Starting phenix.real_space_refine on Tue Feb 20 03:54:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwq_29515/02_2024/8fwq_29515_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwq_29515/02_2024/8fwq_29515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwq_29515/02_2024/8fwq_29515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwq_29515/02_2024/8fwq_29515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwq_29515/02_2024/8fwq_29515_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwq_29515/02_2024/8fwq_29515_updated.pdb" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 148 5.16 5 Na 1 4.78 5 C 17140 2.51 5 N 4366 2.21 5 O 5146 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 58": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 503": "NH1" <-> "NH2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ARG 800": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 503": "NH1" <-> "NH2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" 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: 26805 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "B" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "C" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "D" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} 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: 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: "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: 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: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "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: 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: "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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "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: 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: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 73 Unusual residues: {' NA': 1, '2J9': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'2J9': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'2J9': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'2J9': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 13.35, per 1000 atoms: 0.50 Number of scatterers: 26805 At special positions: 0 Unit cell: (97.125, 160.025, 201.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 Na 1 11.00 F 4 9.00 O 5146 8.00 N 4366 7.00 C 17140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.04 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS B 595 " distance=2.11 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.00 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.04 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.04 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS D 595 " distance=1.95 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.00 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.04 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " 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=0, symmetry=0 Links applied BETA1-3 " NAG F 2 " - " BMA F 3 " " BMA I 3 " - " BMA I 4 " " NAG O 2 " - " BMA O 3 " " BMA R 3 " - " BMA R 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG A1002 " - " ASN A 546 " " NAG A1003 " - " ASN A 423 " " NAG A1004 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 423 " " NAG B1003 " - " ASN B 412 " " NAG C1002 " - " ASN C 275 " " NAG C1003 " - " ASN C 546 " " NAG C1004 " - " ASN C 423 " " NAG C1005 " - " ASN C 412 " " NAG D1002 " - " ASN D 275 " " NAG D1003 " - " ASN D 423 " " NAG D1004 " - " ASN D 412 " " NAG E 1 " - " ASN A 751 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN A 430 " " NAG H 1 " - " ASN A 67 " " NAG I 1 " - " ASN B 546 " " NAG J 1 " - " ASN B 751 " " NAG K 1 " - " ASN B 378 " " NAG L 1 " - " ASN B 430 " " NAG M 1 " - " ASN B 67 " " NAG N 1 " - " ASN C 751 " " NAG O 1 " - " ASN C 378 " " NAG P 1 " - " ASN C 430 " " NAG Q 1 " - " ASN C 67 " " NAG R 1 " - " ASN D 546 " " NAG S 1 " - " ASN D 751 " " NAG T 1 " - " ASN D 378 " " NAG U 1 " - " ASN D 430 " " NAG V 1 " - " ASN D 67 " Time building additional restraints: 9.90 Conformation dependent library (CDL) restraints added in 5.0 seconds 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 26 sheets defined 39.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'A' and resid 52 through 66 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 112 through 124 removed outlier: 4.286A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 166 removed outlier: 4.051A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.549A pdb=" N LEU A 182 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.532A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Proline residue: A 192 - end of helix No H-bonds generated for 'chain 'A' and resid 186 through 193' Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 232 through 243 removed outlier: 3.627A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 287 through 299 removed outlier: 3.923A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.888A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 removed outlier: 3.759A pdb=" N MET A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.775A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.768A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 561 through 584 removed outlier: 3.512A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 631 through 661 removed outlier: 3.557A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 689 through 696 Processing helix chain 'A' and resid 700 through 711 removed outlier: 4.103A pdb=" N LYS A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 730 removed outlier: 3.604A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 748 removed outlier: 4.195A pdb=" N VAL A 745 " --> pdb=" O THR A 741 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 removed outlier: 4.136A pdb=" N ILE A 778 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 782 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 783 " --> pdb=" O ILE A 780 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 786 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 822 through 849 removed outlier: 3.646A pdb=" N LEU A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 66 Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'B' and resid 112 through 125 removed outlier: 3.689A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 removed outlier: 4.021A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 186 through 193 removed outlier: 3.691A pdb=" N ALA B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Proline residue: B 192 - end of helix Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.543A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 243 removed outlier: 3.708A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'B' and resid 287 through 299 removed outlier: 3.555A pdb=" N SER B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.599A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 365 removed outlier: 3.698A pdb=" N MET B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 462 through 473 removed outlier: 3.595A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 521 through 524 No H-bonds generated for 'chain 'B' and resid 521 through 524' Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 561 through 584 removed outlier: 3.734A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 608 through 619 removed outlier: 3.736A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 658 removed outlier: 3.666A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 674 No H-bonds generated for 'chain 'B' and resid 671 through 674' Processing helix chain 'B' and resid 689 through 695 Processing helix chain 'B' and resid 700 through 710 removed outlier: 3.610A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 730 removed outlier: 3.580A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 748 removed outlier: 3.570A pdb=" N GLU B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 748 " --> pdb=" O PHE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 788 removed outlier: 3.520A pdb=" N LEU B 785 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 798 removed outlier: 3.791A pdb=" N LYS B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 849 removed outlier: 3.565A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 66 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 112 through 124 removed outlier: 4.286A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 166 removed outlier: 4.051A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.548A