Starting phenix.real_space_refine on Tue Feb 20 03:54:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg6_32478/02_2024/7wg6_32478.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg6_32478/02_2024/7wg6_32478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg6_32478/02_2024/7wg6_32478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg6_32478/02_2024/7wg6_32478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg6_32478/02_2024/7wg6_32478.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg6_32478/02_2024/7wg6_32478.pdb" } resolution = 3.4 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= 0.005 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 17093 2.51 5 N 4370 2.21 5 O 5228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 154": "OE1" <-> "OE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 142": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26808 Number of models: 1 Model: "" Number of chains: 27 Chain: "B" Number of atoms: 8611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8611 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8586 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 54, 'TRANS': 1037} Chain breaks: 6 Chain: "D" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.95, per 1000 atoms: 0.52 Number of scatterers: 26808 At special positions: 0 Unit cell: (147.66, 138.03, 221.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 5228 8.00 N 4370 7.00 C 17093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1201 " - " ASN A 148 " " NAG A1202 " - " ASN A 17 " " NAG A1203 " - " ASN A 343 " " NAG A1204 " - " ASN A 61 " " NAG A1205 " - " ASN A 603 " " NAG A1206 " - " ASN A 657 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 709 " " NAG B1201 " - " ASN B 125 " " NAG B1202 " - " ASN B 17 " " NAG B1203 " - " ASN B 343 " " NAG B1204 " - " ASN B 61 " " NAG B1205 " - " ASN B 603 " " NAG B1206 " - " ASN B 657 " " NAG B1207 " - " ASN B 616 " " NAG B1208 " - " ASN B 709 " " NAG C1201 " - " ASN C 122 " " NAG C1202 " - " ASN C 17 " " NAG C1203 " - " ASN C 343 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 657 " " NAG C1207 " - " ASN C 616 " " NAG C1208 " - " ASN C 709 " " NAG E 1 " - " ASN B 331 " " NAG F 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN A 236 " " NAG L 1 " - " ASN A 331 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG R 1 " - " ASN C 236 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.06 Conformation dependent library (CDL) restraints added in 4.8 seconds 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 46 sheets defined 24.9% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.825A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.134A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 5.113A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.770A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.637A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.301A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.760A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.675A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 removed outlier: 3.708A pdb=" N PHE B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 881 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.750A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.580A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.934A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 984 removed outlier: 3.895A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.137A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.278A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.549A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.930A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.706A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.929A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.516A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.740A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.535A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.695A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.786A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.685A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.676A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.105A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.842A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1033 removed outlier: 3.923A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 5.113A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.910A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.175A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.251A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.645A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.622A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.961A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.624A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.707A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 882 removed outlier: 3.570A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.649A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.793A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.660A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.960A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.036A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.453A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.059A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.616A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 