: B 332 MET cc_start: 0.8111 (tpt) cc_final: 0.7778 (tpt) REVERT: B 345 HIS cc_start: 0.8071 (t70) cc_final: 0.7714 (t-90) REVERT: B 625 LYS cc_start: 0.8991 (mttt) cc_final: 0.8765 (mtpm) REVERT: C 124 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6971 (mpt) REVERT: C 156 ASN cc_start: 0.6471 (OUTLIER) cc_final: 0.5784 (p0) REVERT: C 210 MET cc_start: 0.7524 (tmm) cc_final: 0.7143 (ttt) REVERT: C 464 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7997 (tm) REVERT: C 524 HIS cc_start: 0.5867 (OUTLIER) cc_final: 0.4233 (p-80) REVERT: D 60 GLN cc_start: 0.8359 (pm20) cc_final: 0.8087 (pm20) REVERT: D 62 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7827 (ptm) REVERT: D 249 MET cc_start: 0.8869 (mtm) cc_final: 0.8611 (mtp) REVERT: D 332 MET cc_start: 0.8110 (tpt) cc_final: 0.7779 (tpt) REVERT: D 345 HIS cc_start: 0.8075 (t70) cc_final: 0.7718 (t-90) REVERT: D 625 LYS cc_start: 0.8993 (mttt) cc_final: 0.8765 (mtpm) outliers start: 59 outliers final: 22 residues processed: 208 average time/residue: 1.2832 time to fit residues: 309.6420 Evaluate side-chains 180 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 527 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 559 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN B 34 HIS B 718 ASN ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN D 34 HIS D 718 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23104 Z= 0.331 Angle : 0.641 10.903 31402 Z= 0.324 Chirality : 0.047 0.377 3528 Planarity : 0.005 0.047 3916 Dihedral : 7.961 59.428 3894 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.04 % Favored : 92.81 % Rotamer: Outliers : 2.94 % Allowed : 16.32 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2700 helix: 0.18 (0.13), residues: 1600 sheet: -0.07 (0.70), residues: 42 loop : -2.06 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 196 HIS 0.009 0.002 HIS D 34 PHE 0.019 0.002 PHE C 546 TYR 0.035 0.002 TYR D 381 ARG 0.004 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 160 time to evaluate : 2.768 Fit side-chains REVERT: A 156 ASN cc_start: 0.6426 (OUTLIER) cc_final: 0.5656 (p0) REVERT: A 210 MET cc_start: 0.7716 (tmm) cc_final: 0.7148 (ttt) REVERT: A 354 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6504 (m-40) REVERT: A 464 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7970 (tm) REVERT: A 502 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5882 (ptm) REVERT: A 524 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.4348 (p-80) REVERT: B 31 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8801 (tptp) REVERT: B 249 MET cc_start: 0.8890 (mtm) cc_final: 0.8619 (mtp) REVERT: B 345 HIS cc_start: 0.8220 (t70) cc_final: 0.7812 (t70) REVERT: B 367 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7996 (p0) REVERT: B 625 LYS cc_start: 0.8971 (mttt) cc_final: 0.8744 (mtpm) REVERT: B 762 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.4988 (t80) REVERT: C 156 ASN cc_start: 0.6419 (OUTLIER) cc_final: 0.5649 (p0) REVERT: C 210 MET cc_start: 0.7715 (tmm) cc_final: 0.7149 (ttt) REVERT: C 354 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6494 (m-40) REVERT: C 464 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7974 (tm) REVERT: C 502 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5884 (ptm) REVERT: C 524 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.4348 (p-80) REVERT: D 31 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8803 (tptp) REVERT: D 249 MET cc_start: 0.8887 (mtm) cc_final: 0.8618 (mtp) REVERT: D 345 HIS cc_start: 0.8220 (t70) cc_final: 0.7811 (t70) REVERT: D 367 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7995 (p0) REVERT: D 625 LYS cc_start: 0.8974 (mttt) cc_final: 0.8746 (mtpm) REVERT: D 762 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.4990 (t80) outliers start: 70 outliers final: 24 residues processed: 212 average time/residue: 1.2417 time to fit residues: 307.2042 Evaluate side-chains 184 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 527 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 189 optimal weight: 0.0000 chunk 146 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN B 34 HIS B 718 ASN ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN D 34 HIS D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23104 Z= 0.222 Angle : 0.599 11.345 31402 Z= 0.300 Chirality : 0.044 0.374 3528 Planarity : 0.004 0.036 3916 Dihedral : 7.731 59.176 3894 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.37 % Favored : 93.48 % Rotamer: Outliers : 2.10 % Allowed : 17.33 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2700 helix: 0.51 (0.14), residues: 1582 sheet: -0.12 (0.71), residues: 42 loop : -1.97 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 196 HIS 0.010 0.001 HIS D 34 PHE 0.026 0.001 PHE A 312 TYR 0.019 0.001 TYR D 381 ARG 0.002 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 