pdb=" N LEU C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 193 removed outlier: 3.532A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Proline residue: C 192 - end of helix No H-bonds generated for 'chain 'C' and resid 186 through 193' Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.627A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 263 No H-bonds generated for 'chain 'C' and resid 261 through 263' Processing helix chain 'C' and resid 267 through 269 No H-bonds generated for 'chain 'C' and resid 267 through 269' Processing helix chain 'C' and resid 287 through 299 removed outlier: 3.923A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.888A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 364 removed outlier: 3.760A pdb=" N MET C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 474 removed outlier: 3.775A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.767A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 524 No H-bonds generated for 'chain 'C' and resid 521 through 524' Processing helix chain 'C' and resid 561 through 584 removed outlier: 3.512A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 580 " --> pdb=" O CYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 619 Processing helix chain 'C' and resid 631 through 661 removed outlier: 3.557A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 689 through 696 Processing helix chain 'C' and resid 700 through 711 removed outlier: 4.103A pdb=" N LYS C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 730 removed outlier: 3.604A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 748 removed outlier: 4.197A pdb=" N VAL C 745 " --> pdb=" O THR C 741 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 787 removed outlier: 4.135A pdb=" N ILE C 778 " --> pdb=" O ARG C 775 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE C 782 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 783 " --> pdb=" O ILE C 780 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN C 786 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 822 through 849 removed outlier: 3.647A pdb=" N LEU C 827 " --> pdb=" O ILE C 823 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 66 Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 112 through 125 removed outlier: 3.690A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 166 removed outlier: 4.021A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 184 Processing helix chain 'D' and resid 186 through 193 removed outlier: 3.691A pdb=" N ALA D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Proline residue: D 192 - end of helix Processing helix chain 'D' and resid 212 through 220 removed outlier: 3.543A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.709A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 287 through 299 removed outlier: 3.555A pdb=" N SER D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 335 removed outlier: 3.599A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 365 removed outlier: 3.698A pdb=" N MET D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 462 through 473 removed outlier: 3.595A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 521 through 524 No H-bonds generated for 'chain 'D' and resid 521 through 524' Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 561 through 584 removed outlier: 3.733A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 588 No H-bonds generated for 'chain 'D' and resid 586 through 588' Processing helix chain 'D' and resid 608 through 619 removed outlier: 3.735A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 658 removed outlier: 3.666A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 674 No H-bonds generated for 'chain 'D' and resid 671 through 674' Processing helix chain 'D' and resid 689 through 695 Processing helix chain 'D' and resid 700 through 710 removed outlier: 3.610A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 730 removed outlier: 3.580A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 748 removed outlier: 3.570A pdb=" N GLU D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 748 " --> pdb=" O PHE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 788 removed outlier: 3.521A pdb=" N LEU D 785 " --> pdb=" O ALA D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 798 removed outlier: 3.792A pdb=" N LYS D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 849 removed outlier: 3.564A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 34 through 43 removed outlier: 3.538A pdb=" N ASP A 79 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 40 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 129 through 131 Processing sheet with id= C, first strand: chain 'A' and resid 173 through 176 removed outlier: 6.400A pdb=" N HIS A 253 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE A 228 " --> pdb=" O HIS A 253 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 255 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A 275 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE A 256 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR A 277 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 392 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A 393 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS A 401 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.937A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 432 through 435 removed outlier: 7.104A pdb=" N THR A 477 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL A 435 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU A 479 " --> pdb=" O VAL A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.934A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 752 through 755 removed outlier: 3.597A pdb=" N ILE A 755 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 735 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 34 through 43 removed outlier: 4.201A pdb=" N GLY B 40 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 129 through 131 Processing sheet with id= J, first strand: chain 'B' and resid 200 through 203 removed outlier: 3.597A pdb=" N VAL B 174 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS B 225 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 175 " --> pdb=" O HIS B 225 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE B 227 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN B 275 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE B 256 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N THR B 277 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 278 through 280 removed outlier: 5.921A pdb=" N SER B 393 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS B 401 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 534 through 536 removed outlier: 3.996A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.139A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 34 through 43 removed outlier: 3.538A pdb=" N ASP C 79 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY C 40 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= P, first strand: chain 'C' and resid 173 through 176 removed outlier: 6.399A pdb=" N HIS C 253 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE C 228 " --> pdb=" O HIS C 253 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 255 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C 275 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE C 256 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR C 277 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 392 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER C 393 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS C 401 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.937A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C 373 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 432 through 435 removed outlier: 7.102A pdb=" N THR C 477 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL C 435 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU C 479 " --> pdb=" O VAL C 435 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.935A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 752 through 755 removed outlier: 3.597A pdb=" N ILE C 755 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 735 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 34 through 43 removed outlier: 4.200A pdb=" N GLY D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 129 through 131 Processing sheet with id= W, first strand: chain 'D' and resid 200 through 203 removed outlier: 3.597A pdb=" N VAL D 174 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS D 225 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL D 175 " --> pdb=" O HIS D 225 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE D 227 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN D 275 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE D 256 " --> pdb=" O ASN D 275 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N THR D 277 " --> pdb=" O PHE D 256 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 278 through 280 removed outlier: 5.921A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 534 through 536 removed outlier: 3.995A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 735 through 738 removed outlier: 4.138A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.42 Time building geometry restraints manager: 10.