Starting phenix.real_space_refine on Mon Mar 18 06:11:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfb_41228/03_2024/8tfb_41228.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfb_41228/03_2024/8tfb_41228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfb_41228/03_2024/8tfb_41228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfb_41228/03_2024/8tfb_41228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfb_41228/03_2024/8tfb_41228.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfb_41228/03_2024/8tfb_41228.pdb" } resolution = 2.99 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= 0.013 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 41863 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Mg 12 5.21 5 S 204 5.16 5 C 26890 2.51 5 N 7104 2.21 5 O 7846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 99": "OD1" <-> "OD2" Residue "Q PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42056 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3501 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3503 Classifications: {'peptide': 443} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "O" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Q" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "V" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "X" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Y" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3504 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 416} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.49, per 1000 atoms: 0.39 Number of scatterers: 42056 At special positions: 0 Unit cell: (152.28, 158.76, 126.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 204 16.00 Mg 12 11.99 O 7846 8.00 N 7104 7.00 C 26890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.87 Conformation dependent library (CDL) restraints added in 5.9 seconds 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9886 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 33 sheets defined 44.6% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.797A pdb=" N MET A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 182 removed outlier: 4.172A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 229 removed outlier: 3.859A pdb=" N TYR A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.544A pdb=" N THR A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 345 through 364 Processing helix chain 'A' and resid 379 through 387 Processing helix chain 'A' and resid 394 through 405 removed outlier: 3.727A pdb=" N GLY A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 413 through 433 removed outlier: 3.791A pdb=" N ALA A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 removed outlier: 3.754A pdb=" N LEU A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.662A pdb=" N GLY B 63 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE B 64 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B 66 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.827A pdb=" N MET B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 182 removed outlier: 3.582A pdb=" N VAL B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 229 removed outlier: 3.871A pdb=" N TYR B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.575A pdb=" N THR B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.712A pdb=" N ARG B 301 " --> pdb=" O ASN B 297 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 302' Processing helix chain 'B' and resid 329 through 333 removed outlier: 3.596A pdb=" N GLY B 332 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 364 Processing helix chain 'B' and resid 379 through 387 Processing helix chain 'B' and resid 394 through 405 removed outlier: 3.732A pdb=" N GLY B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 413 Processing helix chain 'B' and resid 413 through 433 removed outlier: 3.829A pdb=" N ALA B 433 " --> pdb=" O ASP B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 444 removed outlier: 3.660A pdb=" N LEU B 440 " --> pdb=" O HIS B 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.984A pdb=" N MET C 126 " --> pdb=" O GLU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 182 removed outlier: 3.575A pdb=" N VAL C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 229 removed outlier: 3.949A pdb=" N TYR C 219 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 285 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.547A pdb=" N THR C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.679A pdb=" N ARG C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.625A pdb=" N GLY C 332 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 364 Processing helix chain 'C' and resid 379 through 387 Processing helix chain 'C' and resid 394 through 404 removed outlier: 3.838A pdb=" N GLY C 404 " --> pdb=" O ASP C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 433 removed outlier: 6.218A pdb=" N GLU C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N HIS C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 433 " --> pdb=" O ASP C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 444 removed outlier: 3.721A pdb=" N LEU C 440 " --> pdb=" O HIS C 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 21 Processing helix chain 'D' and resid 44 through 53 removed outlier: 4.628A pdb=" N GLU D 48 " --> pdb=" O GLU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 66 removed outlier: 3.548A pdb=" N GLN D 62 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE D 64 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR D 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 59 through 66' Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.975A pdb=" N MET D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 183 removed outlier: 4.146A pdb=" N ASP D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 228 removed outlier: 3.938A pdb=" N TYR D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 285 Processing helix chain 'D' and resid 288 through 293 removed outlier: 3.595A pdb=" N THR D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 removed outlier: 3.668A pdb=" N ARG D 301 " --> pdb=" O ASN D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 Processing helix chain 'D' and resid 345 through 364 Processing helix chain 'D' and resid 374 through 378 Processing helix chain 'D' and resid 379 through 387 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.764A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 405 " --> pdb=" O GLU D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 413 Processing helix chain 'D' and resid 413 through 432 Processing helix chain 'D' and resid 436 through 444 removed outlier: 3.674A pdb=" N LEU D 440 " --> pdb=" O HIS D 436 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 21 Processing helix chain 'L' and resid 45 through 53 Processing helix chain 'L' and resid 59 through 66 removed outlier: 3.631A pdb=" N GLY L 63 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE L 64 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR L 65 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG L 66 " --> pdb=" O GLY L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 127 Processing helix chain 'L' and resid 166 through 183 removed outlier: 4.121A pdb=" N ASP L 170 " --> pdb=" O ASP L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 228 removed outlier: 3.882A pdb=" N TYR L 219 " --> pdb=" O VAL L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 285 Processing helix chain 'L' and resid 288 through 293 removed outlier: 3.591A pdb=" N THR L 292 " --> pdb=" O PHE L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 301 Processing helix chain 'L' and resid 329 through 333 Processing helix chain 'L' and resid 345 through 364 Processing helix chain 'L' and resid 379 through 387 Processing helix chain 'L' and resid 394 through 404 removed outlier: 3.720A pdb=" N GLY L 404 " --> pdb=" O ASP L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 413 Processing helix chain 'L' and resid 413 through 432 Processing helix chain 'L' and resid 436 through 444 removed outlier: 3.728A pdb=" N LEU L 440 " --> pdb=" O HIS L 436 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 21 Processing helix chain 'M' and resid 45 through 53 Processing helix chain 'M' and resid 59 through 61 No H-bonds generated for 'chain 'M' and resid 59 through 61' Processing helix chain 'M' and resid 111 through 126 removed outlier: 3.923A pdb=" N MET M 126 " --> pdb=" O GLU M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 182 removed outlier: 3.592A pdb=" N VAL M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 228 removed outlier: 3.867A pdb=" N TYR M 219 " --> pdb=" O VAL M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 285 Processing helix chain 'M' and resid 288 through 293 removed outlier: 3.559A pdb=" N THR M 292 " --> pdb=" O PHE M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 302 removed outlier: 3.699A pdb=" N ARG M 301 " --> pdb=" O ASN M 297 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 302 " --> pdb=" O SER M 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 302' Processing helix chain 'M' and resid 329 through 333 removed outlier: 3.619A pdb=" N GLY M 332 " --> pdb=" O ARG M 329 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 364 Processing helix chain 'M' and resid 379 through 387 Processing helix chain 'M' and resid 394 through 404 removed outlier: 3.844A pdb=" N GLY M 404 " --> pdb=" O ASP M 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 413 Processing helix chain 'M' and resid 413 through 432 Processing helix chain 'M' and resid 436 through 444 removed outlier: 3.704A pdb=" N LEU M 440 " --> pdb=" O HIS M 436 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 21 Processing helix chain 'O' and resid 45 through 53 Processing helix chain 'O' and resid 59 through 66 removed outlier: 3.539A pdb=" N GLY O 63 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE O 64 " --> pdb=" O ILE O 61 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR O 65 " --> pdb=" O GLN O 62 