153 time to evaluate : 2.630 Fit side-chains REVERT: A 124 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7044 (mpm) REVERT: A 210 MET cc_start: 0.7715 (tmm) cc_final: 0.7135 (ttt) REVERT: A 354 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6619 (m-40) REVERT: A 502 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6152 (ptm) REVERT: A 524 HIS cc_start: 0.6290 (OUTLIER) cc_final: 0.4628 (p-80) REVERT: B 31 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8780 (tptp) REVERT: B 39 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8730 (tt) REVERT: B 249 MET cc_start: 0.8876 (mtm) cc_final: 0.8608 (mtp) REVERT: B 332 MET cc_start: 0.8025 (tpt) cc_final: 0.7671 (tpp) REVERT: B 345 HIS cc_start: 0.8229 (t70) cc_final: 0.7859 (t70) REVERT: B 625 LYS cc_start: 0.8957 (mttt) cc_final: 0.8737 (mtpm) REVERT: B 762 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.4978 (t80) REVERT: C 124 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7045 (mpm) REVERT: C 210 MET cc_start: 0.7717 (tmm) cc_final: 0.7138 (ttt) REVERT: C 354 ASN cc_start: 0.7023 (OUTLIER) cc_final: 0.6617 (m-40) REVERT: C 502 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6154 (ptm) REVERT: C 524 HIS cc_start: 0.6288 (OUTLIER) cc_final: 0.4627 (p-80) REVERT: D 31 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8780 (tptp) REVERT: D 39 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8728 (tt) REVERT: D 249 MET cc_start: 0.8878 (mtm) cc_final: 0.8607 (mtp) REVERT: D 332 MET cc_start: 0.8021 (tpt) cc_final: 0.7673 (tpp) REVERT: D 345 HIS cc_start: 0.8231 (t70) cc_final: 0.7862 (t70) REVERT: D 625 LYS cc_start: 0.8960 (mttt) cc_final: 0.8738 (mtpm) REVERT: D 762 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.4980 (t80) outliers start: 50 outliers final: 18 residues processed: 190 average time/residue: 1.3195 time to fit residues: 290.5009 Evaluate side-chains 179 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 527 ASN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 34 HIS B 718 ASN C 574 GLN D 34 HIS D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23104 Z= 0.162 Angle : 0.576 10.524 31402 Z= 0.285 Chirality : 0.043 0.373 3528 Planarity : 0.004 0.034 3916 Dihedral : 7.419 59.952 3894 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.07 % Favored : 93.78 % Rotamer: Outliers : 1.93 % Allowed : 17.49 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2700 helix: 0.71 (0.14), residues: 1580 sheet: -0.02 (0.73), residues: 42 loop : -1.88 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.011 0.001 HIS D 34 PHE 0.024 0.001 PHE A 312 TYR 0.014 0.001 TYR A 578 ARG 0.001 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 162 time to evaluate : 2.693 Fit side-chains REVERT: A 124 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6902 (mpt) REVERT: A 210 MET cc_start: 0.7721 (tmm) cc_final: 0.7131 (ttt) REVERT: A 354 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6636 (m-40) REVERT: A 502 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6144 (ptm) REVERT: A 524 HIS cc_start: 0.6231 (OUTLIER) cc_final: 0.4571 (p-80) REVERT: B 31 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8784 (tptp) REVERT: B 249 MET cc_start: 0.8847 (mtm) cc_final: 0.8600 (mtp) REVERT: B 332 MET cc_start: 0.7983 (tpt) cc_final: 0.7666 (tpp) REVERT: B 345 HIS cc_start: 0.8233 (t70) cc_final: 0.7858 (t70) REVERT: B 762 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.4983 (t80) REVERT: C 124 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6902 (mpt) REVERT: C 210 MET cc_start: 0.7720 (tmm) cc_final: 0.7133 (ttt) REVERT: C 354 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.6688 (m-40) REVERT: C 502 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6143 (ptm) REVERT: C 524 HIS cc_start: 0.6231 (OUTLIER) cc_final: 0.4572 (p-80) REVERT: D 31 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8783 (tptp) REVERT: D 249 MET cc_start: 0.8846 (mtm) cc_final: 0.8598 (mtp) REVERT: D 332 MET cc_start: 0.7979 (tpt) cc_final: 0.7667 (tpp) REVERT: D 345 HIS cc_start: 0.8236 (t70) cc_final: 0.7860 (t70) REVERT: D 762 PHE cc_start: 0.6067 (OUTLIER) cc_final: 0.4984 (t80) outliers start: 46 outliers final: 14 residues processed: 196 average time/residue: 1.2858 time to fit residues: 292.5490 Evaluate side-chains 174 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 240 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 718 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 718 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23104 Z= 0.252 Angle : 0.617 10.332 31402 Z= 0.306 Chirality : 0.045 0.366 3528 Planarity : 0.004 0.044 3916 Dihedral : 7.446 59.741 3894 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.59 % Favored : 93.26 % Rotamer: Outliers : 1.72 % Allowed : 18.33 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2700 helix: 0.71 (0.14), residues: 