203 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 228 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 205 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 226 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.519A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.146A pdb=" N ARG B 239 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE B 106 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN B 241 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TRP B 104 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 243 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.464A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.733A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.963A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.815A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.597A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.370A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.637A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.562A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.678A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.792A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 203 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 229 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER A 205 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N HIS A 207 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N LEU A 225 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 36 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.731A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.799A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.514A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.702A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.577A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.607A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 451 through 454 removed outlier: 4.661A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.993A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.234A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.746A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.996A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.718A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.725A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 203 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 229 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N SER C 205 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.559A pdb=" N ILE C 105 " --> pdb=" O GLN C 241 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.347A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.968A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.784A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.949A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.619A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.542A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 735 through 736 removed outlier: 3.626A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.567A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2514 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: 11.07 Time building geometry restraints manager: 10.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4288 1.30 - 1.43: 7639 1.43 - 1.57: 15345 1.57 - 1.70: 0 1.70 - 1.83: 147 Bond restraints: 27419 Sorted by residual: bond pdb=" C PHE B 192 " pdb=" O PHE B 192 " ideal model delta sigma weight residual 1.234 1.169 0.065 1.18e-02 7.18e+03 3.04e+01 bond pdb=" CA SER B 205 " pdb=" CB SER B 205 " ideal model delta sigma weight residual 1.533 1.448 0.085 1.66e-02 3.63e+03 2.64e+01 bond pdb=" N ASP B 178 " pdb=" CA ASP B 178 " ideal model delta sigma weight residual 1.458 1.489 -0.031 6.30e-03 2.52e+04 2.39e+01 bond pdb=" C PHE B 194 " pdb=" O PHE B 194 " ideal model delta sigma weight residual 1.234 1.177 0.056 1.17e-02 7.31e+03 2.31e+01 bond pdb=" N ARG A 319 " pdb=" CA ARG A 319 " ideal model delta sigma weight residual 1.457 1.517 -0.059 1.29e-02 6.01e+03 2.12e+01 ... (remaining 27414 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.51: 460 104.51 - 111.96: 13550 111.96 - 119.40: 9105 119.40 - 126.85: 13897 126.85 - 134.30: 274 Bond angle restraints: 37286 Sorted by residual: angle pdb=" C GLU B 226 " pdb=" CA GLU B 226 " pdb=" CB GLU B 226 " ideal model delta sigma weight residual 108.68 97.06 11.62 1.39e+00 5.18e-01 6.99e+01 angle pdb=" N PRO A 322 " pdb=" CA PRO A 322 " pdb=" C PRO A 322 " ideal model delta sigma weight residual 110.80 122.28 -11.48 1.51e+00 4.39e-01 5.78e+01 angle pdb=" CA PHE B 201 " pdb=" C PHE B 201 " pdb=" O PHE B 201 " ideal model delta sigma weight residual 121.16 113.64 7.52 1.13e+00 7.83e-01 4.43e+01 angle pdb=" C ARG A 319 " pdb=" CA ARG A 319 " pdb=" CB ARG A 319 " ideal model delta sigma weight residual 110.42 97.26 13.16 1.99e+00 2.53e-01 4.37e+01 angle pdb=" CA PHE B 201 " pdb=" CB PHE B 201 " pdb=" CG PHE B 201 " ideal model delta sigma weight residual 113.80 120.25 -6.45 1.00e+00 1.00e+00 4.16e+01 ... (remaining 37281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 16136 24.65 - 49.31: 