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG O 66 " --> pdb=" O GLY O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 125 Processing helix chain 'O' and resid 167 through 182 removed outlier: 3.631A pdb=" N VAL O 171 " --> pdb=" O ARG O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 229 removed outlier: 3.869A pdb=" N TYR O 219 " --> pdb=" O VAL O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 271 through 285 Processing helix chain 'O' and resid 288 through 293 removed outlier: 3.520A pdb=" N THR O 292 " --> pdb=" O PHE O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 302 removed outlier: 3.756A pdb=" N ARG O 301 " --> pdb=" O ASN O 297 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU O 302 " --> pdb=" O SER O 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 297 through 302' Processing helix chain 'O' and resid 329 through 333 removed outlier: 3.562A pdb=" N GLY O 332 " --> pdb=" O ARG O 329 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 364 Processing helix chain 'O' and resid 374 through 378 Processing helix chain 'O' and resid 379 through 387 Processing helix chain 'O' and resid 394 through 405 removed outlier: 3.736A pdb=" N GLY O 404 " --> pdb=" O ASP O 400 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER O 405 " --> pdb=" O GLU O 401 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 413 removed outlier: 3.518A pdb=" N LYS O 409 " --> pdb=" O SER O 405 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 433 removed outlier: 3.825A pdb=" N ALA O 433 " --> pdb=" O ASP O 429 " (cutoff:3.500A) Processing helix chain 'O' and resid 436 through 444 removed outlier: 3.730A pdb=" N LEU O 440 " --> pdb=" O HIS O 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 21 Processing helix chain 'P' and resid 45 through 53 Processing helix chain 'P' and resid 59 through 66 removed outlier: 3.551A pdb=" N GLN P 62 " --> pdb=" O SER P 59 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY P 63 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE P 64 " --> pdb=" O ILE P 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR P 65 " --> pdb=" O GLN P 62 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG P 66 " --> pdb=" O GLY P 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 59 through 66' Processing helix chain 'P' and resid 111 through 125 Processing helix chain 'P' and resid 167 through 183 removed outlier: 3.623A pdb=" N VAL P 171 " --> pdb=" O ARG P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 228 removed outlier: 3.917A pdb=" N TYR P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 271 through 285 Processing helix chain 'P' and resid 288 through 293 removed outlier: 3.568A pdb=" N THR P 292 " --> pdb=" O PHE P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 301 Processing helix chain 'P' and resid 329 through 333 removed outlier: 3.552A pdb=" N GLY P 332 " --> pdb=" O ARG P 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 364 Processing helix chain 'P' and resid 374 through 378 Processing helix chain 'P' and resid 379 through 387 Processing helix chain 'P' and resid 394 through 405 removed outlier: 3.766A pdb=" N GLY P 404 " --> pdb=" O ASP P 400 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER P 405 " --> pdb=" O GLU P 401 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 432 removed outlier: 3.505A pdb=" N LYS P 409 " --> pdb=" O SER P 405 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU P 414 " --> pdb=" O GLU P 410 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N HIS P 415 " --> pdb=" O ALA P 411 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL P 416 " --> pdb=" O LEU P 412 " (cutoff:3.500A) Processing helix chain 'P' and resid 436 through 444 removed outlier: 3.717A pdb=" N LEU P 440 " --> pdb=" O HIS P 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 21 Processing helix chain 'Q' and resid 45 through 53 Processing helix chain 'Q' and resid 59 through 61 No H-bonds generated for 'chain 'Q' and resid 59 through 61' Processing helix chain 'Q' and resid 111 through 126 removed outlier: 3.893A pdb=" N MET Q 126 " --> pdb=" O GLU Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 183 removed outlier: 3.603A pdb=" N VAL Q 171 " --> pdb=" O ARG Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 229 removed outlier: 3.892A pdb=" N TYR Q 219 " --> pdb=" O VAL Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 271 through 285 Processing helix chain 'Q' and resid 288 through 293 removed outlier: 3.538A pdb=" N THR Q 292 " --> pdb=" O PHE Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 302 removed outlier: 3.679A pdb=" N ARG Q 301 " --> pdb=" O ASN Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 329 through 333 Processing helix chain 'Q' and resid 345 through 364 Processing helix chain 'Q' and resid 374 through 378 Processing helix chain 'Q' and resid 379 through 387 Processing helix chain 'Q' and resid 394 through 404 removed outlier: 3.641A pdb=" N GLY Q 404 " --> pdb=" O ASP Q 400 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 413 Processing helix chain 'Q' and resid 413 through 433 removed outlier: 3.812A pdb=" N ALA Q 433 " --> pdb=" O ASP Q 429 " (cutoff:3.500A) Processing helix chain 'Q' and resid 436 through 444 removed outlier: 3.721A pdb=" N LEU Q 440 " --> pdb=" O HIS Q 436 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 21 Processing helix chain 'V' and resid 45 through 53 Processing helix chain 'V' and resid 59 through 61 No H-bonds generated for 'chain 'V' and resid 59 through 61' Processing helix chain 'V' and resid 62 through 66 removed outlier: 4.087A pdb=" N THR V 65 " --> pdb=" O GLN V 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG V 66 " --> pdb=" O GLY V 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 62 through 66' Processing helix chain 'V' and resid 111 through 126 removed outlier: 3.780A pdb=" N MET V 126 " --> pdb=" O GLU V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 167 through 183 removed outlier: 3.579A pdb=" N VAL V 171 " --> pdb=" O ARG V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 207 through 229 removed outlier: 3.919A pdb=" N TYR V 219 " --> pdb=" O VAL V 215 " (cutoff:3.500A) Processing helix chain 'V' and resid 271 through 285 Processing helix chain 'V' and resid 288 through 293 removed outlier: 3.539A pdb=" N THR V 292 " --> pdb=" O PHE V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 297 through 302 removed outlier: 3.689A pdb=" N ARG V 301 " --> pdb=" O ASN V 297 " (cutoff:3.500A) Processing helix chain 'V' and resid 329 through 333 removed outlier: 3.665A pdb=" N GLY V 332 " --> pdb=" O ARG V 329 " (cutoff:3.500A) Processing helix chain 'V' and resid 345 through 364 Processing helix chain 'V' and resid 379 through 387 Processing helix chain 'V' and resid 394 through 405 removed outlier: 3.722A pdb=" N GLY V 404 " --> pdb=" O ASP V 400 " (cutoff:3.500A) Processing helix chain 'V' and resid 405 through 433 removed outlier: 6.208A pdb=" N GLU V 414 " --> pdb=" O GLU V 410 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N HIS V 415 " --> pdb=" O ALA V 411 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL V 416 " --> pdb=" O LEU V 412 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA V 433 " --> pdb=" O ASP V 429 " (cutoff:3.500A) Processing helix chain 'V' and resid 436 through 444 removed outlier: 3.694A pdb=" N LEU V 440 " --> pdb=" O HIS V 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 21 Processing helix chain 'X' and resid 45 through 53 Processing helix chain 'X' and resid 59 through 61 No H-bonds generated for 'chain 'X' and resid 59 through 61' Processing helix chain 'X' and resid 62 through 66 removed outlier: 4.295A pdb=" N THR X 65 " --> pdb=" O GLN X 62 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG X 66 " --> pdb=" O GLY X 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 62 through 66' Processing helix chain 'X' and resid 111 through 126 removed outlier: 3.657A pdb=" N MET X 126 " --> pdb=" O GLU X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 167 through 183 removed outlier: 3.553A pdb=" N VAL X 171 " --> pdb=" O ARG X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 228 removed outlier: 3.882A pdb=" N TYR X 219 " --> pdb=" O VAL X 215 " (cutoff:3.500A) Processing helix chain 'X' and resid 271 through 285 Processing helix chain 'X' and resid 288 through 293 removed outlier: 3.597A pdb=" N THR X 292 " --> pdb=" O PHE X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 295 through 301 Processing helix chain 'X' and resid 329 through 333 removed outlier: 3.598A pdb=" N GLY X 332 " --> pdb=" O ARG X 329 " (cutoff:3.500A) Processing helix chain 'X' and resid 345 through 364 Processing helix chain 'X' and resid 379 through 387 Processing helix chain 'X' and resid 394 through 404 removed outlier: 3.737A pdb=" N GLY X 404 " --> pdb=" O ASP X 400 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 413 Processing helix chain 'X' and resid 413 through 432 Processing helix chain 'X' and resid 436 through 444 removed outlier: 3.677A pdb=" N LEU X 440 " --> pdb=" O HIS X 436 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 21 Processing helix chain 'Y' and resid 45 through 53 Processing helix chain 'Y' and resid 59 through 61 No H-bonds generated for 'chain 'Y' and resid 59 through 61' Processing helix chain 'Y' and resid 62 through 66 removed outlier: 4.176A pdb=" N THR Y 65 " --> pdb=" O GLN Y 62 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG Y 66 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 62 through 66' Processing helix chain 'Y' and resid 111 through 127 removed outlier: 3.553A pdb=" N MET Y 126 " --> pdb=" O GLU Y 122 " (cutoff:3.500A) Processing helix chain 'Y' and resid 167 through 183 removed outlier: 3.583A pdb=" N VAL Y 171 " --> pdb=" O ARG Y 167 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY Y 183 " --> pdb=" O LEU Y 179 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 229 removed outlier: 3.910A pdb=" N TYR Y 219 " --> pdb=" O VAL Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 