1568 sheet: -0.05 (0.73), residues: 42 loop : -1.86 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.012 0.001 HIS B 34 PHE 0.024 0.001 PHE A 312 TYR 0.029 0.002 TYR B 381 ARG 0.002 0.000 ARG D 697 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 2.805 Fit side-chains REVERT: A 354 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6859 (m-40) REVERT: A 502 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6070 (ptm) REVERT: A 524 HIS cc_start: 0.6308 (OUTLIER) cc_final: 0.4644 (p-80) REVERT: B 31 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8789 (tptp) REVERT: B 249 MET cc_start: 0.8868 (mtm) cc_final: 0.8611 (mtp) REVERT: B 332 MET cc_start: 0.7975 (tpt) cc_final: 0.7621 (tpp) REVERT: B 334 THR cc_start: 0.9120 (t) cc_final: 0.8871 (t) REVERT: B 345 HIS cc_start: 0.8267 (t70) cc_final: 0.7893 (t70) REVERT: C 354 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6857 (m-40) REVERT: C 502 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6075 (ptm) REVERT: C 524 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.4643 (p-80) REVERT: D 31 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8790 (tptp) REVERT: D 249 MET cc_start: 0.8868 (mtm) cc_final: 0.8610 (mtp) REVERT: D 332 MET cc_start: 0.7974 (tpt) cc_final: 0.7623 (tpp) REVERT: D 334 THR cc_start: 0.9121 (t) cc_final: 0.8872 (t) REVERT: D 345 HIS cc_start: 0.8273 (t70) cc_final: 0.7898 (t70) outliers start: 41 outliers final: 16 residues processed: 177 average time/residue: 1.3898 time to fit residues: 284.0856 Evaluate side-chains 165 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 574 GLN B 34 HIS B 718 ASN C 194 GLN C 574 GLN D 34 HIS D 718 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23104 Z= 0.185 Angle : 0.599 11.962 31402 Z= 0.295 Chirality : 0.043 0.365 3528 Planarity : 0.004 0.033 3916 Dihedral : 7.242 59.950 3894 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.37 % Favored : 93.48 % Rotamer: Outliers : 1.43 % Allowed : 18.71 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2700 helix: 0.80 (0.14), residues: 1580 sheet: 0.01 (0.73), residues: 42 loop : -1.79 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 104 HIS 0.012 0.001 HIS D 34 PHE 0.025 0.001 PHE A 546 TYR 0.019 0.001 TYR A 224 ARG 0.001 0.000 ARG B 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 2.494 Fit side-chains REVERT: A 124 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.7052 (mpm) REVERT: A 210 MET cc_start: 0.7729 (tmm) cc_final: 0.7081 (tmt) REVERT: A 354 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6974 (m-40) REVERT: A 502 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6254 (ptm) REVERT: A 524 HIS cc_start: 0.6300 (OUTLIER) cc_final: 0.4681 (p-80) REVERT: B 31 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8792 (tptp) REVERT: B 249 MET cc_start: 0.8853 (mtm) cc_final: 0.8598 (mtp) REVERT: B 332 MET cc_start: 0.7937 (tpt) cc_final: 0.7649 (tpp) REVERT: B 345 HIS cc_start: 0.8247 (t70) cc_final: 0.7887 (t70) REVERT: C 124 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.7050 (mpm) REVERT: C 210 MET cc_start: 0.7727 (tmm) cc_final: 0.7080 (tmt) REVERT: C 354 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.6981 (m-40) REVERT: C 502 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6255 (ptm) REVERT: C 524 HIS cc_start: 0.6299 (OUTLIER) cc_final: 0.4680 (p-80) REVERT: D 31 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8792 (tptp) REVERT: D 249 MET cc_start: 0.8852 (mtm) cc_final: 0.8599 (mtp) REVERT: D 332 MET cc_start: 0.7932 (tpt) cc_final: 0.7650 (tpp) REVERT: D 345 HIS cc_start: 0.8251 (t70) cc_final: 0.7890 (t70) outliers start: 34 outliers final: 16 residues processed: 168 average time/residue: 1.3545 time to fit residues: 262.1774 Evaluate side-chains 164 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 218 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 34 HIS B 718 ASN C 574 GLN D 34 HIS D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.144228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086660 restraints weight = 38420.926| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.63 r_work: 0.2892 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23104 Z= 0.164 Angle : 0.584 11.137 31402 Z= 0.288 Chirality : 0.042 0.365 3528 Planarity : 0.004 0.033 3916 Dihedral : 6.978 59.453 3894 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.37 % Favored : 93.48 % Rotamer: Outliers : 1.60 % Allowed : 18.67 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2700 helix: 0.91 (0.14), residues: 1588 sheet: 0.27 (0.75), residues: 42 loop : -1.70 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.012 0.001 HIS D 34 PHE 0.023 0.001 PHE A 312 TYR 0.034 0.001 TYR A 224 ARG 0.001 0.000 ARG B 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7010.55 seconds wall clock time: 126 minutes 56.08 seconds (7616.08 seconds total)