932 49.31 - 73.96: 137 73.96 - 98.61: 49 98.61 - 123.27: 21 Dihedral angle restraints: 17275 sinusoidal: 7674 harmonic: 9601 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 155.43 -62.43 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" C ILE B 210 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " pdb=" CB ILE B 210 " ideal model delta harmonic sigma weight residual -122.00 -139.83 17.83 0 2.50e+00 1.60e-01 5.09e+01 dihedral pdb=" C LYS B 202 " pdb=" N LYS B 202 " pdb=" CA LYS B 202 " pdb=" CB LYS B 202 " ideal model delta harmonic sigma weight residual -122.60 -104.85 -17.75 0 2.50e+00 1.60e-01 5.04e+01 ... (remaining 17272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 4283 0.124 - 0.247: 96 0.247 - 0.371: 25 0.371 - 0.494: 6 0.494 - 0.618: 4 Chirality restraints: 4414 Sorted by residual: chirality pdb=" CA ILE B 210 " pdb=" N ILE B 210 " pdb=" C ILE B 210 " pdb=" CB ILE B 210 " both_signs ideal model delta sigma weight residual False 2.43 1.82 0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" CA PRO B 227 " pdb=" N PRO B 227 " pdb=" C PRO B 227 " pdb=" CB PRO B 227 " both_signs ideal model delta sigma weight residual False 2.72 2.11 0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" CB VAL B 193 " pdb=" CA VAL B 193 " pdb=" CG1 VAL B 193 " pdb=" CG2 VAL B 193 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.58e+00 ... (remaining 4411 not shown) Planarity restraints: 4756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 318 " -0.022 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C PHE A 318 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE A 318 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG A 319 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 617 " 0.020 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C CYS C 617 " -0.067 2.00e-02 2.50e+03 pdb=" O CYS C 617 " 0.025 2.00e-02 2.50e+03 pdb=" N THR C 618 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 146 " -0.028 2.00e-02 2.50e+03 2.16e-02 7.00e+00 pdb=" CG HIS C 146 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS C 146 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS C 146 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 146 " -0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS C 146 " -0.006 2.00e-02 2.50e+03 ... (remaining 4753 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 436 2.66 - 3.22: 24433 3.22 - 3.78: 37791 3.78 - 4.34: 50197 4.34 - 4.90: 84779 Nonbonded interactions: 197636 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.097 2.440 nonbonded pdb=" OG SER A 98 " pdb=" O GLU A 180 " model vdw 2.102 2.440 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.168 2.440 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.192 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OG1 THR B 114 " model vdw 2.207 2.440 ... (remaining 197631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 140 or (resid 141 through 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 627 or resid 633 th \ rough 702 or resid 704 through 1162 or resid 1201 through 1208)) selection = (chain 'B' and (resid 14 through 627 or resid 633 through 702 or resid 704 throu \ gh 1162 or resid 1201 through 1208)) selection = (chain 'C' and (resid 14 through 140 or (resid 141 through 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 1162 or resid 1201 \ through 1208)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'P' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.690 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 69.440 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.005 0.085 27419 Z= 0.313 Angle : 0.787 13.162 37286 Z= 0.457 Chirality : 0.059 0.618 4414 Planarity : 0.004 0.061 4713 Dihedral : 15.841 123.266 10972 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.33 % Favored : 93.33 % Rotamer: Outliers : 1.88 % Allowed : 1.11 % Favored : 97.01 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.13 (0.14), residues: 3254 helix: 0.91 (0.20), residues: 701 sheet: 0.08 (0.20), residues: 664 loop : -1.81 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 64 HIS 0.010 0.001 HIS C 146 PHE 0.033 0.001 PHE B 201 TYR 0.033 0.001 TYR B 204 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 339 time to evaluate : 2.850 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: B 84 LEU cc_start: 0.7795 (mt) cc_final: 0.7495 (mt) REVERT: B 150 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.6272 (tptp) REVERT: B 182 LYS cc_start: 0.0261 (OUTLIER) cc_final: -0.0022 (pptt) REVERT: B 216 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.5733 (mp0) REVERT: B 220 GLN cc_start: 0.7907 (tt0) cc_final: 0.7684 (tt0) REVERT: B 305 SER cc_start: 0.9194 (t) cc_final: 0.8843 (p) REVERT: B 467 ASP cc_start: 0.7548 (p0) cc_final: 0.7224 (p0) REVERT: B 523 THR cc_start: 0.8075 (m) cc_final: 0.7785 (p) REVERT: B 547 LYS cc_start: 0.8166 (mttt) cc_final: 0.7958 (mttp) REVERT: B 569 ILE cc_start: 0.8889 (tt) cc_final: 0.8685 (tt) REVERT: B 886 TRP cc_start: 0.8344 (p90) cc_final: 0.7983 (p90) REVERT: B 887 THR cc_start: 0.9145 (p) cc_final: 0.8815 (t) REVERT: A 134 GLN cc_start: 0.7784 (tp40) cc_final: 0.7476 (tm-30) REVERT: A 498 ARG cc_start: 0.7468 (ptp-110) cc_final: 0.7096 (mtm-85) REVERT: A 673 SER cc_start: 0.8418 (t) cc_final: 0.7702 (p) REVERT: A 814 