271 through 285 Processing helix chain 'Y' and resid 288 through 293 removed outlier: 3.538A pdb=" N THR Y 292 " --> pdb=" O PHE Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 295 through 301 Processing helix chain 'Y' and resid 329 through 333 removed outlier: 3.575A pdb=" N GLY Y 332 " --> pdb=" O ARG Y 329 " (cutoff:3.500A) Processing helix chain 'Y' and resid 345 through 364 Processing helix chain 'Y' and resid 379 through 387 Processing helix chain 'Y' and resid 394 through 404 removed outlier: 3.735A pdb=" N GLY Y 404 " --> pdb=" O ASP Y 400 " (cutoff:3.500A) Processing helix chain 'Y' and resid 405 through 413 Processing helix chain 'Y' and resid 413 through 433 removed outlier: 3.807A pdb=" N ALA Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) Processing helix chain 'Y' and resid 436 through 444 removed outlier: 3.701A pdb=" N LEU Y 440 " --> pdb=" O HIS Y 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.130A pdb=" N ALA A 92 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 24 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 11.835A pdb=" N VAL A 93 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N PHE A 81 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N ARG A 95 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N SER A 79 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 97 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 72 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 56 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 142 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 129 through 142 current: chain 'A' and resid 197 through 201 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 197 through 201 current: chain 'A' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 258 through 259 current: chain 'A' and resid 323 through 324 Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 42 removed outlier: 7.682A pdb=" N ALA B 94 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE B 25 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 96 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR B 27 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY B 98 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 11.820A pdb=" N VAL B 93 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N PHE B 81 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N ARG B 95 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N SER B 79 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 97 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 142 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 128 through 142 current: chain 'B' and resid 197 through 201 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 197 through 201 current: chain 'B' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 258 through 259 current: chain 'B' and resid 323 through 324 Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 42 removed outlier: 6.136A pdb=" N ALA C 92 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 24 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N VAL C 93 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 10.588A pdb=" N PHE C 81 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N ARG C 95 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N SER C 79 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU C 97 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AA9, first strand: chain 'C' and resid 128 through 142 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 128 through 142 current: chain 'C' and resid 197 through 202 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 197 through 202 current: chain 'C' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 258 through 259 current: chain 'C' and resid 323 through 324 Processing sheet with id=AB1, first strand: chain 'D' and resid 40 through 42 removed outlier: 6.120A pdb=" N ALA D 92 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 24 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 11.633A pdb=" N VAL D 93 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N PHE D 81 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N ARG D 95 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N SER D 79 " --> pdb=" O ARG D 95 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D 97 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 30 Processing sheet with id=AB3, first strand: chain 'D' and resid 129 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 129 through 142 current: chain 'D' and resid 197 through 202 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 197 through 202 current: chain 'D' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 258 through 259 current: chain 'D' and resid 323 through 324 Processing sheet with id=AB4, first strand: chain 'L' and resid 40 through 42 removed outlier: 6.096A pdb=" N ALA L 92 " --> pdb=" O VAL L 22 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE L 24 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 11.851A pdb=" N VAL L 93 " --> pdb=" O PHE L 81 " (cutoff:3.500A) removed outlier: 10.715A pdb=" N PHE L 81 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N ARG L 95 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N SER L 79 " --> pdb=" O ARG L 95 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU L 97 " --> pdb=" O ASP L 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AB6, first strand: chain 'L' and resid 129 through 142 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 129 through 142 current: chain 'L' and resid 197 through 202 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 197 through 202 current: chain 'L' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 258 through 259 current: chain 'L' and resid 323 through 324 Processing sheet with id=AB7, first strand: chain 'M' and resid 40 through 42 removed outlier: 7.687A pdb=" N ALA M 94 " --> pdb=" O LYS M 23 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE M 25 " --> pdb=" O ALA M 94 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE M 96 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR M 27 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N GLY M 98 " --> pdb=" O THR M 27 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N VAL M 93 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N PHE M 81 " --> pdb=" O VAL M 93 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N ARG M 95 " --> pdb=" O SER M 79 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N SER M 79 " --> pdb=" O ARG M 95 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU M 97 " --> pdb=" O ASP M 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 29 through 30 Processing sheet with id=AB9, first strand: chain 'M' and resid 128 through 142 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 128 through 142 current: chain 'M' and resid 197 through 202 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 197 through 202 current: chain 'M' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 258 through 259 current: chain 'M' and resid 323 through 324 Processing sheet with id=AC1, first strand: chain 'O' and resid 36 through 42 removed outlier: 3.632A pdb=" N TRP O 39 " --> pdb=" O THR O 27 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA O 94 " --> pdb=" O LYS O 23 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE O 25 " --> pdb=" O ALA O 94 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE O 96 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR O 27 " --> pdb=" O ILE O 96 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLY O 98 " --> pdb=" O THR O 27 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE O 29 " --> pdb=" O GLY O 98 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N VAL O 100 " --> pdb=" O PHE O 29 " (cutoff:3.500A) removed outlier: 11.856A pdb=" N VAL O 93 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE O 81 " --> pdb=" O VAL O 93 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N ARG O 95 " --> pdb=" O SER O 79 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N SER O 79 " --> pdb=" O ARG O 95 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU O 97 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 128 through 142 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 128 through 142 current: chain 'O' and resid 197 through 201 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 197 through 201 current: chain 'O' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 258 through 259 current: chain 'O' and resid 323 through 324 Processing sheet with id=AC3, first strand: chain 'P' and resid 36 through 42 removed outlier: 3.679A pdb=" N TRP P 39 " --> pdb=" O THR P 27 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA P 92 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE P 24 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY P 98 " --> pdb=" O GLN P 28 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR P 30 " --> pdb=" O GLY P 98 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N VAL P 100 " --> pdb=" O THR P 30 " (cutoff:3.500A) removed outlier: 11.573A pdb=" N VAL P 93 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N PHE P 81 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N ARG P 95 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N SER P 79 " --> pdb=" O ARG P 95 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU P 97 " --> pdb=" O ASP P 77 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET P 72 " --> pdb=" O PHE P 56 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 128 through 142 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 128 through 142 current: chain 'P' and resid 197 through 202 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 197 through 202 current: chain 'P' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 258 through 259 current: chain 'P' and resid 323 through 324 Processing sheet with id=AC5, first strand: chain 'Q' and resid 40 through 42 removed outlier: 6.158A pdb=" N ALA Q 92 " --> pdb=" O VAL Q 22 