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7479 1.33 - 1.46: 6257 1.46 - 1.58: 13400 1.58 - 1.70: 20 1.70 - 1.82: 252 Bond restraints: 27408 Sorted by residual: bond pdb=" OAA 2J9 C1001 " pdb=" SAP 2J9 C1001 " ideal model delta sigma weight residual 1.452 1.655 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAA 2J9 B1004 " pdb=" SAP 2J9 B1004 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAA 2J9 A1005 " pdb=" SAP 2J9 A1005 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAA 2J9 D1001 " pdb=" SAP 2J9 D1001 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAB 2J9 D1001 " pdb=" SAP 2J9 D1001 " ideal model delta sigma weight residual 1.452 1.649 -0.197 2.00e-02 2.50e+03 9.69e+01 ... (remaining 27403 not shown) Histogram of bond angle deviations from ideal: 59.80 - 77.98: 12 77.98 - 96.16: 0 96.16 - 114.35: 17071 114.35 - 132.53: 19989 132.53 - 150.72: 74 Bond angle restraints: 37146 Sorted by residual: angle pdb=" CAH 2J9 C1001 " pdb=" CAN 2J9 C1001 " pdb=" NAO 2J9 C1001 " ideal model delta sigma weight residual 117.67 150.72 -33.05 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CAH 2J9 A1005 " pdb=" CAN 2J9 A1005 " pdb=" NAO 2J9 A1005 " ideal model delta sigma weight residual 117.67 150.22 -32.55 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAH 2J9 B1004 " pdb=" CAN 2J9 B1004 " pdb=" NAO 2J9 B1004 " ideal model delta sigma weight residual 117.67 149.90 -32.23 3.00e+00 1.11e-01 1.15e+02 angle pdb=" CAH 2J9 D1001 " pdb=" CAN 2J9 D1001 " pdb=" NAO 2J9 D1001 " ideal model delta sigma weight residual 117.67 149.83 -32.16 3.00e+00 1.11e-01 1.15e+02 angle pdb=" CAG 2J9 D1001 " pdb=" CAN 2J9 D1001 " pdb=" NAO 2J9 D1001 " ideal model delta sigma weight residual 118.82 150.21 -31.39 3.00e+00 1.11e-01 1.09e+02 ... (remaining 37141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 16131 22.84 - 45.69: 597 45.69 - 68.53: 184 68.53 - 91.38: 78 91.38 - 114.22: 146 Dihedral angle restraints: 17136 sinusoidal: 7652 harmonic: 9484 Sorted by residual: dihedral pdb=" CA TYR B 478 " pdb=" C TYR B 478 " pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta harmonic sigma weight residual -180.00 -129.67 -50.33 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA TYR D 478 " pdb=" C TYR D 478 " pdb=" N GLU D 479 " pdb=" CA GLU D 479 " ideal model delta harmonic sigma weight residual -180.00 -129.68 -50.32 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ALA B 422 " pdb=" C ALA B 422 " pdb=" N ASN B 423 " pdb=" CA ASN B 423 " ideal model delta harmonic sigma weight residual -180.00 -140.25 -39.75 0 5.00e+00 4.00e-02 6.32e+01 ... (remaining 17133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.463: 4299 0.463 - 0.926: 9 0.926 - 1.389: 1 1.389 - 1.852: 1 1.852 - 2.315: 4 Chirality restraints: 4314 Sorted by residual: chirality pdb=" CAN 2J9 C1001 " pdb=" CAG 2J9 C1001 " pdb=" CAH 2J9 C1001 " pdb=" NAO 2J9 C1001 " both_signs ideal model delta sigma weight residual True 2.32 0.00 2.32 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CAN 2J9 D1001 " pdb=" CAG 2J9 D1001 " pdb=" CAH 2J9 D1001 " pdb=" NAO 2J9 D1001 " both_signs ideal model delta sigma weight residual True 2.32 0.01 2.31 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CAN 2J9 B1004 " pdb=" CAG 2J9 B1004 " pdb=" CAH 2J9 B1004 " pdb=" NAO 2J9 B1004 " both_signs ideal model delta sigma weight residual True 2.32 -0.01 2.31 2.00e-01 2.50e+01 1.33e+02 ... (remaining 4311 not shown) Planarity restraints: 4650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 300 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C ARG B 300 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG B 300 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 301 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 300 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ARG D 300 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG D 300 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU D 301 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 300 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ARG C 300 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG C 300 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU C 301 " -0.020 2.00e-02 2.50e+03 ... (remaining 4647 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4111 2.75 - 3.29: 25643 3.29 - 3.83: 44494 3.83 - 4.36: 52503 4.36 - 4.90: 87535 Nonbonded interactions: 214286 Sorted by model distance: nonbonded pdb=" OG SER C 554 " pdb=" O ASN C 819 " model vdw 2.216 2.440 nonbonded pdb=" OG SER A 554 " pdb=" O ASN A 819 " model vdw 2.216 2.440 nonbonded pdb=" O SER A 632 " pdb=" OG SER B 834 " model vdw 2.245 2.440 nonbonded pdb=" OG SER B 585 " pdb=" OE1 GLU C 841 " model vdw 2.256 2.440 nonbonded pdb=" O SER C 100 " pdb=" OG SER C 344 " model vdw 2.256 2.440 ... (remaining 214281 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 33 through 850 or resid 1002 through 1003)) selection = (chain 'B' and (resid 33 through 850 or resid 1002 through 1003)) selection = (chain 'C' and (resid 33 through 850 or resid 1002 through 1003)) selection = (chain 'D' and (resid 33 through 850 or resid 1002 through 1003)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.400 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: 12.970 Check model and map are aligned: 0.410 Set scattering table: 0.280 Process input model: 66.990 Find NCS groups from input model: 2.320 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: 0.000 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: 88.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.009 0.203 27408 Z= 0.606 Angle : 1.212 33.045 37146 Z= 0.605 Chirality : 0.101 2.315 4314 Planarity : 0.007 0.070 4618 Dihedral : 18.586 114.222 11010 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.87 % Favored : 91.45 % Rotamer: Outliers : 0.28 % Allowed : 3.94 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.11), residues: 3264 helix: -3.56 (0.08), residues: 1332 sheet: -2.94 (0.22), residues: 426 loop : -3.06 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP C 134 HIS 0.013 0.003 HIS B 253 PHE 0.022 0.003 PHE B 446 TYR 0.023 0.003 TYR D 702 ARG 0.015 0.001 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 560 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7044 (mtm) cc_final: 0.6771 (mtt) REVERT: A 57 PHE cc_start: 0.8817 (t80) cc_final: 0.8216 (t80) REVERT: A 155 SER cc_start: 0.9226 (m) cc_final: 0.8772 (p) REVERT: A 156 LEU cc_start: 0.9327 (mt) cc_final: 0.9003 (mt) REVERT: A 172 VAL cc_start: 0.9459 (t) cc_final: 0.9127 (m) REVERT: A 571 CYS cc_start: 0.9092 (m) cc_final: 0.8804 (t) REVERT: A 650 SER cc_start: 0.9122 (m) cc_final: 0.8805 (t) REVERT: B 627 MET cc_start: 0.8609 (mmt) cc_final: 0.8269 (mmm) REVERT: B 633 THR cc_start: 0.8738 (p) cc_final: 0.8252 (t) REVERT: B 811 GLU cc_start: 0.8593 (pt0) cc_final: 0.8308 (pm20) REVERT: C 50 MET cc_start: 0.7134 (mtm) cc_final: 0.6850 (mtt) REVERT: C 57 PHE cc_start: 0.8849 (t80) cc_final: 0.8200 (t80) REVERT: C 155 SER cc_start: 0.9252 (m) cc_final: 0.8767 (p) REVERT: C 156 LEU cc_start: 0.9401 (mt) cc_final: 0.9058 (mt) REVERT: C 172 VAL cc_start: 0.9511 (t) cc_final: 0.9178 (m) REVERT: C 247 MET cc_start: 0.7991 (mtp) cc_final: 0.7051 (mtm) REVERT: C 514 VAL cc_start: 0.8782 (t) cc_final: 0.8468 (p) REVERT: C 571 CYS cc_start: 0.8959 (m) cc_final: 0.8617 (t) REVERT: C 650 SER cc_start: 0.9137 (m) cc_final: 0.8830 (t) REVERT: C 691 MET cc_start: 0.8817 (ptm) cc_final: 0.8572 (ptt) REVERT: C 786 GLN cc_start: 0.8716 (tp40) cc_final: 0.8491 (tt0) REVERT: D 229 ASP cc_start: 0.8375 (t70) cc_final: 0.8147 (t70) REVERT: D 478 TYR cc_start: 0.7762 (p90) cc_final: 0.6713 (p90) REVERT: D 627 MET cc_start: 0.8651 (mmt) cc_final: 0.8013 (mmt) REVERT: D 633 THR cc_start: 0.8794 (p) cc_final: 0.8458 (t) REVERT: D 694 PHE cc_start: 0.8548 (m-80) cc_final: 0.8081 (m-10) REVERT: D 705 MET cc_start: 0.8796 (mtp) cc_final: 0.8334 (mtp) REVERT: D 709 MET cc_start: 0.8967 (mtp) cc_final: 0.8662 (ptp) REVERT: D 750 CYS cc_start: 0.7693 (m) cc_final: 0.7492 (t) REVERT: D 811 GLU cc_start: 0.8553 (pt0) cc_final: 0.8218 (pm20) outliers start: 8 outliers final: 0 residues processed: 566 average time/residue: 0.3807 time to fit residues: 338.0118 Evaluate side-chains 289 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 136 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 189 optimal weight: 20.0000 chunk 294 optimal weight: 0.8980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 141 ASN A 165 GLN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 350 HIS A 456 ASN A 497 GLN A 591 ASN A 593 HIS A 596 ASN A 604 ASN A 610 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 350 HIS B 456 ASN B 495 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN B 802 ASN B 819 ASN C 136 HIS C 141 ASN C 165 GLN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN C 350 HIS C 456 ASN C 497 GLN C 591 ASN C 593 HIS C 596 ASN C 604 ASN C 610 ASN C 622 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 350 HIS D 456 ASN D 495 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN ** D 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27408 Z= 0.257 Angle : 0.834 11.831 37146 Z= 0.401 Chirality : 0.055 0.645 4314 Planarity : 0.005 0.055 4618 Dihedral : 18.728 139.898 4834 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.69 % Favored : 91.97 % Rotamer: Outliers : 2.64 % Allowed : 10.21 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.13), residues: 3264 helix: -1.48 (0.12), residues: 1384 sheet: -2.63 (0.22), residues: 462 loop : -2.82 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 706 HIS 0.006 0.001 HIS C 225 PHE 0.021 0.002 PHE C 584 TYR 0.026 0.002 TYR B 478 ARG 0.008 0.001 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 328 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6473 (mm-30) REVERT: A 57 PHE cc_start: 0.8822 (t80) cc_final: 0.8356 (t80) REVERT: A 323 MET cc_start: 0.8500 (tpp) cc_final: 0.8271 (tpp) REVERT: A 534 MET cc_start: 0.8598 (tpp) cc_final: 0.8075 (ttm) REVERT: A 565 MET cc_start: 0.8683 (mmt) cc_final: 0.7840 (mpp) REVERT: A 571 CYS cc_start: 0.9256 (m) cc_final: 0.8981 (t) REVERT: A 621 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8632 (mm-40) REVERT: A 704 LYS cc_start: 0.9462 (mmmt) cc_final: 0.9176 (tptm) REVERT: B 223 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6575 (mt-10) REVERT: B 234 MET cc_start: 0.8430 (mmp) cc_final: 0.8086 (ttm) REVERT: B 247 MET cc_start: 0.7580 (mtt) cc_final: 0.7244 (mmt) REVERT: B 248 MET cc_start: 0.8072 (mmm) cc_final: 0.7827 (mmm) REVERT: B 311 LEU cc_start: 0.9011 (mp) cc_final: 0.8739 (mt) REVERT: B 322 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9254 (mm) REVERT: B 536 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8671 (pt) REVERT: B 633 THR cc_start: 0.8692 (p) cc_final: 0.8422 (t) REVERT: B 705 MET cc_start: 0.8982 (mtp) cc_final: 0.8755 (ptp) REVERT: B 794 MET cc_start: 0.9328 (mtt) cc_final: 0.9034 (mtt) REVERT: B 810 LYS cc_start: 0.7489 (ptmm) cc_final: 0.7278 (mmtm) REVERT: C 53 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6153 (mm-30) REVERT: C 57 PHE cc_start: 0.8830 (t80) cc_final: 0.8386 (t80) REVERT: C 565 MET cc_start: 0.8669 (mmt) cc_final: 0.7912 (mpp) REVERT: C 571 CYS cc_start: 0.9225 (m) cc_final: 0.8846 (t) REVERT: C 741 THR cc_start: 0.8910 (p) cc_final: 0.8642 (t) REVERT: C 774 TYR cc_start: 0.5946 (m-80) cc_final: 0.5282 (m-10) REVERT: C 786 GLN cc_start: 0.8592 (tp40) cc_final: 0.8254 (tp-100) REVERT: D 152 ASP cc_start: 0.7767 (t0) cc_final: 0.7539 (t0) REVERT: D 223 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6578 (mt-10) REVERT: D 234 MET cc_start: 0.8339 (mmp) cc_final: 0.8099 (ttm) REVERT: D 247 MET cc_start: 0.7616 (mtm) cc_final: 0.7034 (mtt) REVERT: D 248 MET cc_start: 0.8152 (mmm) cc_final: 0.7828 (mmm) REVERT: D 311 LEU cc_start: 0.9007 (mp) cc_final: 0.8772 (mt) REVERT: D 322 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9254 (mm) REVERT: D 469 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7711 (tp30) REVERT: D 536 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8363 (pp) REVERT: D 554 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.8075 (p) REVERT: D 633 THR cc_start: 0.8812 (p) cc_final: 0.8479 (t) REVERT: D 665 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7378 (pp20) REVERT: D 691 MET cc_start: 0.8933 (tmm) cc_final: 0.8710 (tmm) REVERT: D 694 PHE cc_start: 0.8538 (m-80) cc_final: 0.8250 (m-80) REVERT: D 705 MET cc_start: 0.8848 (mtp) cc_final: 0.8407 (mtp) REVERT: D 709 MET cc_start: 0.8910 (mtp) cc_final: 0.8675 (mtm) REVERT: D 811 GLU cc_start: 0.8509 (pt0) cc_final: 0.8260 (pm20) outliers start: 75 outliers final: 33 residues processed: 377 average time/residue: 0.3512 time to fit residues: 219.2709 Evaluate side-chains 299 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 259 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 200 optimal weight: 0.1980 chunk 81 optimal weight: 20.0000 chunk 294 optimal weight: 0.9980 chunk 318 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 292 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 HIS ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27408 Z= 0.213 Angle : 0.779 11.291 37146 Z= 0.365 Chirality : 0.052 0.537 4314 Planarity : 0.005 0.064 4618 Dihedral : 15.798 140.746 4834 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.20 % Favored : 92.52 % Rotamer: Outliers : 3.38 % Allowed : 10.95 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.14), residues: 3264 helix: -0.42 (0.13), residues: 1394 sheet: -2.40 (0.22), residues: 474 loop : -2.61 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 169 HIS 0.008 0.001 HIS A 225 PHE 0.017 0.001 PHE B 228 TYR 0.046 0.001 TYR D 478 ARG 0.009 0.000 ARG C 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 284 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6531 (mm-30) REVERT: A 57 PHE cc_start: 0.8830 (t80) cc_final: 0.8333 (t80) REVERT: A 274 VAL cc_start: 0.4856 (OUTLIER) cc_final: 0.4481 (t) REVERT: A 450 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6768 (t70) REVERT: A 565 MET cc_start: 0.8794 (mmt) cc_final: 0.8047 (mpp) REVERT: A 571 CYS cc_start: 0.9234 (m) cc_final: 0.8998 (t) REVERT: A 649 SER cc_start: 0.9280 (m) cc_final: 0.8840 (t) REVERT: A 677 GLN cc_start: 0.8207 (mp-120) cc_final: 0.8000 (mp10) REVERT: A 687 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7394 (p0) REVERT: A 704 LYS cc_start: 0.9396 (mmmt) cc_final: 0.9164 (tptm) REVERT: A 752 LEU cc_start: 0.9000 (mt) cc_final: 0.8765 (mt) REVERT: B 90 GLU cc_start: 0.8332 (tt0) cc_final: 0.7860 (tt0) REVERT: B 130 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8678 (tp) REVERT: B 223 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6531 (mt-10) REVERT: B 234 MET cc_start: 0.8383 (mmp) cc_final: 0.8100 (ttm) REVERT: B 247 MET cc_start: 0.7500 (mtt) cc_final: 0.7208 (mmt) REVERT: B 311 LEU cc_start: 0.9011 (mp) cc_final: 0.8783 (mt) REVERT: B 322 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9242 (mm) REVERT: B 323 MET cc_start: 0.8980 (tpp) cc_final: 0.8471 (ttm) REVERT: B 468 ARG cc_start: 0.8620 (ttp80) cc_final: 0.7723 (mmm-85) REVERT: B 478 TYR cc_start: 0.7541 (p90) cc_final: 0.6743 (p90) REVERT: B 536 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8415 (pp) REVERT: B 565 MET cc_start: 0.8022 (mmt) cc_final: 0.7773 (mmp) REVERT: B 633 THR cc_start: 0.8685 (p) cc_final: 0.8374 (t) REVERT: B 665 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7258 (tm-30) REVERT: B 738 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8088 (mm-30) REVERT: C 57 PHE cc_start: 0.8856 (t80) cc_final: 0.8327 (t80) REVERT: C 534 MET cc_start: 0.8595 (tpp) cc_final: 0.8151 (ttm) REVERT: C 565 MET cc_start: 0.8701 (mmt) cc_final: 0.7967 (mpp) REVERT: C 571 CYS cc_start: 0.9219 (m) cc_final: 0.8902 (t) REVERT: C 649 SER cc_start: 0.9059 (m) cc_final: 0.8608 (t) REVERT: C 752 LEU cc_start: 0.9056 (mt) cc_final: 0.8826 (mt) REVERT: C 786 GLN cc_start: 0.8548 (tp40) cc_final: 0.8171 (tp-100) REVERT: D 223 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6027 (mt-10) REVERT: D 234 MET cc_start: 0.8322 (mmp) cc_final: 0.8085 (ttm) REVERT: D 248 MET cc_start: 0.8098 (mmm) cc_final: 0.7819 (mmm) REVERT: D 311 LEU cc_start: 0.8970 (mp) cc_final: 0.8749 (mt) REVERT: D 322 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9214 (mm) REVERT: D 323 MET cc_start: 0.9054 (tpp) cc_final: 0.8558 (ttm) REVERT: D 469 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7742 (tp30) REVERT: D 501 MET cc_start: 0.8937 (mmm) cc_final: 0.8701 (mmm) REVERT: D 536 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8512 (pp) REVERT: D 565 MET cc_start: 0.8110 (mmt) cc_final: 0.7886 (mmp) REVERT: D 627 MET cc_start: 0.8803 (mmm) cc_final: 0.8058 (mtt) REVERT: D 633 THR cc_start: 0.8760 (p) cc_final: 0.8394 (t) REVERT: D 665 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7319 (pp20) REVERT: D 694 PHE cc_start: 0.8515 (m-80) cc_final: 0.8213 (m-80) REVERT: D 705 MET cc_start: 0.8939 (mtp) cc_final: 0.8466 (mtp) REVERT: D 738 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8053 (mm-30) REVERT: D 811 GLU cc_start: 0.8691 (pt0) cc_final: 0.8441 (pm20) outliers start: 96 outliers final: 45 residues processed: 345 average time/residue: 0.3435 time to fit residues: 198.1534 Evaluate side-chains 308 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 254 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 793 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 2.9990 chunk 221 optimal weight: 0.0010 chunk 152 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 295 optimal weight: 0.0060 chunk 313 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 overall best weight: 0.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27408 Z= 0.174 Angle : 0.734 11.362 37146 Z= 0.340 Chirality : 0.050 0.515 4314 Planarity : 0.004 0.060 4618 Dihedral : 13.396 140.139 4834 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.08 % Favored : 92.62 % Rotamer: Outliers : 2.54 % Allowed : 12.43 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3264 helix: 0.11 (0.14), residues: 1394 sheet: -1.80 (0.25), residues: 416 loop : -2.37 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 169 HIS 0.004 0.001 HIS B 253 PHE 0.013 0.001 PHE A 224 TYR 0.019 0.001 TYR A 733 ARG 0.006 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 284 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8816 (t80) cc_final: 0.8276 (t80) REVERT: A 234 MET cc_start: 0.8341 (mpp) cc_final: 0.8088 (mpp) REVERT: A 450 ASP cc_start: 0.7018 (OUTLIER) cc_final: 0.6777 (t70) REVERT: A 534 MET cc_start: 0.8489 (tpp) cc_final: 0.8112 (ttm) REVERT: A 565 MET cc_start: 0.8769 (mmt) cc_final: 0.8025 (mpp) REVERT: A 649 SER cc_start: 0.9115 (m) cc_final: 0.8797 (t) REVERT: A 677 GLN cc_start: 0.8188 (mp-120) cc_final: 0.7956 (mp10) REVERT: A 704 LYS cc_start: 0.9369 (mmmt) cc_final: 0.9141 (tptt) REVERT: B 90 GLU cc_start: 0.8306 (tt0) cc_final: 0.7884 (tt0) REVERT: B 130 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8456 (tt) REVERT: B 218 MET cc_start: 0.8424 (tpp) cc_final: 0.8156 (tpp) REVERT: B 234 MET cc_start: 0.8385 (mmp) cc_final: 0.8159 (ttm) REVERT: B 322 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9175 (mm) REVERT: B 323 MET cc_start: 0.8916 (tpp) cc_final: 0.8594 (tpp) REVERT: B 329 VAL cc_start: 0.8570 (t) cc_final: 0.8366 (p) REVERT: B 360 MET cc_start: 0.7998 (mmm) cc_final: 0.7753 (mmm) REVERT: B 468 ARG cc_start: 0.8655 (ttp80) cc_final: 0.7807 (mmm160) REVERT: B 536 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8279 (pp) REVERT: B 633 THR cc_start: 0.8639 (p) cc_final: 0.8319 (t) REVERT: B 665 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7189 (pp20) REVERT: B 705 MET cc_start: 0.9134 (mtp) cc_final: 0.8855 (ptp) REVERT: B 738 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7961 (mm-30) REVERT: B 770 MET cc_start: 0.8803 (tpt) cc_final: 0.8590 (mmt) REVERT: C 57 PHE cc_start: 0.8851 (t80) cc_final: 0.8322 (t80) REVERT: C 245 MET cc_start: 0.8180 (ppp) cc_final: 0.7470 (ppp) REVERT: C 347 CYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5567 (p) REVERT: C 450 ASP cc_start: 0.6697 (p0) cc_final: 0.6352 (t70) REVERT: C 565 MET cc_start: 0.8710 (mmt) cc_final: 0.7947 (mpp) REVERT: C 571 CYS cc_start: 0.9221 (m) cc_final: 0.8924 (t) REVERT: C 645 LEU cc_start: 0.8684 (tp) cc_final: 0.8421 (tt) REVERT: C 649 SER cc_start: 0.9029 (m) cc_final: 0.8800 (t) REVERT: C 740 THR cc_start: 0.9273 (p) cc_final: 0.8981 (t) REVERT: C 786 GLN cc_start: 0.8523 (tp40) cc_final: 0.8288 (tt0) REVERT: D 90 GLU cc_start: 0.8542 (tt0) cc_final: 0.8072 (tt0) REVERT: D 218 MET cc_start: 0.7935 (tpp) cc_final: 0.7651 (tpp) REVERT: D 247 MET cc_start: 0.7327 (mtm) cc_final: 0.7096 (mtt) REVERT: D 248 MET cc_start: 0.8053 (mmm) cc_final: 0.7758 (mmm) REVERT: D 322 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9185 (mm) REVERT: D 323 MET cc_start: 0.9019 (tpp) cc_final: 0.8307 (tpp) REVERT: D 501 MET cc_start: 0.9041 (mmm) cc_final: 0.8396 (mmm) REVERT: D 536 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8315 (pp) REVERT: D 565 MET cc_start: 0.7995 (mmt) cc_final: 0.7765 (mmp) REVERT: D 627 MET cc_start: 0.8734 (mmm) cc_final: 0.8039 (mtt) REVERT: D 633 THR cc_start: 0.8671 (p) cc_final: 0.8319 (t) REVERT: D 665 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7377 (pp20) REVERT: D 694 PHE cc_start: 0.8505 (m-80) cc_final: 0.8214 (m-80) REVERT: D 705 MET cc_start: 0.9100 (mtp) cc_final: 0.8473 (mtp) REVERT: D 738 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7892 (mm-30) REVERT: D 811 GLU cc_start: 0.8740 (pt0) cc_final: 0.8480 (pm20) outliers start: 72 outliers final: 33 residues processed: 330 average time/residue: 0.3413 time to fit residues: 187.8759 Evaluate side-chains 287 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 247 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 793 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 233 optimal weight: 0.4980 chunk 129 optimal weight: 0.0980 chunk 267 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 549 ASN ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27408 Z= 0.212 Angle : 0.725 12.308 37146 Z= 0.338 Chirality : 0.050 0.529 4314 Planarity : 0.004 0.064 4618 Dihedral : 12.188 140.763 4834 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.32 % Favored : 92.46 % Rotamer: Outliers : 3.20 % Allowed : 12.61 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.44 (0.15), residues: 3264 helix: 0.44 (0.14), residues: 1378 sheet: -1.60 (0.25), residues: 436 loop : -2.15 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 169 HIS 0.005 0.001 HIS C 225 PHE 0.015 0.001 PHE D 708 TYR 0.020 0.001 TYR B 478 ARG 0.005 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 262 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9239 (mm) REVERT: A 57 PHE cc_start: 0.8851 (t80) cc_final: 0.8391 (t80) REVERT: A 234 MET cc_start: 0.8526 (mpp) cc_final: 0.8146 (mpp) REVERT: A 450 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6716 (t70) REVERT: A 501 MET cc_start: 0.8555 (mmm) cc_final: 0.8036 (tpt) REVERT: A 565 MET cc_start: 0.8788 (mmt) cc_final: 0.8121 (mpp) REVERT: A 645 LEU cc_start: 0.8651 (tp) cc_final: 0.8308 (tt) REVERT: A 649 SER cc_start: 0.9150 (m) cc_final: 0.8802 (t) REVERT: A 705 MET cc_start: 0.8750 (mmp) cc_final: 0.8510 (mmm) REVERT: A 742 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8697 (mt) REVERT: B 90 GLU cc_start: 0.8333 (tt0) cc_final: 0.7890 (tt0) REVERT: B 130 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8588 (tp) REVERT: B 223 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6513 (mt-10) REVERT: B 234 MET cc_start: 0.8437 (mmp) cc_final: 0.8139 (ttm) REVERT: B 322 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9244 (mm) REVERT: B 468 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8010 (mmm160) REVERT: B 536 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8316 (pp) REVERT: B 633 THR cc_start: 0.8662 (p) cc_final: 0.8334 (t) REVERT: B 665 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7187 (pp20) REVERT: B 738 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8041 (mm-30) REVERT: C 55 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8925 (mm) REVERT: C 57 PHE cc_start: 0.8868 (t80) cc_final: 0.8400 (t80) REVERT: C 245 MET cc_start: 0.8041 (ppp) cc_final: 0.7475 (ppp) REVERT: C 347 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5668 (p) REVERT: C 450 ASP cc_start: 0.6700 (p0) cc_final: 0.6346 (t70) REVERT: C 534 MET cc_start: 0.8483 (tpp) cc_final: 0.8132 (ttm) REVERT: C 565 MET cc_start: 0.8751 (mmt) cc_final: 0.7973 (mpp) REVERT: C 571 CYS cc_start: 0.9198 (m) cc_final: 0.8956 (t) REVERT: C 645 LEU cc_start: 0.8930 (tp) cc_final: 0.8659 (tt) REVERT: C 649 SER cc_start: 0.9119 (m) cc_final: 0.8828 (t) REVERT: C 709 MET cc_start: 0.9005 (mtm) cc_final: 0.8368 (mtt) REVERT: C 786 GLN cc_start: 0.8534 (tp40) cc_final: 0.8200 (tt0) REVERT: D 90 GLU cc_start: 0.8579 (tt0) cc_final: 0.8110 (tt0) REVERT: D 223 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6594 (mt-10) REVERT: D 248 MET cc_start: 0.8041 (mmm) cc_final: 0.7762 (mmm) REVERT: D 322 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9210 (mm) REVERT: D 360 MET cc_start: 0.7892 (mmm) cc_final: 0.7487 (mmm) REVERT: D 536 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8410 (pp) REVERT: D 565 MET cc_start: 0.8046 (mmt) cc_final: 0.7809 (mmp) REVERT: D 627 MET cc_start: 0.8786 (mmm) cc_final: 0.8112 (mtt) REVERT: D 633 THR cc_start: 0.8752 (p) cc_final: 0.8366 (t) REVERT: D 665 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7403 (pp20) REVERT: D 694 PHE cc_start: 0.8532 (m-80) cc_final: 0.8187 (m-80) REVERT: D 705 MET cc_start: 0.9057 (mtp) cc_final: 0.8470 (mtp) REVERT: D 738 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7989 (mm-30) REVERT: D 770 MET cc_start: 0.8856 (tpt) cc_final: 0.8520 (mmt) outliers start: 91 outliers final: 52 residues processed: 326 average time/residue: 0.3252 time to fit residues: 179.5111 Evaluate side-chains 300 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 238 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 3.9990 chunk 282 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 183 optimal weight: 0.0020 chunk 77 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 260 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27408 Z= 0.162 Angle : 0.713 13.083 37146 Z= 0.325 Chirality : 0.049 0.502 4314 Planarity : 0.004 0.057 4618 Dihedral : 11.501 140.581 4834 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.02 % Favored : 92.80 % Rotamer: Outliers : 2.92 % Allowed : 13.70 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.28 (0.15), residues: 3264 helix: 0.63 (0.14), residues: 1396 sheet: -1.63 (0.25), residues: 448 loop : -2.13 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 169 HIS 0.004 0.001 HIS B 253 PHE 0.012 0.001 PHE D 579 TYR 0.015 0.001 TYR B 478 ARG 0.003 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 273 time to evaluate : 3.003 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: A 57 PHE cc_start: 0.8821 (t80) cc_final: 0.8345 (t80) REVERT: A 245 MET cc_start: 0.8103 (ppp) cc_final: 0.7385 (ppp) REVERT: A 347 CYS cc_start: 0.6292 (OUTLIER) cc_final: 0.5912 (p) REVERT: A 450 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6577 (t70) REVERT: A 534 MET cc_start: 0.8334 (tpp) cc_final: 0.7965 (ttm) REVERT: A 565 MET cc_start: 0.8783 (mmt) cc_final: 0.8080 (mpp) REVERT: A 645 LEU cc_start: 0.8630 (tp) cc_final: 0.8217 (tt) REVERT: A 649 SER cc_start: 0.9136 (m) cc_final: 0.8894 (t) REVERT: A 691 MET cc_start: 0.8571 (ptp) cc_final: 0.8358 (ptp) REVERT: A 705 MET cc_start: 0.9075 (mmp) cc_final: 0.8617 (mmp) REVERT: B 90 GLU cc_start: 0.8328 (tt0) cc_final: 0.7883 (tt0) REVERT: B 130 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 223 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6472 (mt-10) REVERT: B 228 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8793 (m-10) REVERT: B 322 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9143 (mm) REVERT: B 323 MET cc_start: 0.8906 (tpp) cc_final: 0.8323 (ttm) REVERT: B 389 LEU cc_start: 0.9264 (mt) cc_final: 0.8849 (mt) REVERT: B 468 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8029 (mmp80) REVERT: B 501 MET cc_start: 0.8665 (mmm) cc_final: 0.7963 (mmm) REVERT: B 536 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8184 (pp) REVERT: B 633 THR cc_start: 0.8629 (p) cc_final: 0.8284 (t) REVERT: B 665 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7188 (pp20) REVERT: B 737 MET cc_start: 0.7335 (tmm) cc_final: 0.6904 (tmm) REVERT: B 738 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7979 (mm-30) REVERT: C 57 PHE cc_start: 0.8873 (t80) cc_final: 0.8396 (t80) REVERT: C 245 MET cc_start: 0.7778 (ppp) cc_final: 0.7223 (ppp) REVERT: C 347 CYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5652 (p) REVERT: C 450 ASP cc_start: 0.6475 (p0) cc_final: 0.6245 (t70) REVERT: C 501 MET cc_start: 0.8487 (mmm) cc_final: 0.8156 (tpt) REVERT: C 534 MET cc_start: 0.8599 (tpp) cc_final: 0.8178 (ttm) REVERT: C 565 MET cc_start: 0.8750 (mmt) cc_final: 0.7972 (mpp) REVERT: C 571 CYS cc_start: 0.9212 (m) cc_final: 0.9007 (t) REVERT: C 645 LEU cc_start: 0.8793 (tp) cc_final: 0.8466 (tt) REVERT: C 649 SER cc_start: 0.9000 (m) cc_final: 0.8794 (t) REVERT: C 740 THR cc_start: 0.9304 (p) cc_final: 0.8934 (t) REVERT: D 90 GLU cc_start: 0.8535 (tt0) cc_final: 0.8047 (tt0) REVERT: D 228 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8917 (m-10) REVERT: D 247 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6837 (mmt) REVERT: D 248 MET cc_start: 0.7962 (mmm) cc_final: 0.7689 (mmm) REVERT: D 322 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9167 (mm) REVERT: D 323 MET cc_start: 0.8941 (tpp) cc_final: 0.8501 (ttm) REVERT: D 536 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8275 (pp) REVERT: D 565 MET cc_start: 0.8004 (mmt) cc_final: 0.7768 (mmp) REVERT: D 633 THR cc_start: 0.8737 (p) cc_final: 0.8332 (t) REVERT: D 665 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7415 (pp20) REVERT: D 694 PHE cc_start: 0.8547 (m-80) cc_final: 0.8202 (m-80) REVERT: D 705 MET cc_start: 0.8996 (mtp) cc_final: 0.8424 (mtp) REVERT: D 737 MET cc_start: 0.7169 (tmm) cc_final: 0.6861 (tmm) REVERT: D 738 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7930 (mm-30) outliers start: 83 outliers final: 50 residues processed: 331 average time/residue: 0.3293 time to fit residues: 183.7913 Evaluate side-chains 299 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 238 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 263 optimal weight: 0.3980 chunk 175 optimal weight: 0.9980 chunk 312 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 818 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27408 Z= 0.198 Angle : 0.731 13.103 37146 Z= 0.335 Chirality : 0.049 0.498 4314 Planarity : 0.004 0.060 4618 Dihedral : 11.031 136.646 4834 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 3.20 % Allowed : 13.52 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3264 helix: 0.72 (0.14), residues: 1394 sheet: -1.52 (0.25), residues: 440 loop : -2.04 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 169 HIS 0.005 0.001 HIS B 253 PHE 0.013 0.001 PHE D 166 TYR 0.014 0.001 TYR B 478 ARG 0.005 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 246 time to evaluate : 3.136 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: A 57 PHE cc_start: 0.8848 (t80) cc_final: 0.8415 (t80) REVERT: A 234 MET cc_start: 0.8857 (mpp) cc_final: 0.8458 (mpp) REVERT: A 245 MET cc_start: 0.8147 (ppp) cc_final: 0.7491 (ppp) REVERT: A 347 CYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5900 (p) REVERT: A 450 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6655 (t70) REVERT: A 501 MET cc_start: 0.8542 (mmm) cc_final: 0.8069 (tpt) REVERT: A 534 MET cc_start: 0.8527 (tpp) cc_final: 0.8036 (ttm) REVERT: A 565 MET cc_start: 0.8817 (mmt) cc_final: 0.8088 (mpp) REVERT: A 649 SER cc_start: 0.9122 (m) cc_final: 0.8824 (t) REVERT: A 691 MET cc_start: 0.8500 (ptp) cc_final: 0.8251 (ptp) REVERT: A 705 MET cc_start: 0.8892 (mmp) cc_final: 0.8648 (mmp) REVERT: A 740 THR cc_start: 0.9353 (p) cc_final: 0.8977 (t) REVERT: B 50 MET cc_start: 0.3333 (ttp) cc_final: 0.2901 (tmm) REVERT: B 90 GLU cc_start: 0.8326 (tt0) cc_final: 0.7910 (tt0) REVERT: B 130 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8563 (tp) REVERT: B 223 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6464 (mt-10) REVERT: B 228 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8832 (m-10) REVERT: B 322 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9163 (mm) REVERT: B 323 MET cc_start: 0.8963 (tpp) cc_final: 0.8491 (ttm) REVERT: B 389 LEU cc_start: 0.9262 (mt) cc_final: 0.8841 (mt) REVERT: B 468 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8042 (mmp80) REVERT: B 536 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8559 (pp) REVERT: B 633 THR cc_start: 0.8643 (p) cc_final: 0.8271 (t) REVERT: B 665 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7125 (pp20) REVERT: B 737 MET cc_start: 0.7444 (tmm) cc_final: 0.7061 (tmm) REVERT: B 800 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.5981 (ttp80) REVERT: C 57 PHE cc_start: 0.8893 (t80) cc_final: 0.8426 (t80) REVERT: C 245 MET cc_start: 0.7790 (ppp) cc_final: 0.7182 (ppp) REVERT: C 347 CYS cc_start: 0.6129 (OUTLIER) cc_final: 0.5677 (p) REVERT: C 450 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.6246 (t70) REVERT: C 501 MET cc_start: 0.8511 (mmm) cc_final: 0.7811 (tpt) REVERT: C 565 MET cc_start: 0.8756 (mmt) cc_final: 0.7999 (mpp) REVERT: C 645 LEU cc_start: 0.8851 (tp) cc_final: 0.8587 (tt) REVERT: C 649 SER cc_start: 0.9062 (m) cc_final: 0.8828 (t) REVERT: C 705 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8552 (mmm) REVERT: C 709 MET cc_start: 0.9041 (mtm) cc_final: 0.8404 (mtt) REVERT: D 90 GLU cc_start: 0.8591 (tt0) cc_final: 0.8105 (tt0) REVERT: D 218 MET cc_start: 0.7959 (tpp) cc_final: 0.7719 (tpp) REVERT: D 228 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8841 (m-10) REVERT: D 248 MET cc_start: 0.8041 (mmm) cc_final: 0.7787 (mmm) REVERT: D 322 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9188 (mm) REVERT: D 323 MET cc_start: 0.8998 (tpp) cc_final: 0.8444 (ttm) REVERT: D 360 MET cc_start: 0.7801 (mmm) cc_final: 0.7495 (mmm) REVERT: D 501 MET cc_start: 0.8818 (mmm) cc_final: 0.8199 (mmm) REVERT: D 536 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8457 (pp) REVERT: D 565 MET cc_start: 0.8021 (mmt) cc_final: 0.7787 (mmp) REVERT: D 633 THR cc_start: 0.8765 (p) cc_final: 0.8347 (t) REVERT: D 665 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7355 (pp20) REVERT: D 694 PHE cc_start: 0.8617 (m-80) cc_final: 0.8252 (m-80) REVERT: D 705 MET cc_start: 0.9009 (mtp) cc_final: 0.8452 (mtp) REVERT: D 737 MET cc_start: 0.7208 (tmm) cc_final: 0.6988 (tmm) REVERT: D 738 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8039 (mm-30) outliers start: 91 outliers final: 58 residues processed: 306 average time/residue: 0.3275 time to fit residues: 169.4677 Evaluate side-chains 303 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 231 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 605 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 198 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27408 Z= 0.188 Angle : 0.731 12.547 37146 Z= 0.336 Chirality : 0.048 0.495 4314 Planarity : 0.004 0.058 4618 Dihedral : 10.600 139.399 4834 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 2.78 % Allowed : 14.58 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3264 helix: 0.86 (0.15), residues: 1390 sheet: -1.41 (0.25), residues: 430 loop : -2.01 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP C 169 HIS 0.005 0.001 HIS B 253 PHE 0.023 0.001 PHE A 584 TYR 0.012 0.001 TYR B 478 ARG 0.003 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 246 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8893 (t80) cc_final: 0.8432 (t80) REVERT: A 234 MET cc_start: 0.8896 (mpp) cc_final: 0.8537 (mpp) REVERT: A 245 MET cc_start: 0.8137 (ppp) cc_final: 0.7536 (ppp) REVERT: A 323 MET cc_start: 0.8325 (mmt) cc_final: 0.8059 (mmt) REVERT: A 347 CYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5875 (p) REVERT: A 450 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6474 (t0) REVERT: A 501 MET cc_start: 0.8551 (mmm) cc_final: 0.7977 (tpt) REVERT: A 534 MET cc_start: 0.8525 (tpp) cc_final: 0.8087 (ttm) REVERT: A 565 MET cc_start: 0.8817 (mmt) cc_final: 0.8059 (mpp) REVERT: A 649 SER cc_start: 0.9155 (m) cc_final: 0.8834 (t) REVERT: A 705 MET cc_start: 0.8930 (mmp) cc_final: 0.8718 (mmm) REVERT: A 740 THR cc_start: 0.9414 (p) cc_final: 0.9062 (t) REVERT: B 50 MET cc_start: 0.3293 (ttp) cc_final: 0.2749 (tmm) REVERT: B 90 GLU cc_start: 0.8382 (tt0) cc_final: 0.7957 (tt0) REVERT: B 223 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: B 228 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8851 (m-10) REVERT: B 322 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9180 (mm) REVERT: B 389 LEU cc_start: 0.9276 (mt) cc_final: 0.8863 (mt) REVERT: B 468 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8054 (mmp80) REVERT: B 536 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8534 (pp) REVERT: B 633 THR cc_start: 0.8649 (p) cc_final: 0.8278 (t) REVERT: B 665 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7125 (pp20) REVERT: B 737 MET cc_start: 0.7423 (tmm) cc_final: 0.7062 (tmm) REVERT: B 800 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.5979 (ttp80) REVERT: C 57 PHE cc_start: 0.8913 (t80) cc_final: 0.8460 (t80) REVERT: C 245 MET cc_start: 0.7765 (ppp) cc_final: 0.7169 (ppp) REVERT: C 347 CYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5613 (p) REVERT: C 501 MET cc_start: 0.8512 (mmm) cc_final: 0.7838 (tpt) REVERT: C 534 MET cc_start: 0.8323 (tpp) cc_final: 0.7930 (ttm) REVERT: C 565 MET cc_start: 0.8743 (mmt) cc_final: 0.7992 (mpp) REVERT: C 649 SER cc_start: 0.9077 (m) cc_final: 0.8854 (t) REVERT: C 740 THR cc_start: 0.9323 (p) cc_final: 0.8967 (t) REVERT: D 90 GLU cc_start: 0.8595 (tt0) cc_final: 0.8105 (tt0) REVERT: D 218 MET cc_start: 0.7964 (tpp) cc_final: 0.7677 (tpp) REVERT: D 228 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8840 (m-10) REVERT: D 247 MET cc_start: 0.7336 (mmt) cc_final: 0.7086 (mmt) REVERT: D 248 MET cc_start: 0.8140 (mmm) cc_final: 0.7894 (mmm) REVERT: D 322 LEU cc_start: 0.9405 (mm) cc_final: 0.9171 (mm) REVERT: D 323 MET cc_start: 0.9070 (tpp) cc_final: 0.8490 (ttm) REVERT: D 360 MET cc_start: 0.7797 (mmm) cc_final: 0.7460 (mmm) REVERT: D 536 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8406 (pp) REVERT: D 627 MET cc_start: 0.8829 (mmm) cc_final: 0.8238 (ttt) REVERT: D 633 THR cc_start: 0.8766 (p) cc_final: 0.8351 (t) REVERT: D 665 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7319 (pp20) REVERT: D 694 PHE cc_start: 0.8610 (m-80) cc_final: 0.8197 (m-80) REVERT: D 705 MET cc_start: 0.9013 (mtp) cc_final: 0.8458 (mtp) REVERT: D 737 MET cc_start: 0.7137 (tmm) cc_final: 0.6846 (tmm) REVERT: D 738 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7991 (mm-30) REVERT: D 770 MET cc_start: 0.8793 (tpt) cc_final: 0.8443 (mmt) REVERT: D 811 GLU cc_start: 0.8358 (pm20) cc_final: 0.8126 (pp20) outliers start: 79 outliers final: 50 residues processed: 302 average time/residue: 0.3277 time to fit residues: 167.5265 Evaluate side-chains 291 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 231 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 chunk 272 optimal weight: 0.9980 chunk 291 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27408 Z= 0.210 Angle : 0.742 12.895 37146 Z= 0.341 Chirality : 0.048 0.486 4314 Planarity : 0.004 0.070 4618 Dihedral : 10.189 138.914 4834 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.44 % Favored : 92.37 % Rotamer: Outliers : 2.68 % Allowed : 14.75 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.96 (0.15), residues: 3264 helix: 0.93 (0.15), residues: 1384 sheet: -1.35 (0.25), residues: 430 loop : -2.00 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.002 TRP C 169 HIS 0.007 0.001 HIS C 225 PHE 0.021 0.001 PHE A 279 TYR 0.013 0.001 TYR A 733 ARG 0.010 0.000 ARG D 431 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 235 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8896 (t80) cc_final: 0.8448 (t80) REVERT: A 234 MET cc_start: 0.8928 (mpp) cc_final: 0.8406 (mpp) REVERT: A 245 MET cc_start: 0.8133 (ppp) cc_final: 0.7556 (ppp) REVERT: A 323 MET cc_start: 0.8402 (mmt) cc_final: 0.8134 (mmt) REVERT: A 347 CYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5773 (p) REVERT: A 450 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6460 (t0) REVERT: A 501 MET cc_start: 0.8549 (mmm) cc_final: 0.7990 (tpt) REVERT: A 534 MET cc_start: 0.8592 (tpp) cc_final: 0.8063 (ttp) REVERT: A 565 MET cc_start: 0.8842 (mmt) cc_final: 0.8072 (mpp) REVERT: A 649 SER cc_start: 0.9197 (m) cc_final: 0.8824 (t) REVERT: A 740 THR cc_start: 0.9394 (p) cc_final: 0.9031 (t) REVERT: B 50 MET cc_start: 0.3380 (ttp) cc_final: 0.2875 (tmm) REVERT: B 90 GLU cc_start: 0.8511 (tt0) cc_final: 0.8052 (tt0) REVERT: B 223 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: B 228 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8889 (m-10) REVERT: B 322 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9196 (mm) REVERT: B 323 MET cc_start: 0.8901 (tpp) cc_final: 0.8603 (ttt) REVERT: B 389 LEU cc_start: 0.9277 (mt) cc_final: 0.8853 (mt) REVERT: B 468 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8024 (mmp80) REVERT: B 501 MET cc_start: 0.8662 (mmm) cc_final: 0.7785 (mmm) REVERT: B 536 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8576 (pp) REVERT: B 633 THR cc_start: 0.8704 (p) cc_final: 0.8324 (t) REVERT: B 665 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7131 (pp20) REVERT: B 737 MET cc_start: 0.7585 (tmm) cc_final: 0.7242 (tmm) REVERT: B 800 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.6015 (ttp80) REVERT: C 57 PHE cc_start: 0.8938 (t80) cc_final: 0.8491 (t80) REVERT: C 234 MET cc_start: 0.8656 (mpp) cc_final: 0.8117 (mpp) REVERT: C 245 MET cc_start: 0.7844 (ppp) cc_final: 0.7188 (ppp) REVERT: C 347 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5662 (p) REVERT: C 501 MET cc_start: 0.8495 (mmm) cc_final: 0.7798 (tpt) REVERT: C 534 MET cc_start: 0.8471 (tpp) cc_final: 0.7952 (ttm) REVERT: C 565 MET cc_start: 0.8751 (mmt) cc_final: 0.8114 (mpp) REVERT: C 649 SER cc_start: 0.9043 (m) cc_final: 0.8707 (t) REVERT: C 691 MET cc_start: 0.8326 (ppp) cc_final: 0.8101 (ppp) REVERT: C 705 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8650 (mmm) REVERT: C 709 MET cc_start: 0.9017 (mtm) cc_final: 0.8476 (mtt) REVERT: C 740 THR cc_start: 0.9334 (p) cc_final: 0.8972 (t) REVERT: D 50 MET cc_start: 0.3276 (tmm) cc_final: 0.2776 (tmm) REVERT: D 90 GLU cc_start: 0.8626 (tt0) cc_final: 0.8151 (tt0) REVERT: D 218 MET cc_start: 0.7999 (tpp) cc_final: 0.7696 (tpp) REVERT: D 228 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8832 (m-10) REVERT: D 247 MET cc_start: 0.7517 (mmt) cc_final: 0.7274 (mmt) REVERT: D 248 MET cc_start: 0.8099 (mmm) cc_final: 0.7864 (mmm) REVERT: D 322 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9210 (mm) REVERT: D 323 MET cc_start: 0.9130 (tpp) cc_final: 0.8577 (ttm) REVERT: D 340 MET cc_start: 0.8591 (mmm) cc_final: 0.8288 (mmm) REVERT: D 360 MET cc_start: 0.7741 (mmm) cc_final: 0.7415 (mmm) REVERT: D 536 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8446 (pp) REVERT: D 565 MET cc_start: 0.8049 (mmt) cc_final: 0.7817 (mmp) REVERT: D 620 MET cc_start: 0.9005 (mmt) cc_final: 0.7069 (mmt) REVERT: D 627 MET cc_start: 0.8881 (mmm) cc_final: 0.8148 (ttt) REVERT: D 633 THR cc_start: 0.8771 (p) cc_final: 0.8338 (t) REVERT: D 665 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7329 (pp20) REVERT: D 694 PHE cc_start: 0.8645 (m-80) cc_final: 0.8197 (m-80) REVERT: D 705 MET cc_start: 0.9018 (mtp) cc_final: 0.8469 (mtp) REVERT: D 737 MET cc_start: 0.7227 (tmm) cc_final: 0.6933 (tmm) REVERT: D 738 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8006 (mm-30) outliers start: 76 outliers final: 57 residues processed: 288 average time/residue: 0.3332 time to fit residues: 167.1293 Evaluate side-chains 297 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 228 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 704 LYS Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 605 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 1.9990 chunk 307 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 322 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27408 Z= 0.207 Angle : 0.741 12.201 37146 Z= 0.342 Chirality : 0.048 0.483 4314 Planarity : 0.004 0.069 4618 Dihedral : 9.858 139.087 4834 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.38 % Favored : 92.43 % Rotamer: Outliers : 2.46 % Allowed : 14.93 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % 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: -0.87 (0.15), residues: 3264 helix: 1.00 (0.15), residues: 1384 sheet: -1.25 (0.26), residues: 430 loop : -1.97 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.002 TRP C 169 HIS 0.006 0.001 HIS B 253 PHE 0.037 0.001 PHE B 606 TYR 0.012 0.001 TYR B 478 ARG 0.002 0.000 ARG D 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8896 (t80) cc_final: 0.8436 (t80) REVERT: A 234 MET cc_start: 0.8968 (mpp) cc_final: 0.8369 (mpp) REVERT: A 245 MET cc_start: 0.8143 (ppp) cc_final: 0.7592 (ppp) REVERT: A 323 MET cc_start: 0.8310 (mmt) cc_final: 0.8051 (mmt) REVERT: A 347 CYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5804 (p) REVERT: A 450 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6434 (t0) REVERT: A 501 MET cc_start: 0.8516 (mmm) cc_final: 0.7953 (tpt) REVERT: A 534 MET cc_start: 0.8604 (tpp) cc_final: 0.8069 (ttp) REVERT: A 565 MET cc_start: 0.8832 (mmt) cc_final: 0.8075 (mpp) REVERT: A 621 GLN cc_start: 0.8606 (tp40) cc_final: 0.8243 (tp40) REVERT: A 649 SER cc_start: 0.9165 (m) cc_final: 0.8805 (t) REVERT: A 740 THR cc_start: 0.9409 (p) cc_final: 0.9009 (t) REVERT: B 50 MET cc_start: 0.3221 (ttp) cc_final: 0.2800 (tmm) REVERT: B 90 GLU cc_start: 0.8563 (tt0) cc_final: 0.8101 (tt0) REVERT: B 218 MET cc_start: 0.8475 (tpp) cc_final: 0.8176 (tpp) REVERT: B 228 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8937 (m-10) REVERT: B 322 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9241 (mm) REVERT: B 323 MET cc_start: 0.8970 (tpp) cc_final: 0.8501 (ttt) REVERT: B 389 LEU cc_start: 0.9286 (mt) cc_final: 0.8865 (mt) REVERT: B 468 ARG cc_start: 0.8786 (ttp80) cc_final: 0.8068 (mmp80) REVERT: B 536 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8575 (pp) REVERT: B 633 THR cc_start: 0.8669 (p) cc_final: 0.8264 (t) REVERT: B 665 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7138 (pp20) REVERT: B 737 MET cc_start: 0.7622 (tmm) cc_final: 0.7258 (tmm) REVERT: B 800 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.5974 (ttp80) REVERT: C 57 PHE cc_start: 0.8944 (t80) cc_final: 0.8532 (t80) REVERT: C 234 MET cc_start: 0.8689 (mpp) cc_final: 0.8144 (mpp) REVERT: C 245 MET cc_start: 0.7843 (ppp) cc_final: 0.7160 (ppp) REVERT: C 347 CYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5644 (p) REVERT: C 501 MET cc_start: 0.8434 (mmm) cc_final: 0.7670 (tpt) REVERT: C 534 MET cc_start: 0.8487 (tpp) cc_final: 0.8021 (ttm) REVERT: C 565 MET cc_start: 0.8745 (mmt) cc_final: 0.8109 (mpp) REVERT: C 621 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8606 (tp40) REVERT: C 649 SER cc_start: 0.9034 (m) cc_final: 0.8694 (t) REVERT: C 709 MET cc_start: 0.9071 (mtm) cc_final: 0.8524 (mtt) REVERT: C 740 THR cc_start: 0.9339 (p) cc_final: 0.9006 (t) REVERT: D 50 MET cc_start: 0.3271 (tmm) cc_final: 0.2772 (tmm) REVERT: D 90 GLU cc_start: 0.8626 (tt0) cc_final: 0.8157 (tt0) REVERT: D 218 MET cc_start: 0.8007 (tpp) cc_final: 0.7678 (tpp) REVERT: D 228 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8839 (m-10) REVERT: D 247 MET cc_start: 0.7620 (mmt) cc_final: 0.7360 (mmt) REVERT: D 248 MET cc_start: 0.8123 (mmm) cc_final: 0.7884 (mmm) REVERT: D 322 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9246 (mm) REVERT: D 323 MET cc_start: 0.9158 (tpp) cc_final: 0.8632 (ttm) REVERT: D 360 MET cc_start: 0.7756 (mmm) cc_final: 0.7432 (mmm) REVERT: D 501 MET cc_start: 0.8654 (mmm) cc_final: 0.7846 (mmm) REVERT: D 536 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8657 (pp) REVERT: D 565 MET cc_start: 0.8056 (mmt) cc_final: 0.7823 (mmp) REVERT: D 620 MET cc_start: 0.9022 (mmt) cc_final: 0.7196 (mmt) REVERT: D 627 MET cc_start: 0.8865 (mmm) cc_final: 0.8140 (ttt) REVERT: D 633 THR cc_start: 0.8859 (p) cc_final: 0.8421 (t) REVERT: D 665 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7262 (pp20) REVERT: D 694 PHE cc_start: 0.8661 (m-80) cc_final: 0.8200 (m-80) REVERT: D 705 MET cc_start: 0.9017 (mtp) cc_final: 0.8472 (mtp) REVERT: D 737 MET cc_start: 0.7228 (tmm) cc_final: 0.6936 (tmm) REVERT: D 770 MET cc_start: 0.8878 (tpt) cc_final: 0.8502 (mmt) outliers start: 70 outliers final: 56 residues processed: 281 average time/residue: 0.3357 time to fit residues: 160.3765 Evaluate side-chains 294 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 228 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 554 SER Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.6980 chunk 273 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 264 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 818 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.084200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.065699 restraints weight = 126469.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066843 restraints weight = 77980.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067337 restraints weight = 62497.923| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27408 Z= 0.169 Angle : 0.725 12.691 37146 Z= 0.331 Chirality : 0.047 0.479 4314 Planarity : 0.004 0.066 4618 Dihedral : 9.463 139.010 4834 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.05 % Favored : 92.77 % Rotamer: Outliers : 2.25 % Allowed : 15.32 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % 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: -0.78 (0.15), residues: 3264 helix: 1.05 (0.15), residues: 1396 sheet: -1.14 (0.26), residues: 430 loop : -1.93 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP C 169 HIS 0.005 0.001 HIS D 253 PHE 0.029 0.001 PHE C 279 TYR 0.016 0.001 TYR A 733 ARG 0.007 0.000 ARG B 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5072.27 seconds wall clock time: 94 minutes 1.40 seconds (5641.40 seconds total)