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7364 (mmtp) REVERT: A 823 PHE cc_start: 0.7822 (m-80) cc_final: 0.7620 (m-80) REVERT: A 886 TRP cc_start: 0.7911 (p90) cc_final: 0.6957 (p90) REVERT: A 1005 GLN cc_start: 0.7363 (tp40) cc_final: 0.6924 (mt0) REVERT: C 30 ASN cc_start: 0.7941 (t0) cc_final: 0.7519 (p0) REVERT: C 52 GLN cc_start: 0.7614 (pm20) cc_final: 0.7295 (pt0) REVERT: C 314 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: C 540 ASN cc_start: 0.7297 (m-40) cc_final: 0.6956 (t0) REVERT: C 955 ASN cc_start: 0.7596 (t0) cc_final: 0.6914 (m-40) REVERT: C 1119 ASN cc_start: 0.7797 (m110) cc_final: 0.7518 (m-40) outliers start: 54 outliers final: 10 residues processed: 386 average time/residue: 0.3830 time to fit residues: 233.3257 Evaluate side-chains 226 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 622 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 155 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN C 148 ASN C 188 ASN C 625 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27419 Z= 0.256 Angle : 0.627 8.996 37286 Z= 0.317 Chirality : 0.047 0.426 4414 Planarity : 0.004 0.059 4713 Dihedral : 9.672 99.928 5043 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.12 % Rotamer: Outliers : 1.53 % Allowed : 10.35 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3254 helix: 0.90 (0.20), residues: 727 sheet: 0.21 (0.20), residues: 664 loop : -1.82 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.008 0.001 HIS B 66 PHE 0.023 0.002 PHE B 906 TYR 0.025 0.002 TYR B 160 ARG 0.006 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.7631 (mt) cc_final: 0.7339 (mt) REVERT: B 236 ASN cc_start: 0.8682 (t0) cc_final: 0.8284 (m-40) REVERT: B 305 SER cc_start: 0.9266 (t) cc_final: 0.8968 (p) REVERT: B 467 ASP cc_start: 0.7454 (p0) cc_final: 0.7225 (p0) REVERT: B 523 THR cc_start: 0.8092 (m) cc_final: 0.7801 (p) REVERT: B 547 LYS cc_start: 0.8187 (mttt) cc_final: 0.7954 (mttt) REVERT: B 569 ILE cc_start: 0.8885 (tt) cc_final: 0.8685 (tt) REVERT: B 1017 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7339 (tt0) REVERT: A 211 ILE cc_start: 0.7461 (mp) cc_final: 0.7150 (pt) REVERT: A 351 TYR cc_start: 0.8513 (p90) cc_final: 0.8090 (p90) REVERT: A 462 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8416 (mmmt) REVERT: A 465 GLU cc_start: 0.7658 (pt0) cc_final: 0.7450 (pt0) REVERT: A 498 ARG cc_start: 0.7503 (ptp-110) cc_final: 0.7148 (mtm-85) REVERT: A 673 SER cc_start: 0.8574 (t) cc_final: 0.7869 (p) REVERT: A 814 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7349 (mmtm) REVERT: A 886 TRP cc_start: 0.7845 (p90) cc_final: 0.7349 (p90) REVERT: A 1005 GLN cc_start: 0.7495 (tp40) cc_final: 0.7088 (mt0) REVERT: C 52 GLN cc_start: 0.7631 (pm20) cc_final: 0.7119 (tt0) REVERT: C 131 CYS cc_start: 0.4114 (t) cc_final: 0.3534 (t) REVERT: C 140 PHE cc_start: 0.8449 (p90) cc_final: 0.8237 (p90) REVERT: C 314 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: C 565 PHE cc_start: 0.7000 (m-10) cc_final: 0.6675 (m-80) REVERT: C 740 MET cc_start: 0.8442 (ttm) cc_final: 0.8111 (ttt) REVERT: C 900 MET cc_start: 0.8157 (mtp) cc_final: 0.7935 (mtm) REVERT: C 955 ASN cc_start: 0.7683 (t0) cc_final: 0.7068 (m-40) outliers start: 44 outliers final: 26 residues processed: 253 average time/residue: 0.3400 time to fit residues: 143.8204 Evaluate side-chains 214 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 297 optimal weight: 0.2980 chunk 321 optimal weight: 0.5980 chunk 264 optimal weight: 8.9990 chunk 295 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 238 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 751 ASN C 625 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27419 Z= 0.181 Angle : 0.568 9.334 37286 Z= 0.285 Chirality : 0.045 0.410 4414 Planarity : 0.004 0.053 4713 Dihedral : 7.793 94.705 5024 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 1.42 % Allowed : 12.60 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.84 (0.14), residues: 3254 helix: 1.18 (0.20), residues: 722 sheet: 0.41 (0.21), residues: 646 loop : -1.70 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.009 0.001 HIS B 207 PHE 0.014 0.001 PHE B 906 TYR 0.018 0.001 TYR B 453 ARG 0.004 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.7574 (mt) cc_final: 0.7301 (mt) REVERT: B 335 LEU cc_start: 0.8810 (mm) cc_final: 0.7799 (tt) REVERT: B 523 THR cc_start: 0.8100 (m) cc_final: 0.7834 (p) REVERT: B 547 LYS cc_start: 0.8246 (mttt) cc_final: 0.7995 (mttp) REVERT: B 915 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8100 (m) REVERT: B 965 GLN cc_start: 0.8249 (tt0) cc_final: 0.7829 (tp40) REVERT: B 1017 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7276 (tt0) REVERT: A 200 TYR cc_start: 0.6523 (m-80) cc_final: 0.5804 (m-80) REVERT: A 351 TYR cc_start: 0.8541 (p90) cc_final: 0.8042 (p90) REVERT: A 462 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8222 (mmmt) REVERT: A 465 GLU cc_start: 0.7517 (pt0) cc_final: 0.7218 (pt0) REVERT: A 498 ARG cc_start: 0.7496 (ptp-110) cc_final: 0.7176 (mtm-85) REVERT: A 673 SER cc_start: 0.8492 (t) cc_final: 0.7798 (p) REVERT: A 814 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7338 (mmtm) REVERT: A 886 TRP cc_start: 0.7895 (p90) cc_final: 0.7404 (p90) REVERT: A 1005 GLN cc_start: 0.7475 (tp40) cc_final: 0.7124 (mt0) REVERT: C 52 GLN cc_start: 0.7674 (pm20) cc_final: 