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE Q 24 " --> pdb=" O ALA Q 92 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N VAL Q 93 " --> pdb=" O PHE Q 81 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N PHE Q 81 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N ARG Q 95 " --> pdb=" O SER Q 79 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N SER Q 79 " --> pdb=" O ARG Q 95 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU Q 97 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET Q 72 " --> pdb=" O PHE Q 56 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE Q 56 " --> pdb=" O MET Q 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 29 through 30 Processing sheet with id=AC7, first strand: chain 'Q' and resid 129 through 142 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 129 through 142 current: chain 'Q' and resid 197 through 202 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 197 through 202 current: chain 'Q' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 258 through 259 current: chain 'Q' and resid 323 through 324 Processing sheet with id=AC8, first strand: chain 'V' and resid 40 through 42 removed outlier: 6.072A pdb=" N ALA V 92 " --> pdb=" O VAL V 22 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE V 24 " --> pdb=" O ALA V 92 " (cutoff:3.500A) removed outlier: 11.819A pdb=" N VAL V 93 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N PHE V 81 " --> pdb=" O VAL V 93 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N ARG V 95 " --> pdb=" O SER V 79 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N SER V 79 " --> pdb=" O ARG V 95 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU V 97 " --> pdb=" O ASP V 77 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET V 72 " --> pdb=" O PHE V 56 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 29 through 30 Processing sheet with id=AD1, first strand: chain 'V' and resid 128 through 142 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 128 through 142 current: chain 'V' and resid 197 through 201 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 197 through 201 current: chain 'V' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 258 through 259 current: chain 'V' and resid 323 through 324 Processing sheet with id=AD2, first strand: chain 'X' and resid 40 through 42 removed outlier: 7.707A pdb=" N ALA X 94 " --> pdb=" O LYS X 23 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE X 25 " --> pdb=" O ALA X 94 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE X 96 " --> pdb=" O ILE X 25 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR X 27 " --> pdb=" O ILE X 96 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLY X 98 " --> pdb=" O THR X 27 " (cutoff:3.500A) removed outlier: 11.664A pdb=" N VAL X 93 " --> pdb=" O PHE X 81 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N PHE X 81 " --> pdb=" O VAL X 93 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N ARG X 95 " --> pdb=" O SER X 79 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N SER X 79 " --> pdb=" O ARG X 95 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU X 97 " --> pdb=" O ASP X 77 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 29 through 30 Processing sheet with id=AD4, first strand: chain 'X' and resid 129 through 142 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 129 through 142 current: chain 'X' and resid 197 through 201 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 197 through 201 current: chain 'X' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 258 through 259 current: chain 'X' and resid 323 through 324 Processing sheet with id=AD5, first strand: chain 'Y' and resid 36 through 42 removed outlier: 3.799A pdb=" N TRP Y 39 " --> pdb=" O THR Y 27 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ALA Y 94 " --> pdb=" O LYS Y 23 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE Y 25 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE Y 96 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR Y 27 " --> pdb=" O ILE Y 96 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLY Y 98 " --> pdb=" O THR Y 27 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE Y 29 " --> pdb=" O GLY Y 98 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N VAL Y 100 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) removed outlier: 11.537A pdb=" N VAL Y 93 " --> pdb=" O PHE Y 81 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N PHE Y 81 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N ARG Y 95 " --> pdb=" O SER Y 79 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N SER Y 79 " --> pdb=" O ARG Y 95 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU Y 97 " --> pdb=" O ASP Y 77 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET Y 72 " --> pdb=" O PHE Y 56 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 129 through 142 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 129 through 142 current: chain 'Y' and resid 197 through 201 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 197 through 201 current: chain 'Y' and resid 258 through 259 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 258 through 259 current: chain 'Y' and resid 323 through 324 1683 hydrogen bonds defined for protein. 4845 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: 12.60 Time building geometry restraints manager: 14.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7078 1.31 - 1.43: 11544 1.43 - 1.56: 24142 1.56 - 1.68: 0 1.68 - 1.81: 348 Bond restraints: 43112 Sorted by residual: bond pdb=" C SER V 405 " pdb=" O SER V 405 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.15e-02 7.56e+03 1.97e+01 bond pdb=" C MET A 402 " pdb=" O MET A 402 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.49e+01 bond pdb=" C MET D 402 " pdb=" O MET D 402 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.28e-02 6.10e+03 1.36e+01 bond pdb=" C MET P 402 " pdb=" O MET P 402 " ideal model delta sigma weight residual 1.236 1.188 0.047 1.29e-02 6.01e+03 1.34e+01 bond pdb=" C MET V 402 " pdb=" O MET V 402 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.29e-02 6.01e+03 1.33e+01 ... (remaining 43107 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.40: 1509 106.40 - 113.30: 22561 113.30 - 120.19: 15074 120.19 - 127.09: 18701 127.09 - 133.99: 541 Bond angle restraints: 58386 Sorted by residual: angle pdb=" C MET A 402 " pdb=" CA MET A 402 " pdb=" CB MET A 402 " ideal model delta sigma weight residual 110.79 121.38 -10.59 1.66e+00 3.63e-01 4.07e+01 angle pdb=" C LYS A 403 " pdb=" CA LYS A 403 " pdb=" CB LYS A 403 " ideal model delta sigma weight residual 110.79 120.56 -9.77 1.66e+00 3.63e-01 3.47e+01 angle pdb=" C MET O 402 " pdb=" CA MET O 402 " pdb=" CB MET O 402 " ideal model delta sigma weight residual 110.37 100.13 10.24 1.78e+00 3.16e-01 3.31e+01 angle pdb=" N LYS A 403 " pdb=" CA LYS A 403 " pdb=" C LYS A 403 " ideal model delta sigma weight residual 111.28 105.68 5.60 1.09e+00 8.42e-01 2.64e+01 angle pdb=" N MET A 402 " pdb=" CA MET A 402 " pdb=" C MET A 402 " ideal model delta sigma weight residual 111.28 105.83 5.45 1.09e+00 8.42e-01 2.50e+01 ... (remaining 58381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 23870 17.69 - 35.38: 1621 35.38 - 53.07: 207 53.07 - 70.76: 103 70.76 - 88.45: 55 Dihedral angle restraints: 25856 sinusoidal: 10450 harmonic: 15406 Sorted by residual: dihedral pdb=" C MET O 402 " pdb=" N MET O 402 " pdb=" CA MET O 402 " pdb=" CB MET O 402 " ideal model delta harmonic sigma weight residual -122.60 -110.07 -12.53 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C MET A 402 " pdb=" N MET A 402 " pdb=" CA MET A 402 " pdb=" CB MET A 402 " ideal model delta harmonic sigma weight residual -122.60 -133.02 10.42 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" CA MET A 402 " pdb=" C MET A 402 " pdb=" N LYS A 403 " pdb=" CA LYS A 403 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 25853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5418 0.060 - 0.120: 784 0.120 - 0.180: 33 0.180 - 0.240: 1 0.240 - 0.299: 3 Chirality restraints: 6239 Sorted by residual: chirality pdb=" CA MET O 402 " pdb=" N MET O 402 " pdb=" C MET O 402 " pdb=" CB MET O 402 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LYS C 403 " pdb=" N LYS C 403 " pdb=" C LYS C 403 " pdb=" CB LYS C 403 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA MET A 402 " pdb=" N MET A 402 " pdb=" C MET A 402 " pdb=" CB MET A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 6236 not shown) Planarity restraints: 7631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 401 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.50e+00 pdb=" C GLU D 401 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU D 401 " -0.015 2.00e-02 2.50e+03 pdb=" N MET D 402 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 401 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C GLU P 401 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU P 401 " 0.015 2.00e-02 2.50e+03 pdb=" N MET P 402 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU V 401 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C GLU V 401 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU V 401 " -0.015 2.00e-02 2.50e+03 pdb=" N MET V 402 " -0.013 2.00e-02 2.50e+03 ... (remaining 7628 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 484 2.65 - 3.21: 38912 3.21 - 3.77: 64259 3.77 - 4.34: 90545 4.34 - 4.90: 151775 Nonbonded interactions: 345975 Sorted by model distance: nonbonded pdb=" OE1 GLU L 199 " pdb="MG MG L 501 " model vdw 2.087 2.170 nonbonded pdb=" OE1 GLU A 199 " pdb="MG MG A 501 " model vdw 2.090 2.170 nonbonded pdb=" OE1 GLU X 199 " pdb="MG MG X 501 " model vdw 2.091 2.170 nonbonded pdb=" OE1 GLU Y 199 " pdb="MG MG Y 501 " model vdw 2.094 2.170 nonbonded pdb=" OE1 GLU B 199 " pdb="MG MG B 501 " model vdw 2.097 2.170 ... (remaining 345970 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 5 through 88 or (resid 89 and (name N or name CA or name C \ or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'B' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 447 or resid 501)) selection = (chain 'C' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'D' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'L' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'M' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'O' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'P' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'Q' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'V' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'X' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) selection = (chain 'Y' and (resid 5 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 88 or (resid 89 and (name N or name \ CA or name C or name O )) or resid 90 through 447 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.410 Construct map_model_manager: 0.050 Extract box with map and model: 5.500 Check model and map are aligned: 0.470 Set scattering table: 0.310 Process input model: 84.930 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 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 : 0.003 0.051 43112 Z= 0.211 Angle : 0.473 10.588 58386 Z= 0.256 Chirality : 0.041 0.299 6239 Planarity : 0.003 0.030 7631 Dihedral : 13.180 88.455 15970 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.12), residues: 5292 helix: 2.21 (0.11), residues: 2040 sheet: -0.19 (0.18), residues: 900 loop : 0.60 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 39 HIS 0.007 0.001 HIS Y 181 PHE 0.016 0.001 PHE X 64 TYR 0.012 0.001 TYR Q 299 ARG 0.002 0.000 ARG V 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 761 time to evaluate : 4.032 Fit side-chains REVERT: A 12 ASP cc_start: 0.6804 (m-30) cc_final: 0.6558 (m-30) REVERT: A 15 GLU cc_start: 0.6797 (tt0) cc_final: 0.6355 (mt-10) REVERT: A 18 LYS cc_start: 0.6486 (ttmm) cc_final: 0.6138 (mptp) REVERT: A 20 ARG cc_start: 0.6948 (mtp85) cc_final: 0.5980 (mtt180) REVERT: A 21 ASP cc_start: 0.6973 (t70) cc_final: 0.6223 (p0) REVERT: A 47 GLU cc_start: 0.7917 (tt0) cc_final: 0.7370 (tp30) REVERT: A 77 ASP cc_start: 0.6670 (t0) cc_final: 0.5836 (t0) REVERT: A 122 GLU cc_start: 0.6602 (tp30) cc_final: 0.5931 (tm-30) REVERT: A 167 ARG cc_start: 0.6511 (ptm-80) cc_final: 0.5084 (mmt90) REVERT: A 185 GLN cc_start: 0.7928 (mt0) cc_final: 0.7702 (mt0) REVERT: A 203 ARG cc_start: 0.6110 (mtp-110) cc_final: 0.5713 (mmm-85) REVERT: A 275 MET cc_start: 0.7516 (mmp) cc_final: 0.7044 (mmm) REVERT: A 358 LEU cc_start: 0.6603 (mt) cc_final: 0.6183 (mt) REVERT: A 389 ARG cc_start: 0.6626 (mmm-85) cc_final: 0.5433 (mtm110) REVERT: A 426 MET cc_start: 0.6516 (mtp) cc_final: 0.6296 (mtp) REVERT: B 12 ASP cc_start: 0.6798 (m-30) cc_final: 0.6554 (m-30) REVERT: B 18 LYS cc_start: 0.6788 (ttpt) cc_final: 0.6065 (mptp) REVERT: B 21 ASP cc_start: 0.7400 (t0) cc_final: 0.6501 (p0) REVERT: B 44 GLU cc_start: 0.8175 (mp0) cc_final: 0.7652 (mp0) REVERT: B 47 GLU cc_start: 0.7766 (tt0) cc_final: 0.7409 (tp30) REVERT: B 121 LYS cc_start: 0.6439 (mttp) cc_final: 0.6070 (ttpp) REVERT: B 167 ARG cc_start: 0.6520 (ttp-110) cc_final: 0.5274 (mmt90) REVERT: B 182 MET cc_start: 0.6695 (mtp) cc_final: 0.6445 (mtp) REVERT: B 185 GLN cc_start: 0.7904 (mt0) cc_final: 0.7681 (mt0) REVERT: B 203 ARG cc_start: 0.6977 (ttt-90) cc_final: 0.6073 (tpt-90) REVERT: B 209 CYS cc_start: 0.6275 (t) cc_final: 0.5921 (t) REVERT: B 402 MET cc_start: 0.7149 (ttt) cc_final: 0.6879 (ttt) REVERT: C 12 ASP cc_start: 0.6806 (m-30) cc_final: 0.6595 (m-30) REVERT: C 15 GLU cc_start: 0.6968 (tt0) cc_final: 0.6642 (mt-10) REVERT: C 18 LYS cc_start: 0.7030 (tttt) cc_final: 0.6460 (mptp) REVERT: C 20 ARG cc_start: 0.6750 (mtp85) cc_final: 0.6155 (ttm170) REVERT: C 21 ASP cc_start: 0.7392 (t70) cc_final: 0.6549 (p0) REVERT: C 44 GLU cc_start: 0.8066 (mp0) cc_final: 0.7682 (mp0) REVERT: C 47 GLU cc_start: 0.7584 (tt0) cc_final: 0.7294 (tp30) REVERT: C 82 ARG cc_start: 0.6320 (mtt-85) cc_final: 0.6058 (ttm-80) REVERT: C 167 ARG cc_start: 0.6422 (ptm-80) cc_final: 0.4961 (mmt90) REVERT: C 185 GLN cc_start: 0.7945 (mt0) cc_final: 0.7551 (mt0) REVERT: C 358 LEU cc_start: 0.6589 (mt) cc_final: 0.6321 (mt) REVERT: C 389 ARG cc_start: 0.6903 (mmm-85) cc_final: 0.5805 (mtm110) REVERT: C 415 HIS cc_start: 0.6957 (t70) cc_final: 0.6420 (t-90) REVERT: D 12 ASP cc_start: 0.6792 (m-30) cc_final: 0.6574 (m-30) REVERT: D 15 GLU cc_start: 0.6897 (tt0) cc_final: 0.6534 (mt-10) REVERT: D 18 LYS cc_start: 0.6991 (ttpt) cc_final: 0.6417 (mptp) REVERT: D 19 GLU cc_start: 0.7478 (tt0) cc_final: 0.7102 (tt0) REVERT: D 20 ARG cc_start: 0.6891 (mtt180) cc_final: 0.6517 (mtm-85) REVERT: D 21 ASP cc_start: 0.7396 (t70) cc_final: 0.6448 (p0) REVERT: D 44 GLU cc_start: 0.8066 (mp0) cc_final: 0.7640 (mp0) REVERT: D 47 GLU cc_start: 0.7714 (tt0) cc_final: 0.7456 (tp30) REVERT: D 62 GLN cc_start: 0.5557 (mt0) cc_final: 0.5333 (mp10) REVERT: D 82 ARG cc_start: 0.6459 (mmt-90) cc_final: 0.5965 (ttm-80) REVERT: D 121 LYS cc_start: 0.6808 (ttmt) cc_final: 0.6191 (ttpp) REVERT: D 125 LYS cc_start: 0.7093 (mttm) cc_final: 0.6810 (mmtm) REVERT: D 130 MET cc_start: 0.7718 (ttm) cc_final: 0.7296 (ttt) REVERT: D 203 ARG cc_start: 0.6343 (mtp-110) cc_final: 0.5746 (mmm-85) REVERT: D 228 LYS cc_start: 0.6716 (mmtt) cc_final: 0.6513 (mmtt) REVERT: D 258 LYS cc_start: 0.6449 (mtpp) cc_final: 0.5933 (mttm) REVERT: L 12 ASP cc_start: 0.6773 (m-30) cc_final: 0.6540 (m-30) REVERT: L 18 LYS cc_start: 0.6511 (ttmm) cc_final: 0.6065 (mptp) REVERT: L 20 ARG cc_start: 0.7255 (mtp85) cc_final: 0.6540 (mtm-85) REVERT: L 47 GLU cc_start: 0.7825 (tt0) cc_final: 0.7403 (tp30) REVERT: L 77 ASP cc_start: 0.6513 (t0) cc_final: 0.5931 (t0) REVERT: L 122 GLU cc_start: 0.6821 (tp30) cc_final: 0.6447 (tp30) REVERT: L 152 GLU cc_start: 0.6146 (mm-30) cc_final: 0.5903 (mp0) REVERT: L 167 ARG cc_start: 0.5969 (ttp80) cc_final: 0.5094 (mmt90) REVERT: L 203 ARG cc_start: 0.6187 (mtp-110) cc_final: 0.5956 (mmm-85) REVERT: L 389 ARG cc_start: 0.6523 (mmm-85) cc_final: 0.5317 (mtm-85) REVERT: L 402 MET cc_start: 0.7287 (ttt) cc_final: 0.7038 (ttt) REVERT: M 10 LYS cc_start: 0.6598 (pttt) cc_final: 0.6366 (pttp) REVERT: M 12 ASP cc_start: 0.6763 (m-30) cc_final: 0.6522 (m-30) REVERT: M 19 GLU cc_start: 0.7702 (tt0) cc_final: 0.7347 (tt0) REVERT: M 20 ARG cc_start: 0.7045 (mtp85) cc_final: 0.6274 (mtm-85) REVERT: M 21 ASP cc_start: 0.7500 (t70) cc_final: 0.6435 (p0) REVERT: M 44 GLU cc_start: 0.8152 (mp0) cc_final: 0.7733 (mp0) REVERT: M 47 GLU cc_start: 0.7771 (tt0) cc_final: 0.7158 (tp30) REVERT: M 62 GLN cc_start: 0.6709 (pt0) cc_final: 0.6342 (mt0) REVERT: M 77 ASP cc_start: 0.6598 (t0) cc_final: 0.6093 (t0) REVERT: M 167 ARG cc_start: 0.6215 (ttp-110) cc_final: 0.5221 (mmt90) REVERT: M 182 MET cc_start: 0.7473 (mtp) cc_final: 0.7253 (mtp) REVERT: M 185 GLN cc_start: 0.7964 (mt0) cc_final: 0.7753 (mt0) REVERT: M 203 ARG cc_start: 0.6161 (ttt-90) cc_final: 0.5749 (mmm-85) REVERT: M 389 ARG cc_start: 0.6659 (mmm-85) cc_final: 0.5482 (mtm-85) REVERT: O 12 ASP cc_start: 0.6645 (m-30) cc_final: 0.6376 (m-30) REVERT: O 15 GLU cc_start: 0.6978 (tt0) cc_final: 0.6490 (mt-10) REVERT: O 18 LYS cc_start: 0.6778 (tttt) cc_final: 0.6247 (mptp) REVERT: O 21 ASP cc_start: 0.7025 (t70) cc_final: 0.6161 (p0) REVERT: O 26 ARG cc_start: 0.6336 (mmt90) cc_final: 0.5881 (mtp180) REVERT: O 44 GLU cc_start: 0.8096 (mp0) cc_final: 0.7789 (mp0) REVERT: O 48 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6794 (mt-10) REVERT: O 167 ARG cc_start: 0.6417 (ttp-110) cc_final: 0.5500 (mmt90) REVERT: O 203 ARG cc_start: 0.6541 (ptm160) cc_final: 0.5999 (ptm160) REVERT: O 258 LYS cc_start: 0.6557 (mtpp) cc_final: 0.6009 (mttm) REVERT: O 275 MET cc_start: 0.7523 (mmp) cc_final: 0.7061 (mmm) REVERT: O 389 ARG cc_start: 0.7032 (mmm-85) cc_final: 0.5691 (mtp-110) REVERT: P 12 ASP cc_start: 0.6832 (m-30) cc_final: 0.6627 (m-30) REVERT: P 15 GLU cc_start: 0.6945 (tt0) cc_final: 0.6462 (mt-10) REVERT: P 18 LYS cc_start: 0.7020 (tttt) cc_final: 0.6490 (mptp) REVERT: P 20 ARG cc_start: 0.7059 (mtt-85) cc_final: 0.6709 (mtt-85) REVERT: P 21 ASP cc_start: 0.7379 (t70) cc_final: 0.6399 (p0) REVERT: P 26 ARG cc_start: 0.5861 (mmt90) cc_final: 0.5513 (mmm160) REVERT: P 44 GLU cc_start: 0.8030 (mp0) cc_final: 0.7650 (mp0) REVERT: P 62 GLN cc_start: 0.5896 (mt0) cc_final: 0.5545 (mp10) REVERT: P 121 LYS cc_start: 0.6448 (ttpt) cc_final: 0.6189 (ttpp) REVERT: P 125 LYS cc_start: 0.7009 (mttp) cc_final: 0.6721 (mmtm) REVERT: P 130 MET cc_start: 0.7695 (ttm) cc_final: 0.7297 (ttm) REVERT: P 185 GLN cc_start: 0.8011 (mt0) cc_final: 0.7580 (mt0) REVERT: P 258 LYS cc_start: 0.6670 (mtpp) cc_final: 0.6216 (mttm) REVERT: P 389 ARG cc_start: 0.6901 (mmm-85) cc_final: 0.5556 (mtm-85) REVERT: Q 12 ASP cc_start: 0.6906 (m-30) cc_final: 0.6656 (m-30) REVERT: Q 15 GLU cc_start: 0.6897 (tt0) cc_final: 0.6459 (mt-10) REVERT: Q 18 LYS cc_start: 0.6837 (ttpt) cc_final: 0.6182 (mptp) REVERT: Q 21 ASP cc_start: 0.7066 (t70) cc_final: 0.6237 (p0) REVERT: Q 26 ARG cc_start: 0.6484 (mtt-85) cc_final: 0.6262 (mtp180) REVERT: Q 44 GLU cc_start: 0.8024 (mp0) cc_final: 0.7677 (mp0) REVERT: Q 47 GLU cc_start: 0.7946 (tt0) cc_final: 0.7472 (tp30) REVERT: Q 73 LYS cc_start: 0.6145 (ttpp) cc_final: 0.5678 (ttmm) REVERT: Q 77 ASP cc_start: 0.6770 (t0) cc_final: 0.5872 (t0) REVERT: Q 121 LYS cc_start: 0.6626 (ttmt) cc_final: 0.6154 (ttpp) REVERT: Q 125 LYS cc_start: 0.6979 (mttm) cc_final: 0.6700 (mtpp) REVERT: Q 167 ARG cc_start: 0.6544 (ptm-80) cc_final: 0.5187 (mmt90) REVERT: Q 203 ARG cc_start: 0.6310 (mtp-110) cc_final: 0.5928 (mmm-85) REVERT: Q 258 LYS cc_start: 0.6519 (mtpp) cc_final: 0.6278 (mtpp) REVERT: Q 389 ARG cc_start: 0.6864 (mmm-85) cc_final: 0.5728 (mtm110) REVERT: Q 426 MET cc_start: 0.6523 (mtp) cc_final: 0.6294 (mtp) REVERT: V 12 ASP cc_start: 0.6824 (m-30) cc_final: 0.6611 (m-30) REVERT: V 15 GLU cc_start: 0.6975 (tt0) cc_final: 0.6641 (mt-10) REVERT: V 18 LYS cc_start: 0.7088 (ttpt) cc_final: 0.6487 (mptp) REVERT: V 20 ARG cc_start: 0.6889 (mtt-85) cc_final: 0.6270 (mtt-85) REVERT: V 21 ASP cc_start: 0.7442 (t0) cc_final: 0.6525 (p0) REVERT: V 44 GLU cc_start: 0.8070 (mp0) cc_final: 0.7523 (mp0) REVERT: V 47 GLU cc_start: 0.7764 (tt0) cc_final: 0.7490 (tp30) REVERT: V 130 MET cc_start: 0.7518 (ttm) cc_final: 0.7208 (ttm) REVERT: V 167 ARG cc_start: 0.6270 (ptm-80) cc_final: 0.4886 (mmt90) REVERT: V 185 GLN cc_start: 0.8028 (mt0) cc_final: 0.7472 (mt0) REVERT: V 203 ARG cc_start: 0.7058 (ttt-90) cc_final: 0.6011 (tpt-90) REVERT: V 209 CYS cc_start: 0.5876 (t) cc_final: 0.5488 (m) REVERT: V 389 ARG cc_start: 0.6552 (mtp180) cc_final: 0.5439 (mtm110) REVERT: X 15 GLU cc_start: 0.7045 (tt0) cc_final: 0.6719 (mt-10) REVERT: X 18 LYS cc_start: 0.6684 (tttp) cc_final: 0.6143 (mptp) REVERT: X 26 ARG cc_start: 0.6198 (ttm-80) cc_final: 0.5451 (ttt90) REVERT: X 41 ILE cc_start: 0.5828 (mt) cc_final: 0.5522 (mm) REVERT: X 44 GLU cc_start: 0.8107 (mp0) cc_final: 0.7714 (mp0) REVERT: X 62 GLN cc_start: 0.6810 (pt0) cc_final: 0.6470 (mt0) REVERT: X 64 PHE cc_start: 0.7392 (p90) cc_final: 0.7182 (p90) REVERT: X 77 ASP cc_start: 0.6665 (t0) cc_final: 0.6210 (t0) REVERT: X 167 ARG cc_start: 0.6240 (ttp-110) cc_final: 0.5002 (mmt90) REVERT: X 203 ARG cc_start: 0.6601 (ttt90) cc_final: 0.5927 (tpt-90) REVERT: X 209 CYS cc_start: 0.6354 (t) cc_final: 0.5975 (t) REVERT: X 389 ARG cc_start: 0.6500 (mtp180) cc_final: 0.5262 (mtm-85) REVERT: X 402 MET cc_start: 0.7193 (ttt) cc_final: 0.6969 (ttt) REVERT: X 446 MET cc_start: 0.8041 (ttm) cc_final: 0.7537 (ttm) REVERT: Y 15 GLU cc_start: 0.6992 (tt0) cc_final: 0.6559 (mt-10) REVERT: Y 18 LYS cc_start: 0.6715 (tttp) cc_final: 0.6343 (mptp) REVERT: Y 20 ARG cc_start: 0.6857 (mtt-85) cc_final: 0.6374 (mtt180) REVERT: Y 21 ASP cc_start: 0.7020 (t70) cc_final: 0.6206 (p0) REVERT: Y 77 ASP cc_start: 0.6784 (t0) cc_final: 0.6091 (t0) REVERT: Y 121 LYS cc_start: 0.6223 (ttpt) cc_final: 0.6008 (ttpp) REVERT: Y 167 ARG cc_start: 0.6553 (ptm-80) cc_final: 0.5203 (mmt90) REVERT: Y 203 ARG cc_start: 0.6684 (ttt90) cc_final: 0.5939 (tpt-90) REVERT: Y 209 CYS cc_start: 0.6092 (t) cc_final: 0.5630 (m) REVERT: Y 275 MET cc_start: 0.7540 (mmp) cc_final: 0.7121 (mmm) REVERT: Y 358 LEU cc_start: 0.6819 (mt) cc_final: 0.6592 (mt) REVERT: Y 389 ARG cc_start: 0.6754 (mtp180) cc_final: 0.5712 (mtm110) outliers start: 0 outliers final: 0 residues processed: 761 average time/residue: 1.5398 time to fit residues: 1382.1255 Evaluate side-chains 473 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 0.7980 chunk 400 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 413 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 251 optimal weight: 0.1980 chunk 308 optimal weight: 10.0000 chunk 479 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 156 GLN A 251 GLN A 415 HIS ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN B 272 GLN B 415 HIS C 156 GLN C 243 ASN C 415 HIS D 243 ASN D 415 HIS L 185 GLN L 415 HIS M 415 HIS O 62 GLN O 156 GLN O 185 GLN O 415 HIS P 243 ASN P 374 ASN P 415 HIS Q 156 GLN Q 185 GLN Q 415 HIS V 243 ASN V 272 GLN V 374 ASN X 185 GLN X 415 HIS Y 62 GLN Y 156 GLN Y 185 GLN Y 243 ASN Y 415 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 43112 Z= 0.221 Angle : 0.485 5.841 58386 Z= 0.257 Chirality : 0.043 0.159 6239 Planarity : 0.004 0.032 7631 Dihedral : 3.969 19.518 5784 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.90 % Allowed : 6.59 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.12), residues: 5292 helix: 2.27 (0.11), residues: 2052 sheet: -0.32 (0.17), residues: 924 loop : 0.53 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 39 HIS 0.008 0.001 HIS P 415 PHE 0.022 0.002 PHE P 64 TYR 0.018 0.001 TYR O 226 ARG 0.005 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 470 time to evaluate : 3.813 Fit side-chains REVERT: A 12 ASP cc_start: 0.6765 (m-30) cc_final: 0.6532 (m-30) REVERT: A 15 GLU cc_start: 0.6788 (tt0) cc_final: 0.6355 (mt-10) REVERT: A 20 ARG cc_start: 0.6651 (mtp85) cc_final: 0.5883 (mtt180) REVERT: A 21 ASP cc_start: 0.6986 (t70) cc_final: 0.6130 (p0) REVERT: A 47 GLU cc_start: 0.7227 (tt0) cc_final: 0.6991 (tp30) REVERT: A 77 ASP cc_start: 0.6795 (t0) cc_final: 0.6142 (t0) REVERT: A 152 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5602 (mp0) REVERT: A 185 GLN cc_start: 0.7931 (mt0) cc_final: 0.7722 (mt0) REVERT: A 203 ARG cc_start: 0.6230 (mtp-110) cc_final: 0.5769 (mmm-85) REVERT: A 358 LEU cc_start: 0.6510 (mt) cc_final: 0.6261 (mt) REVERT: A 389 ARG cc_start: 0.6696 (mmm-85) cc_final: 0.5564 (mtm110) REVERT: B 15 GLU cc_start: 0.6934 (tt0) cc_final: 0.6414 (mt-10) REVERT: B 21 ASP cc_start: 0.7376 (t0) cc_final: 0.6567 (p0) REVERT: B 44 GLU cc_start: 0.8115 (mp0) cc_final: 0.7472 (mp0) REVERT: B 47 GLU cc_start: 0.7554 (tt0) cc_final: 0.7209 (tp30) REVERT: B 73 LYS cc_start: 0.6591 (ttpp) cc_final: 0.5922 (ttpt) REVERT: B 77 ASP cc_start: 0.6896 (t0) cc_final: 0.6375 (t0) REVERT: B 104 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6784 (p0) REVERT: B 152 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5757 (mp0) REVERT: B 185 GLN cc_start: 0.7954 (mt0) cc_final: 0.7709 (mt0) REVERT: B 203 ARG cc_start: 0.6897 (ttt-90) cc_final: 0.6048 (tpt-90) REVERT: B 402 MET cc_start: 0.6926 (ttt) cc_final: 0.6594 (ttt) REVERT: C 12 ASP cc_start: 0.6833 (m-30) cc_final: 0.6619 (m-30) REVERT: C 15 GLU cc_start: 0.7006 (tt0) cc_final: 0.6697 (mt-10) REVERT: C 20 ARG cc_start: 0.6803 (mtp85) cc_final: 0.5843 (mtm-85) REVERT: C 21 ASP cc_start: 0.7359 (t70) cc_final: 0.6490 (p0) REVERT: C 44 GLU cc_start: 0.7948 (mp0) cc_final: 0.7562 (mp0) REVERT: C 47 GLU cc_start: 0.7260 (tt0) cc_final: 0.7016 (tp30) REVERT: C 82 ARG cc_start: 0.6366 (mtt-85) cc_final: 0.5975 (ttm-80) REVERT: C 358 LEU cc_start: 0.6300 (mt) cc_final: 0.6032 (mt) REVERT: C 389 ARG cc_start: 0.6928 (mmm-85) cc_final: 0.5777 (mtm110) REVERT: D 12 ASP cc_start: 0.6792 (m-30) cc_final: 0.6589 (m-30) REVERT: D 15 GLU cc_start: 0.6769 (tt0) cc_final: 0.6454 (mt-10) REVERT: D 18 LYS cc_start: 0.6966 (ttpt) cc_final: 0.6329 (mptp) REVERT: D 21 ASP cc_start: 0.7386 (t70) cc_final: 0.6444 (p0) REVERT: D 44 GLU cc_start: 0.7978 (mp0) cc_final: 0.7695 (mp0) REVERT: D 62 GLN cc_start: 0.5734 (mt0) cc_final: 0.5413 (mp10) REVERT: D 121 LYS cc_start: 0.6780 (ttmt) cc_final: 0.6305 (ttpp) REVERT: D 130 MET cc_start: 0.8052 (ttm) cc_final: 0.7810 (ttp) REVERT: D 152 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5824 (mp0) REVERT: D 203 ARG cc_start: 0.6607 (mtp-110) cc_final: 0.6055 (mmm-85) REVERT: D 258 LYS cc_start: 0.6443 (mtpp) cc_final: 0.5913 (mttm) REVERT: D 402 MET cc_start: 0.6976 (ttt) cc_final: 0.6732 (ttt) REVERT: L 15 GLU cc_start: 0.6792 (tt0) cc_final: 0.6234 (mt-10) REVERT: L 20 ARG cc_start: 0.7132 (mtp85) cc_final: 0.6361 (mtm-85) REVERT: L 47 GLU cc_start: 0.7489 (tt0) cc_final: 0.7275 (mm-30) REVERT: L 73 LYS cc_start: 0.6427 (ttpp) cc_final: 0.5801 (ttpt) REVERT: L 77 ASP cc_start: 0.6829 (t0) cc_final: 0.6316 (t0) REVERT: L 104 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6831 (p0) REVERT: L 130 MET cc_start: 0.8072 (ttm) cc_final: 0.7839 (ttm) REVERT: L 203 ARG cc_start: 0.6196 (mtp-110) cc_final: 0.5891 (mmm-85) REVERT: L 389 ARG cc_start: 0.6545 (mmm-85) cc_final: 0.5299 (mtm-85) REVERT: L 446 MET cc_start: 0.7971 (ttm) cc_final: 0.7322 (ttm) REVERT: M 10 LYS cc_start: 0.6673 (pttt) cc_final: 0.6460 (pttp) REVERT: M 12 ASP cc_start: 0.6752 (m-30) cc_final: 0.6546 (m-30) REVERT: M 20 ARG cc_start: 0.7136 (mtp85) cc_final: 0.6410 (mtm-85) REVERT: M 44 GLU cc_start: 0.8063 (mp0) cc_final: 0.7695 (mp0) REVERT: M 47 GLU cc_start: 0.7286 (tt0) cc_final: 0.6982 (mm-30) REVERT: M 73 LYS cc_start: 0.6378 (ttpt) cc_final: 0.5922 (ttpt) REVERT: M 77 ASP cc_start: 0.6893 (t0) cc_final: 0.6414 (t0) REVERT: M 104 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6806 (p0) REVERT: M 152 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5543 (mp0) REVERT: M 185 GLN cc_start: 0.7959 (mt0) cc_final: 0.7639 (mt0) REVERT: M 203 ARG cc_start: 0.6508 (ttt-90) cc_final: 0.5902 (mmm-85) REVERT: M 374 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.7061 (t0) REVERT: M 389 ARG cc_start: 0.6708 (mmm-85) cc_final: 0.5452 (mtm-85) REVERT: O 10 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5602 (ptmm) REVERT: O 12 ASP cc_start: 0.6743 (m-30) cc_final: 0.6538 (m-30) REVERT: O 15 GLU cc_start: 0.6900 (tt0) cc_final: 0.6360 (mt-10) REVERT: O 26 ARG cc_start: 0.6429 (mmt90) cc_final: 0.6089 (mtp85) REVERT: O 48 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6469 (mt-10) REVERT: O 55 MET cc_start: 0.8038 (mmm) cc_final: 0.7792 (mmt) REVERT: O 77 ASP cc_start: 0.6623 (t0) cc_final: 0.6062 (t0) REVERT: O 152 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5637 (mp0) REVERT: O 203 ARG cc_start: 0.6701 (ptm160) cc_final: 0.6049 (ptm160) REVERT: O 258 LYS cc_start: 0.6595 (mtpp) cc_final: 0.6101 (mttm) REVERT: O 389 ARG cc_start: 0.6954 (mmm-85) cc_final: 0.5600 (mtp-110) REVERT: P 12 ASP cc_start: 0.6812 (m-30) cc_final: 0.6611 (m-30) REVERT: P 15 GLU cc_start: 0.6961 (tt0) cc_final: 0.6535 (mt-10) REVERT: P 18 LYS cc_start: 0.6885 (tttt) cc_final: 0.6319 (mptp) REVERT: P 20 ARG cc_start: 0.7076 (mtt-85) cc_final: 0.6769 (mtt-85) REVERT: P 21 ASP cc_start: 0.7408 (t70) cc_final: 0.6483 (p0) REVERT: P 26 ARG cc_start: 0.5894 (mmt90) cc_final: 0.5499 (mmm160) REVERT: P 48 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6228 (pt0) REVERT: P 62 GLN cc_start: 0.5984 (mt0) cc_final: 0.5563 (mp10) REVERT: P 73 LYS cc_start: 0.6179 (ttpt) cc_final: 0.5911 (ttmm) REVERT: P 203 ARG cc_start: 0.7132 (mmm-85) cc_final: 0.6921 (mtp-110) REVERT: P 258 LYS cc_start: 0.6756 (mtpp) cc_final: 0.6220 (mttm) REVERT: P 389 ARG cc_start: 0.6962 (mmm-85) cc_final: 0.5603 (mtm-85) REVERT: Q 12 ASP cc_start: 0.7006 (m-30) cc_final: 0.6798 (m-30) REVERT: Q 15 GLU cc_start: 0.6843 (tt0) cc_final: 0.6418 (mt-10) REVERT: Q 18 LYS cc_start: 0.6818 (ttpt) cc_final: 0.6222 (mptp) REVERT: Q 21 ASP cc_start: 0.6956 (t70) cc_final: 0.6063 (p0) REVERT: Q 26 ARG cc_start: 0.6410 (mtt-85) cc_final: 0.6172 (mtp85) REVERT: Q 44 GLU cc_start: 0.7951 (mp0) cc_final: 0.7578 (mp0) REVERT: Q 47 GLU cc_start: 0.7278 (tt0) cc_final: 