0.7254 (tt0) REVERT: C 131 CYS cc_start: 0.4512 (t) cc_final: 0.3964 (t) REVERT: C 140 PHE cc_start: 0.8504 (p90) cc_final: 0.8274 (p90) REVERT: C 314 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: C 565 PHE cc_start: 0.7109 (m-10) cc_final: 0.6820 (m-10) REVERT: C 740 MET cc_start: 0.8396 (ttm) cc_final: 0.7989 (ttt) REVERT: C 752 LEU cc_start: 0.8465 (tt) cc_final: 0.7875 (mt) REVERT: C 900 MET cc_start: 0.8102 (mtp) cc_final: 0.7867 (mtm) REVERT: C 955 ASN cc_start: 0.7652 (t0) cc_final: 0.7023 (m-40) outliers start: 41 outliers final: 25 residues processed: 235 average time/residue: 0.3357 time to fit residues: 133.5494 Evaluate side-chains 207 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 887 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 316 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 282 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 165 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27419 Z= 0.253 Angle : 0.595 10.569 37286 Z= 0.297 Chirality : 0.050 1.249 4414 Planarity : 0.004 0.055 4713 Dihedral : 6.993 91.848 5018 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.27 % Rotamer: Outliers : 2.19 % Allowed : 14.62 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.87 (0.14), residues: 3254 helix: 1.17 (0.20), residues: 713 sheet: 0.33 (0.20), residues: 664 loop : -1.70 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 64 HIS 0.008 0.001 HIS B 207 PHE 0.022 0.002 PHE B 133 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 184 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 ASN cc_start: 0.6921 (m-40) cc_final: 0.6429 (t0) REVERT: B 335 LEU cc_start: 0.8803 (mm) cc_final: 0.7808 (tt) REVERT: B 350 VAL cc_start: 0.6777 (OUTLIER) cc_final: 0.6574 (t) REVERT: B 408 ARG cc_start: 0.7697 (pmt-80) cc_final: 0.7338 (ppt170) REVERT: B 523 THR cc_start: 0.8087 (m) cc_final: 0.7854 (p) REVERT: B 547 LYS cc_start: 0.8288 (mttt) cc_final: 0.8070 (mttp) REVERT: B 886 TRP cc_start: 0.8767 (p90) cc_final: 0.8402 (p90) REVERT: B 965 GLN cc_start: 0.8299 (tt0) cc_final: 0.7879 (tp40) REVERT: B 969 LYS cc_start: 0.8551 (mttp) cc_final: 0.8322 (mtpp) REVERT: B 1017 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7318 (tt0) REVERT: A 351 TYR cc_start: 0.8590 (p90) cc_final: 0.8138 (p90) REVERT: A 462 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8164 (mmmt) REVERT: A 498 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.7157 (mtm-85) REVERT: A 673 SER cc_start: 0.8558 (t) cc_final: 0.7854 (p) REVERT: A 779 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 814 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7365 (mmtm) REVERT: A 886 TRP cc_start: 0.8055 (p90) cc_final: 0.7451 (p90) REVERT: A 960 ASN cc_start: 0.8110 (t0) cc_final: 0.7909 (t0) REVERT: A 1005 GLN cc_start: 0.7539 (tp40) cc_final: 0.7132 (mt0) REVERT: C 52 GLN cc_start: 0.7628 (pm20) cc_final: 0.7211 (tt0) REVERT: C 126 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7736 (m) REVERT: C 140 PHE cc_start: 0.8570 (p90) cc_final: 0.8248 (p90) REVERT: C 565 PHE cc_start: 0.7165 (m-10) cc_final: 0.6935 (m-10) REVERT: C 740 MET cc_start: 0.8449 (ttm) cc_final: 0.7955 (ttt) REVERT: C 900 MET cc_start: 0.8149 (mtp) cc_final: 0.7932 (mtm) REVERT: C 955 ASN cc_start: 0.7719 (t0) cc_final: 0.7115 (m-40) outliers start: 63 outliers final: 44 residues processed: 235 average time/residue: 0.3424 time to fit residues: 134.9375 Evaluate side-chains 221 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 218 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 161 optimal weight: 0.5980 chunk 283 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 183 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN A 66 HIS A 165 ASN C 137 ASN C 321 GLN C 625 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27419 Z= 0.181 Angle : 0.554 11.666 37286 Z= 0.277 Chirality : 0.044 0.396 4414 Planarity : 0.004 0.051 4713 Dihedral : 6.709 90.990 5013 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 2.22 % Allowed : 15.14 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.76 (0.15), residues: 3254 helix: 1.34 (0.20), residues: 711 sheet: 0.29 (0.20), residues: 691 loop : -1.65 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.009 0.001 HIS B 207 PHE 0.013 0.001 PHE A1121 TYR 0.018 0.001 TYR B 453 ARG 0.003 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 188 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ASN cc_start: 0.6892 (m-40) cc_final: 0.6375 (t0) REVERT: B 298 GLU cc_start: 0.8016 (tp30) cc_final: 0.7650 (tt0) REVERT: B 335 LEU cc_start: 0.8816 (mm) cc_final: 0.7832 (tt) REVERT: B 402 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7386 (pt) REVERT: B 408 ARG cc_start: 0.7703 (pmt-80) cc_final: 0.7305 (ppt170) REVERT: B 523 THR cc_start: 0.8102 (m) cc_final: 0.7890 (p) REVERT: B 547 LYS cc_start: 0.8274 (mttt) cc_final: 0.8010 (mttp) REVERT: B 811 LYS cc_start: 0.6388 (tttm) cc_final: 0.6066 (mttp) REVERT: B 886 TRP cc_start: 0.8753 (p90) cc_final: 0.8417 (p90) REVERT: B 965 GLN cc_start: 0.8270 (tt0) cc_final: 0.7879 (tp40) REVERT: B 969 LYS cc_start: 0.8529 (mttp) cc_final: 0.8309 (mtpp) REVERT: B 1017 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7262 (tt0) REVERT: A 351 TYR cc_start: 0.8583 (p90) cc_final: 0.8164 (p90) REVERT: A 465 GLU cc_start: 0.7408 (pt0) cc_final: 0.7173 (pt0) REVERT: A 498 ARG cc_start: 0.7488 (ptp-110) cc_final: 0.7131 (mtm-85) REVERT: A 586 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: A 673 SER cc_start: 0.8538 (t) cc_final: 0.7832 (p) REVERT: A 814 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7360 (mmtm) REVERT: A 886 TRP cc_start: 0.7936 (p90) cc_final: 0.7362 (p90) REVERT: A 1005 GLN cc_start: 0.7536 (tp40) cc_final: 0.7171 (mt0) REVERT: C 52 GLN cc_start: 0.7618 (pm20) cc_final: 0.7225 (tt0) REVERT: C 126 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7770 (m) REVERT: C 131 CYS cc_start: 0.4535 (t) cc_final: 0.3906 (t) REVERT: C 140 PHE cc_start: 0.8479 (p90) cc_final: 0.8131 (p90) REVERT: C 200 TYR cc_start: 0.7932 (m-80) cc_final: 0.7611 (m-80) REVERT: C 565 PHE cc_start: 0.7153 (m-10) cc_final: 0.6921 (m-10) REVERT: C 900 MET cc_start: 0.8015 (mtp) cc_final: 0.7758 (mtm) REVERT: C 955 ASN cc_start: 0.7674 (t0) cc_final: 0.7137 (m-40) outliers start: 64 outliers final: 39 residues processed: 244 average time/residue: 0.3335 time to fit residues: 137.3326 Evaluate side-chains 221 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 0.7980 chunk 284 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 316 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B1101 HIS A 66 HIS A 165 ASN C 125 ASN C 625 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27419 Z= 0.273 Angle : 0.596 9.709 37286 Z= 0.298 Chirality : 0.046 0.404 4414 Planarity : 0.004 0.054 4713 Dihedral : 6.231 89.514 5013 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.85 % Favored : 93.09 % Rotamer: Outliers : 2.53 % Allowed : 16.25 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.87 (0.14), residues: 3254 helix: 1.22 (0.20), residues: 712 sheet: 0.16 (0.20), residues: 694 loop : -1.69 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.006 0.001 HIS B 207 PHE 0.022 0.002 PHE B 133 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 181 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8436 (t) cc_final: 0.8169 (p) REVERT: B 335 LEU cc_start: 0.8757 (mm) cc_final: 0.7856 (tt) REVERT: B 523 THR cc_start: 0.8136 (m) cc_final: 0.7929 (p) REVERT: B 547 LYS cc_start: 0.8361 (mttt) cc_final: 0.8046 (mttp) REVERT: B 965 GLN cc_start: 0.8269 (tt0) cc_final: 0.7878 (tp40) REVERT: B 969 LYS cc_start: 0.8564 (mttp) cc_final: 0.8328 (mtpp) REVERT: B 1141 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6352 (mt) REVERT: A 351 TYR cc_start: 0.8619 (p90) cc_final: 0.8257 (p90) REVERT: A 462 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8103 (mmmt) REVERT: A 465 GLU cc_start: 0.7463 (pt0) cc_final: 0.7161 (pt0) REVERT: A 498 ARG cc_start: 0.7455 (ptp-110) cc_final: 0.7098 (mtm-85) REVERT: A 586 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: A 673 SER cc_start: 0.8471 (t) cc_final: 0.7784 (p) REVERT: A 779 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7941 (tm-30) REVERT: A 814 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7384 (mmtm) REVERT: A 1005 GLN cc_start: 0.7586 (tp40) cc_final: 0.7213 (mt0) REVERT: C 52 GLN cc_start: 0.7591 (pm20) cc_final: 0.7178 (tt0) REVERT: C 126 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7844 (m) REVERT: C 131 CYS cc_start: 0.4677 (t) cc_final: 0.4082 (t) REVERT: C 140 PHE cc_start: 0.8602 (p90) cc_final: 0.8264 (p90) REVERT: C 200 TYR cc_start: 0.7985 (m-80) cc_final: 0.7601 (m-80) REVERT: C 900 MET cc_start: 0.8101 (mtp) cc_final: 0.7852 (mtm) REVERT: C 955 ASN cc_start: 0.7723 (t0) cc_final: 0.7203 (m-40) outliers start: 73 outliers final: 52 residues processed: 245 average time/residue: 0.3340 time to fit residues: 138.1056 Evaluate side-chains 228 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 173 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 180 optimal weight: 0.0570 chunk 231 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 266 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 315 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 422 ASN A 66 HIS A 165 ASN C 125 ASN C 196 ASN C 207 HIS C 580 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27419 Z= 0.184 Angle : 0.546 9.755 37286 Z= 0.274 Chirality : 0.044 0.391 4414 Planarity : 0.004 0.053 4713 Dihedral : 5.997 88.620 5013 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 2.33 % Allowed : 16.91 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.78 (0.15), residues: 3254 helix: 1.39 (0.20), residues: 711 sheet: 0.17 (0.19), residues: 713 loop : -1.67 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.008 0.001 HIS B 207 PHE 0.015 0.001 PHE B 168 TYR 0.018 0.001 TYR B 453 ARG 0.002 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 181 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8437 (t) cc_final: 0.8049 (m) REVERT: B 335 LEU cc_start: 0.8806 (mm) cc_final: 0.7919 (tt) REVERT: B 402 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7318 (pt) REVERT: B 465 GLU cc_start: 0.7735 (tt0) cc_final: 0.7485 (tt0) REVERT: B 547 LYS cc_start: 0.8331 (mttt) cc_final: 0.8019 (mttp) REVERT: B 811 LYS cc_start: 0.6387 (tttm) cc_final: 0.6073 (mttp) REVERT: B 965 GLN cc_start: 0.8281 (tt0) cc_final: 0.7916 (tp40) REVERT: B 969 LYS cc_start: 0.8551 (mttp) cc_final: 0.8318 (mtpp) REVERT: A 351 TYR cc_start: 0.8609 (p90) cc_final: 0.8237 (p90) REVERT: A 462 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8037 (mmmt) REVERT: A 465 GLU cc_start: 0.7398 (pt0) cc_final: 0.7081 (pt0) REVERT: A 498 ARG cc_start: 0.7503 (ptp-110) cc_final: 0.7136 (mtm-85) REVERT: A 586 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: A 673 SER cc_start: 0.8452 (t) cc_final: 0.7797 (p) REVERT: A 814 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7374 (mmtm) REVERT: A 1005 GLN cc_start: 0.7562 (tp40) cc_final: 0.7178 (mt0) REVERT: C 52 GLN cc_start: 0.7580 (pm20) cc_final: 0.7199 (tt0) REVERT: C 126 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7850 (m) REVERT: C 131 CYS cc_start: 0.4556 (t) cc_final: 0.3951 (t) REVERT: C 140 PHE cc_start: 0.8604 (p90) cc_final: 0.8278 (p90) REVERT: C 200 TYR cc_start: 0.7926 (m-80) cc_final: 0.7562 (m-80) REVERT: C 900 MET cc_start: 0.8072 (mtp) cc_final: 0.7841 (mtm) REVERT: C 955 ASN cc_start: 0.7659 (t0) cc_final: 0.7135 (m-40) outliers start: 67 outliers final: 51 residues processed: 240 average time/residue: 0.3341 time to fit residues: 136.6020 Evaluate side-chains 229 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 175 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 188 optimal weight: 0.0980 chunk 94 optimal weight: 0.0870 chunk 61 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 155 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS C 125 ASN C 207 HIS C 580 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27419 Z= 0.139 Angle : 0.527 9.877 37286 Z= 0.263 Chirality : 0.043 0.380 4414 Planarity : 0.004 0.051 4713 Dihedral : 5.760 87.204 5010 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 2.12 % Allowed : 17.29 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.62 (0.15), residues: 3254 helix: 1.53 (0.20), residues: 719 sheet: 0.29 (0.20), residues: 703 loop : -1.59 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.010 0.001 HIS B 207 PHE 0.028 0.001 PHE B 133 TYR 0.018 0.001 TYR B 453 ARG 0.003 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 183 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8413 (t) cc_final: 0.8057 (m) REVERT: B 298 GLU cc_start: 0.7990 (tp30) cc_final: 0.7523 (tt0) REVERT: B 402 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7267 (pt) REVERT: B 465 GLU cc_start: 0.7731 (tt0) cc_final: 0.7436 (tt0) REVERT: B 547 LYS cc_start: 0.8310 (mttt) cc_final: 0.8011 (mttp) REVERT: B 811 LYS cc_start: 0.6372 (tttm) cc_final: 0.6067 (mttp) REVERT: B 965 GLN cc_start: 0.8262 (tt0) cc_final: 0.7930 (tp40) REVERT: B 969 LYS cc_start: 0.8531 (mttp) cc_final: 0.8307 (mtpp) REVERT: B 1017 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7248 (tt0) REVERT: B 1141 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6267 (mt) REVERT: A 351 TYR cc_start: 0.8576 (p90) cc_final: 0.8193 (p90) REVERT: A 462 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7991 (mmmt) REVERT: A 465 GLU cc_start: 0.7416 (pt0) cc_final: 0.7082 (pt0) REVERT: A 498 ARG cc_start: 0.7541 (ptp-110) cc_final: 0.7157 (mtm-85) REVERT: A 586 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: A 673 SER cc_start: 0.8446 (t) cc_final: 0.7791 (p) REVERT: A 814 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7371 (mmtm) REVERT: A 1005 GLN cc_start: 0.7526 (tp40) cc_final: 0.7149 (mt0) REVERT: C 52 GLN cc_start: 0.7577 (pm20) cc_final: 0.7200 (tt0) REVERT: C 126 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7879 (m) REVERT: C 131 CYS cc_start: 0.4563 (t) cc_final: 0.3954 (t) REVERT: C 140 PHE cc_start: 0.8575 (p90) cc_final: 0.8249 (p90) REVERT: C 200 TYR cc_start: 0.7873 (m-80) cc_final: 0.7525 (m-80) REVERT: C 900 MET cc_start: 0.8037 (mtp) cc_final: 0.7794 (mtm) REVERT: C 955 ASN cc_start: 0.7609 (t0) cc_final: 0.7053 (m-40) outliers start: 61 outliers final: 45 residues processed: 234 average time/residue: 0.3324 time to fit residues: 131.0392 Evaluate side-chains 228 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 179 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 chunk 293 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 265 optimal weight: 20.0000 chunk 277 optimal weight: 3.9990 chunk 292 optimal weight: 0.3980 chunk 192 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS A 66 HIS C 125 ASN C 207 HIS C 580 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27419 Z= 0.182 Angle : 0.537 9.812 37286 Z= 0.268 Chirality : 0.044 0.383 4414 Planarity : 0.004 0.051 4713 Dihedral : 5.669 85.642 5010 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 2.05 % Allowed : 17.53 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.62 (0.15), residues: 3254 helix: 1.55 (0.20), residues: 718 sheet: 0.30 (0.19), residues: 703 loop : -1.60 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.010 0.001 HIS B 207 PHE 0.026 0.001 PHE B 133 TYR 0.018 0.001 TYR B 453 ARG 0.002 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 181 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8478 (t) cc_final: 0.8116 (m) REVERT: B 335 LEU cc_start: 0.8854 (mm) cc_final: 0.7845 (tt) REVERT: B 465 GLU cc_start: 0.7639 (tt0) cc_final: 0.7317 (tt0) REVERT: B 547 LYS cc_start: 0.8320 (mttt) cc_final: 0.8021 (mttp) REVERT: B 811 LYS cc_start: 0.6381 (tttm) cc_final: 0.6078 (mttp) REVERT: B 965 GLN cc_start: 0.8275 (tt0) cc_final: 0.7947 (tp40) REVERT: B 969 LYS cc_start: 0.8528 (mttp) cc_final: 0.8306 (mtpp) REVERT: B 1017 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7271 (tt0) REVERT: B 1141 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6310 (mt) REVERT: A 351 TYR cc_start: 0.8617 (p90) cc_final: 0.8224 (p90) REVERT: A 420 ASP cc_start: 0.7521 (t70) cc_final: 0.7291 (t70) REVERT: A 462 LYS cc_start: 0.8312 (mmmt) cc_final: 0.7981 (mmmt) REVERT: A 465 GLU cc_start: 0.7435 (pt0) cc_final: 0.7079 (pt0) REVERT: A 498 ARG cc_start: 0.7501 (ptp-110) cc_final: 0.7166 (mtm-85) REVERT: A 586 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: A 673 SER cc_start: 0.8460 (t) cc_final: 0.7809 (p) REVERT: A 814 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7406 (mmtm) REVERT: A 1005 GLN cc_start: 0.7554 (tp40) cc_final: 0.7148 (mt0) REVERT: C 52 GLN cc_start: 0.7591 (pm20) cc_final: 0.7212 (tt0) REVERT: C 126 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7891 (m) REVERT: C 131 CYS cc_start: 0.4572 (t) cc_final: 0.4264 (t) REVERT: C 140 PHE cc_start: 0.8571 (p90) cc_final: 0.8243 (p90) REVERT: C 200 TYR cc_start: 0.7980 (m-80) cc_final: 0.7600 (m-80) REVERT: C 900 MET cc_start: 0.8081 (mtp) cc_final: 0.7849 (mtm) REVERT: C 955 ASN cc_start: 0.7674 (t0) cc_final: 0.7089 (m-40) outliers start: 59 outliers final: 47 residues processed: 229 average time/residue: 0.3494 time to fit residues: 134.9309 Evaluate side-chains 225 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 147 optimal weight: 0.1980 chunk 215 optimal weight: 0.0370 chunk 325 optimal weight: 10.0000 chunk 299 optimal weight: 0.6980 chunk 259 optimal weight: 30.0000 chunk 26 optimal weight: 0.0970 chunk 200 optimal weight: 1.9990 chunk 159 optimal weight: 0.0570 chunk 206 optimal weight: 1.9990 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS A 66 HIS C 125 ASN C 196 ASN C 207 HIS C 955 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27419 Z= 0.133 Angle : 0.517 9.792 37286 Z= 0.258 Chirality : 0.043 0.367 4414 Planarity : 0.004 0.051 4713 Dihedral : 5.462 83.164 5010 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 1.81 % Allowed : 17.74 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 (0.15), residues: 3254 helix: 1.72 (0.20), residues: 722 sheet: 0.46 (0.20), residues: 691 loop : -1.54 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.010 0.001 HIS B 207 PHE 0.032 0.001 PHE B 342 TYR 0.023 0.001 TYR B 170 ARG 0.003 0.000 ARG B 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 191 time to evaluate : 3.087 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8504 (t) cc_final: 0.8173 (m) REVERT: B 298 GLU cc_start: 0.7854 (tp30) cc_final: 0.7409 (tt0) REVERT: B 335 LEU cc_start: 0.8839 (mm) cc_final: 0.7828 (tt) REVERT: B 547 LYS cc_start: 0.8267 (mttt) cc_final: 0.7981 (mttp) REVERT: B 586 ASP cc_start: 0.7824 (t0) cc_final: 0.7512 (t0) REVERT: B 811 LYS cc_start: 0.6347 (tttm) cc_final: 0.6065 (mttp) REVERT: B 965 GLN cc_start: 0.8273 (tt0) cc_final: 0.7968 (tp40) REVERT: B 969 LYS cc_start: 0.8508 (mttp) cc_final: 0.8306 (mtpp) REVERT: B 1017 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7237 (tt0) REVERT: B 1141 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6265 (mt) REVERT: A 177 MET cc_start: 0.2322 (mmp) cc_final: 0.0462 (ptt) REVERT: A 351 TYR cc_start: 0.8577 (p90) cc_final: 0.8172 (p90) REVERT: A 462 LYS cc_start: 0.8307 (mmmt) cc_final: 0.7980 (mmmt) REVERT: A 465 GLU cc_start: 0.7395 (pt0) cc_final: 0.7032 (pt0) REVERT: A 498 ARG cc_start: 0.7552 (ptp-110) cc_final: 0.7229 (mtm-85) REVERT: A 586 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: A 673 SER cc_start: 0.8434 (t) cc_final: 0.7775 (p) REVERT: A 814 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7370 (mmtm) REVERT: A 1005 GLN cc_start: 0.7474 (tp40) cc_final: 0.7097 (mt0) REVERT: C 52 GLN cc_start: 0.7597 (pm20) cc_final: 0.7211 (tt0) REVERT: C 126 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8015 (m) REVERT: C 140 PHE cc_start: 0.8545 (p90) cc_final: 0.8222 (p90) REVERT: C 200 TYR cc_start: 0.7897 (m-80) cc_final: 0.7535 (m-80) REVERT: C 900 MET cc_start: 0.8017 (mtp) cc_final: 0.7762 (mtm) REVERT: C 955 ASN cc_start: 0.7481 (t0) cc_final: 0.6989 (m-40) REVERT: C 1010 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7850 (mm110) outliers start: 52 outliers final: 43 residues processed: 233 average time/residue: 0.3451 time to fit residues: 136.5782 Evaluate side-chains 222 residues out of total 2886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 259 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.184826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145745 restraints weight = 33961.653| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.85 r_work: 0.3301 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 27419 Z= 0.360 Angle : 0.699 59.132 37286 Z= 0.385 Chirality : 0.049 0.471 4414 Planarity : 0.004 0.051 4713 Dihedral : 5.467 81.684 5010 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 1.81 % Allowed : 18.06 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.50 (0.15), residues: 3254 helix: 1.65 (0.20), residues: 722 sheet: 0.44 (0.20), residues: 693 loop : -1.54 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.008 0.001 HIS B 207 PHE 0.017 0.001 PHE B 194 TYR 0.017 0.002 TYR B 453 ARG 0.003 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4779.02 seconds wall clock time: 88 minutes 39.91 seconds (5319.91 seconds total)