0.7051 (tp30) REVERT: Q 77 ASP cc_start: 0.6901 (t0) cc_final: 0.6293 (t0) REVERT: Q 121 LYS cc_start: 0.6634 (ttmt) cc_final: 0.6198 (ttpp) REVERT: Q 152 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5537 (mp0) REVERT: Q 203 ARG cc_start: 0.6525 (mtp-110) cc_final: 0.5877 (mmm-85) REVERT: Q 258 LYS cc_start: 0.6723 (mtpp) cc_final: 0.6485 (mtpp) REVERT: Q 389 ARG cc_start: 0.6879 (mmm-85) cc_final: 0.5711 (mtm110) REVERT: V 15 GLU cc_start: 0.6953 (tt0) cc_final: 0.6635 (mt-10) REVERT: V 18 LYS cc_start: 0.6931 (ttpt) cc_final: 0.6398 (mptp) REVERT: V 20 ARG cc_start: 0.6718 (mtt-85) cc_final: 0.6240 (mtt-85) REVERT: V 21 ASP cc_start: 0.7335 (t0) cc_final: 0.6497 (p0) REVERT: V 44 GLU cc_start: 0.7998 (mp0) cc_final: 0.7375 (mp0) REVERT: V 47 GLU cc_start: 0.7482 (tt0) cc_final: 0.7266 (tp30) REVERT: V 62 GLN cc_start: 0.5817 (OUTLIER) cc_final: 0.5608 (mp10) REVERT: V 104 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6763 (p0) REVERT: V 130 MET cc_start: 0.7988 (ttm) cc_final: 0.7748 (ttm) REVERT: V 152 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5687 (mp0) REVERT: V 185 GLN cc_start: 0.7990 (mt0) cc_final: 0.7754 (mt0) REVERT: V 203 ARG cc_start: 0.7019 (ttt-90) cc_final: 0.6033 (tpt-90) REVERT: X 15 GLU cc_start: 0.7099 (tt0) cc_final: 0.6781 (mt-10) REVERT: X 26 ARG cc_start: 0.6226 (ttm-80) cc_final: 0.5576 (ttt90) REVERT: X 64 PHE cc_start: 0.7452 (p90) cc_final: 0.7250 (p90) REVERT: X 73 LYS cc_start: 0.6430 (ttpp) cc_final: 0.5815 (ttpt) REVERT: X 77 ASP cc_start: 0.6954 (t0) cc_final: 0.6463 (t0) REVERT: X 104 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6835 (p0) REVERT: X 203 ARG cc_start: 0.6622 (ttt90) cc_final: 0.5834 (tpt-90) REVERT: X 389 ARG cc_start: 0.6513 (mtp180) cc_final: 0.5262 (mtm-85) REVERT: X 402 MET cc_start: 0.6943 (ttt) cc_final: 0.6670 (ttt) REVERT: X 446 MET cc_start: 0.8118 (ttm) cc_final: 0.7556 (ttm) REVERT: Y 15 GLU cc_start: 0.6899 (tt0) cc_final: 0.6503 (mt-10) REVERT: Y 77 ASP cc_start: 0.6941 (t0) cc_final: 0.6241 (t0) REVERT: Y 152 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5436 (mp0) REVERT: Y 185 GLN cc_start: 0.8239 (mt0) cc_final: 0.7933 (mt0) REVERT: Y 203 ARG cc_start: 0.6686 (ttt90) cc_final: 0.5912 (tpt-90) REVERT: Y 389 ARG cc_start: 0.6706 (mtp180) cc_final: 0.5690 (mtm110) outliers start: 85 outliers final: 24 residues processed: 531 average time/residue: 1.4772 time to fit residues: 932.8285 Evaluate side-chains 446 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 405 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 268 THR Chi-restraints excluded: chain M residue 104 ASP Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 268 THR Chi-restraints excluded: chain M residue 374 ASN Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 104 ASP Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain P residue 48 GLU Chi-restraints excluded: chain P residue 268 THR Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 268 THR Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 268 THR Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 104 ASP Chi-restraints excluded: chain X residue 268 THR Chi-restraints excluded: chain Y residue 104 ASP Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 373 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 399 optimal weight: 5.9990 chunk 326 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 480 optimal weight: 6.9990 chunk 518 optimal weight: 6.9990 chunk 427 optimal weight: 3.9990 chunk 476 optimal weight: 0.0050 chunk 163 optimal weight: 0.9990 chunk 385 optimal weight: 6.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 227 HIS B 62 GLN B 148 ASN C 156 GLN C 227 HIS ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS L 185 GLN O 156 GLN O 185 GLN P 185 GLN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 GLN Q 185 GLN Q 227 HIS V 148 ASN V 227 HIS V 415 HIS Y 156 GLN Y 227 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 43112 Z= 0.314 Angle : 0.520 9.477 58386 Z= 0.274 Chirality : 0.045 0.165 6239 Planarity : 0.004 0.039 7631 Dihedral : 4.214 19.103 5784 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.28 % Allowed : 7.71 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.12), residues: 5292 helix: 2.09 (0.11), residues: 2040 sheet: -0.54 (0.17), residues: 912 loop : 0.24 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 39 HIS 0.008 0.001 HIS O 227 PHE 0.030 0.002 PHE A 64 TYR 0.019 0.002 TYR M 219 ARG 0.005 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 404 time to evaluate : 3.798 Fit side-chains REVERT: A 12 ASP cc_start: 0.6844 (m-30) cc_final: 0.6610 (m-30) REVERT: A 15 GLU cc_start: 0.6778 (tt0) cc_final: 0.6339 (mt-10) REVERT: A 20 ARG cc_start: 0.6700 (mtp85) cc_final: 0.6091 (mtt180) REVERT: A 47 GLU cc_start: 0.7270 (tt0) cc_final: 0.7020 (tp30) REVERT: A 152 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5484 (mp0) REVERT: A 185 GLN cc_start: 0.8000 (mt0) cc_final: 0.7795 (mt0) REVERT: A 203 ARG cc_start: 0.6284 (mtp-110) cc_final: 0.5862 (mmm-85) REVERT: A 389 ARG cc_start: 0.6570 (mmm-85) cc_final: 0.5355 (mtm110) REVERT: B 15 GLU cc_start: 0.6928 (tt0) cc_final: 0.6388 (mt-10) REVERT: B 21 ASP cc_start: 0.7331 (t70) cc_final: 0.7126 (t70) REVERT: B 44 GLU cc_start: 0.8074 (mp0) cc_final: 0.7465 (mp0) REVERT: B 47 GLU cc_start: 0.7468 (tt0) cc_final: 0.7154 (tp30) REVERT: B 73 LYS cc_start: 0.6359 (ttpp) cc_final: 0.5725 (ttpt) REVERT: B 121 LYS cc_start: 0.6468 (mttp) cc_final: 0.6169 (ttpp) REVERT: B 167 ARG cc_start: 0.6111 (ttp-110) cc_final: 0.5155 (mmt90) REVERT: B 185 GLN cc_start: 0.7930 (mt0) cc_final: 0.7684 (mt0) REVERT: B 203 ARG cc_start: 0.6844 (ttt-90) cc_final: 0.5982 (tpt-90) REVERT: B 266 THR cc_start: 0.6052 (m) cc_final: 0.5387 (p) REVERT: B 402 MET cc_start: 0.6896 (ttt) cc_final: 0.6535 (ttt) REVERT: C 12 ASP cc_start: 0.6881 (m-30) cc_final: 0.6678 (m-30) REVERT: C 15 GLU cc_start: 0.7001 (tt0) cc_final: 0.6741 (mt-10) REVERT: C 18 LYS cc_start: 0.6890 (tttt) cc_final: 0.6323 (mptp) REVERT: C 20 ARG cc_start: 0.6996 (mtp85) cc_final: 0.5929 (mtm-85) REVERT: C 21 ASP cc_start: 0.7411 (t70) cc_final: 0.6509 (p0) REVERT: C 44 GLU cc_start: 0.7799 (mp0) cc_final: 0.7464 (mp0) REVERT: C 47 GLU cc_start: 0.7274 (tt0) cc_final: 0.6989 (tp30) REVERT: C 104 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7083 (p0) REVERT: C 152 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5479 (mp0) REVERT: C 167 ARG cc_start: 0.5850 (ptm-80) cc_final: 0.5610 (ptt90) REVERT: C 389 ARG cc_start: 0.6689 (mmm-85) cc_final: 0.5438 (mtm110) REVERT: D 5 LYS cc_start: 0.4564 (OUTLIER) cc_final: 0.4206 (ttpt) REVERT: D 12 ASP cc_start: 0.6840 (m-30) cc_final: 0.6635 (m-30) REVERT: D 15 GLU cc_start: 0.6740 (tt0) cc_final: 0.6463 (mt-10) REVERT: D 18 LYS cc_start: 0.6933 (ttpt) cc_final: 0.6311 (mptp) REVERT: D 21 ASP cc_start: 0.7476 (t70) cc_final: 0.6523 (p0) REVERT: D 44 GLU cc_start: 0.7907 (mp0) cc_final: 0.7405 (mp0) REVERT: D 62 GLN cc_start: 0.5822 (mt0) cc_final: 0.5433 (mp10) REVERT: D 104 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6964 (p0) REVERT: D 152 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5449 (mp0) REVERT: D 156 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8028 (mm110) REVERT: D 258 LYS cc_start: 0.6435 (mtpp) cc_final: 0.6117 (mtpp) REVERT: L 15 GLU cc_start: 0.6793 (tt0) cc_final: 0.6251 (mt-10) REVERT: L 20 ARG cc_start: 0.7060 (mtp85) cc_final: 0.6247 (mtm-85) REVERT: L 47 GLU cc_start: 0.7554 (tt0) cc_final: 0.7172 (tp30) REVERT: L 62 GLN cc_start: 0.6008 (OUTLIER) cc_final: 0.5769 (mp10) REVERT: L 72 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6960 (mtt) REVERT: L 73 LYS cc_start: 0.6375 (ttpp) cc_final: 0.5744 (ttpt) REVERT: L 203 ARG cc_start: 0.6266 (mtp-110) cc_final: 0.5927 (mmm-85) REVERT: L 389 ARG cc_start: 0.6480 (mmm-85) cc_final: 0.5261 (mtm-85) REVERT: L 402 MET cc_start: 0.6868 (ttt) cc_final: 0.6565 (ttt) REVERT: M 10 LYS cc_start: 0.6575 (pttt) cc_final: 0.6339 (pttp) REVERT: M 20 ARG cc_start: 0.6964 (mtp85) cc_final: 0.6152 (mtm-85) REVERT: M 44 GLU cc_start: 0.8003 (mp0) cc_final: 0.7494 (mp0) REVERT: M 47 GLU cc_start: 0.7250 (tt0) cc_final: 0.6780 (tp30) REVERT: M 62 GLN cc_start: 0.6511 (pt0) cc_final: 0.6306 (mt0) REVERT: M 152 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5673 (mp0) REVERT: M 167 ARG cc_start: 0.5750 (ttp-110) cc_final: 0.4931 (mmt90) REVERT: M 185 GLN cc_start: 0.7989 (mt0) cc_final: 0.7670 (mt0) REVERT: M 203 ARG cc_start: 0.6516 (ttt-90) cc_final: 0.5765 (mmm-85) REVERT: M 374 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7100 (t0) REVERT: M 389 ARG cc_start: 0.6616 (mmm-85) cc_final: 0.5286 (mtm-85) REVERT: O 12 ASP cc_start: 0.6813 (m-30) cc_final: 0.6578 (m-30) REVERT: O 15 GLU cc_start: 0.6963 (tt0) cc_final: 0.6440 (mt-10) REVERT: O 26 ARG cc_start: 0.6090 (mmt90) cc_final: 0.5572 (mmm160) REVERT: O 48 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6653 (mt-10) REVERT: O 152 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5522 (mp0) REVERT: O 203 ARG cc_start: 0.6884 (ptm160) cc_final: 0.6243 (ptt90) REVERT: O 204 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: O 209 CYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5645 (m) REVERT: O 258 LYS cc_start: 0.6697 (mtpp) cc_final: 0.6238 (mttm) REVERT: P 12 ASP cc_start: 0.6849 (m-30) cc_final: 0.6633 (m-30) REVERT: P 15 GLU cc_start: 0.7015 (tt0) cc_final: 0.6603 (mt-10) REVERT: P 18 LYS cc_start: 0.6918 (tttt) cc_final: 0.6341 (mptp) REVERT: P 20 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6844 (mtt-85) REVERT: P 21 ASP cc_start: 0.7487 (t70) cc_final: 0.6566 (p0) REVERT: P 26 ARG cc_start: 0.6211 (mmt90) cc_final: 0.5902 (mmm160) REVERT: P 48 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6291 (pt0) REVERT: P 62 GLN cc_start: 0.5963 (mt0) cc_final: 0.5585 (mp10) REVERT: P 73 LYS cc_start: 0.6221 (ttpt) cc_final: 0.5884 (ttmm) REVERT: P 104 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6896 (p0) REVERT: P 152 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5520 (mp0) REVERT: P 156 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8068 (mm110) REVERT: P 203 ARG cc_start: 0.7116 (mmm-85) cc_final: 0.6905 (mtp-110) REVERT: P 258 LYS cc_start: 0.6578 (mtpp) cc_final: 0.5988 (mttm) REVERT: P 389 ARG cc_start: 0.6751 (mmm-85) cc_final: 0.5512 (mtm110) REVERT: P 402 MET cc_start: 0.7150 (ttt) cc_final: 0.6830 (ttt) REVERT: Q 12 ASP cc_start: 0.6920 (m-30) cc_final: 0.6676 (m-30) REVERT: Q 15 GLU cc_start: 0.6816 (tt0) cc_final: 0.6426 (mt-10) REVERT: Q 18 LYS cc_start: 0.6701 (ttpt) cc_final: 0.6075 (mptp) REVERT: Q 26 ARG cc_start: 0.6506 (mtt-85) cc_final: 0.6185 (mtp85) REVERT: Q 44 GLU cc_start: 0.7817 (mp0) cc_final: 0.7443 (mp0) REVERT: Q 47 GLU cc_start: 0.7168 (tt0) cc_final: 0.6890 (tp30) REVERT: Q 152 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: Q 203 ARG cc_start: 0.6479 (mtp-110) cc_final: 0.5883 (mmm-85) REVERT: Q 209 CYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5613 (m) REVERT: Q 389 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.5601 (mtm110) REVERT: V 15 GLU cc_start: 0.6930 (tt0) cc_final: 0.6680 (mt-10) REVERT: V 18 LYS cc_start: 0.6919 (ttpt) cc_final: 0.6382 (mptp) REVERT: V 20 ARG cc_start: 0.6837 (mtt-85) cc_final: 0.6349 (mtm-85) REVERT: V 21 ASP cc_start: 0.7533 (t70) cc_final: 0.6662 (p0) REVERT: V 47 GLU cc_start: 0.7540 (tt0) cc_final: 0.7310 (tp30) REVERT: V 62 GLN cc_start: 0.5943 (OUTLIER) cc_final: 0.5703 (mp10) REVERT: V 104 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6817 (p0) REVERT: V 121 LYS cc_start: 0.6465 (OUTLIER) cc_final: 0.6166 (ttpp) REVERT: V 152 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5399 (mp0) REVERT: V 156 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8004 (mm110) REVERT: V 167 ARG cc_start: 0.5962 (ptm-80) cc_final: 0.5726 (ptt90) REVERT: V 203 ARG cc_start: 0.7009 (ttt-90) cc_final: 0.6061 (tpt-90) REVERT: X 15 GLU cc_start: 0.7094 (tt0) cc_final: 0.6820 (mt-10) REVERT: X 26 ARG cc_start: 0.6104 (ttm-80) cc_final: 0.5466 (ttt90) REVERT: X 73 LYS cc_start: 0.6306 (ttpp) cc_final: 0.5692 (ttpt) REVERT: X 104 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6982 (p0) REVERT: X 203 ARG cc_start: 0.6651 (ttt90) cc_final: 0.5771 (tpt-90) REVERT: X 402 MET cc_start: 0.6991 (ttt) cc_final: 0.6662 (ttt) REVERT: Y 15 GLU cc_start: 0.6930 (tt0) cc_final: 0.6558 (mt-10) REVERT: Y 26 ARG cc_start: 0.6226 (ttm-80) cc_final: 0.5997 (mtp180) REVERT: Y 152 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5447 (mp0) REVERT: Y 203 ARG cc_start: 0.6712 (ttt90) cc_final: 0.5954 (tpt-90) outliers start: 102 outliers final: 41 residues processed: 476 average time/residue: 1.5282 time to fit residues: 862.9118 Evaluate side-chains 437 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 372 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 182 MET Chi-restraints excluded: chain L residue 226 TYR Chi-restraints excluded: chain L residue 268 THR Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain M residue 48 GLU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 226 TYR Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 268 THR Chi-restraints excluded: chain M residue 374 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 104 ASP Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 204 PHE Chi-restraints excluded: chain O residue 209 CYS Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain P residue 48 GLU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 104 ASP Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 268 THR Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 209 CYS Chi-restraints excluded: chain Q residue 268 THR Chi-restraints excluded: chain V residue 12 ASP Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 72 MET Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 121 LYS Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 226 TYR Chi-restraints excluded: chain V residue 268 THR Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 104 ASP Chi-restraints excluded: chain X residue 226 TYR Chi-restraints excluded: chain X residue 268 THR Chi-restraints excluded: chain Y residue 104 ASP Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 268 THR Chi-restraints excluded: chain Y residue 373 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 0.9980 chunk 361 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 482 optimal weight: 2.9990 chunk 510 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 456 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 156 GLN A 227 HIS C 227 HIS ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS L 185 GLN O 156 GLN O 185 GLN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 GLN Q 185 GLN Q 227 HIS V 185 GLN V 227 HIS Y 62 GLN Y 156 GLN Y 185 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 43112 Z= 0.137 Angle : 0.431 5.742 58386 Z= 0.227 Chirality : 0.041 0.153 6239 Planarity : 0.003 0.030 7631 Dihedral : 3.876 18.899 5784 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.72 % Allowed : 9.16 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.12), residues: 5292 helix: 2.32 (0.11), residues: 2040 sheet: -0.55 (0.17), residues: 972 loop : 0.15 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 39 HIS 0.003 0.001 HIS C 415 PHE 0.023 0.001 PHE P 64 TYR 0.016 0.001 TYR M 219 ARG 0.004 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 428 time to evaluate : 4.577 Fit side-chains REVERT: A 12 ASP cc_start: 0.6778 (m-30) cc_final: 0.6546 (m-30) REVERT: A 15 GLU cc_start: 0.6788 (tt0) cc_final: 0.6371 (mt-10) REVERT: A 20 ARG cc_start: 0.6671 (mtp85) cc_final: 0.5969 (mtt180) REVERT: A 21 ASP cc_start: 0.7029 (t70) cc_final: 0.6217 (p0) REVERT: A 47 GLU cc_start: 0.7135 (tt0) cc_final: 0.6932 (tp30) REVERT: A 152 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5570 (mp0) REVERT: A 203 ARG cc_start: 0.6300 (mtp-110) cc_final: 0.5969 (mmm-85) REVERT: A 226 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: A 389 ARG cc_start: 0.6497 (mmm-85) cc_final: 0.5286 (mtm110) REVERT: B 15 GLU cc_start: 0.6944 (tt0) cc_final: 0.6395 (mt-10) REVERT: B 44 GLU cc_start: 0.8084 (mp0) cc_final: 0.7421 (mp0) REVERT: B 73 LYS cc_start: 0.6324 (ttpp) cc_final: 0.5751 (ttpt) REVERT: B 104 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6935 (p0) REVERT: B 121 LYS cc_start: 0.6426 (mttp) cc_final: 0.6159 (ttpp) REVERT: B 185 GLN cc_start: 0.7892 (mt0) cc_final: 0.7569 (mt0) REVERT: B 203 ARG cc_start: 0.6795 (ttt-90) cc_final: 0.5903 (tpt-90) REVERT: B 402 MET cc_start: 0.6949 (ttt) cc_final: 0.6573 (ttt) REVERT: C 15 GLU cc_start: 0.6978 (tt0) cc_final: 0.6730 (mt-10) REVERT: C 20 ARG cc_start: 0.7070 (mtp85) cc_final: 0.6026 (mtm-85) REVERT: C 21 ASP cc_start: 0.7550 (t70) cc_final: 0.6604 (p0) REVERT: C 44 GLU cc_start: 0.7798 (mp0) cc_final: 0.7286 (mp0) REVERT: C 47 GLU cc_start: 0.7154 (tt0) cc_final: 0.6909 (tp30) REVERT: C 82 ARG cc_start: 0.5965 (mtt-85) cc_final: 0.5686 (ttm-80) REVERT: C 104 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6873 (p0) REVERT: C 152 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5351 (mp0) REVERT: C 389 ARG cc_start: 0.6664 (mmm-85) cc_final: 0.5412 (mtm110) REVERT: D 15 GLU cc_start: 0.6772 (tt0) cc_final: 0.6512 (mt-10) REVERT: D 18 LYS cc_start: 0.6811 (ttpt) cc_final: 0.6229 (mptp) REVERT: D 21 ASP cc_start: 0.7543 (t70) cc_final: 0.6647 (p0) REVERT: D 44 GLU cc_start: 0.7845 (mp0) cc_final: 0.7312 (mp0) REVERT: D 62 GLN cc_start: 0.5842 (mt0) cc_final: 0.5517 (mp10) REVERT: D 152 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.5388 (mp0) REVERT: D 156 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8180 (mm110) REVERT: D 181 HIS cc_start: 0.6872 (t70) cc_final: 0.6125 (t70) REVERT: D 258 LYS cc_start: 0.6548 (mtpp) cc_final: 0.6229 (mtpp) REVERT: L 15 GLU cc_start: 0.6853 (tt0) cc_final: 0.6335 (mt-10) REVERT: L 20 ARG cc_start: 0.7180 (mtp85) cc_final: 0.6388 (mtm-85) REVERT: L 72 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7151 (mtt) REVERT: L 73 LYS cc_start: 0.6263 (ttpp) cc_final: 0.5710 (ttpt) REVERT: L 152 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5692 (mp0) REVERT: L 156 GLN cc_start: 0.8143 (mp10) cc_final: 0.7714 (mm110) REVERT: L 203 ARG cc_start: 0.6248 (mtp-110) cc_final: 0.5897 (mmm-85) REVERT: L 355 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5987 (mmm160) REVERT: L 389 ARG cc_start: 0.6517 (mmm-85) cc_final: 0.5248 (mtm-85) REVERT: L 402 MET cc_start: 0.6826 (ttt) cc_final: 0.6534 (ttt) REVERT: L 446 MET cc_start: 0.7899 (ttm) cc_final: 0.7356 (ttm) REVERT: M 20 ARG cc_start: 0.6975 (mtp85) cc_final: 0.6146 (mtm-85) REVERT: M 44 GLU cc_start: 0.7967 (mp0) cc_final: 0.7462 (mp0) REVERT: M 47 GLU cc_start: 0.7266 (tt0) cc_final: 0.6996 (mm-30) REVERT: M 77 ASP cc_start: 0.6656 (t0) cc_final: 0.6415 (t0) REVERT: M 156 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7514 (mt0) REVERT: M 185 GLN cc_start: 0.7978 (mt0) cc_final: 0.7661 (mt0) REVERT: M 203 ARG cc_start: 0.6579 (ttt-90) cc_final: 0.5772 (mmm-85) REVERT: M 389 ARG cc_start: 0.6625 (mmm-85) cc_final: 0.5287 (mtm-85) REVERT: O 12 ASP cc_start: 0.6791 (m-30) cc_final: 0.6585 (m-30) REVERT: O 15 GLU cc_start: 0.6912 (tt0) cc_final: 0.6440 (mt-10) REVERT: O 26 ARG cc_start: 0.6091 (mmt90) cc_final: 0.5713 (mtp180) REVERT: O 48 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6465 (mt-10) REVERT: O 55 MET cc_start: 0.7717 (mmm) cc_final: 0.7340 (mmt) REVERT: O 152 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5583 (mp0) REVERT: O 203 ARG cc_start: 0.6906 (ptm160) cc_final: 0.6274 (ptt90) REVERT: O 258 LYS cc_start: 0.6596 (mtpp) cc_final: 0.6098 (mttm) REVERT: P 12 ASP cc_start: 0.6827 (m-30) cc_final: 0.6624 (m-30) REVERT: P 15 GLU cc_start: 0.6971 (tt0) cc_final: 0.6529 (mt-10) REVERT: P 18 LYS cc_start: 0.6838 (tttt) cc_final: 0.6269 (mptp) REVERT: P 20 ARG cc_start: 0.7145 (mtt-85) cc_final: 0.6845 (mtt-85) REVERT: P 21 ASP cc_start: 0.7482 (t70) cc_final: 0.6607 (p0) REVERT: P 26 ARG cc_start: 0.6058 (mmt90) cc_final: 0.5815 (mmm160) REVERT: P 73 LYS cc_start: 0.6194 (ttpt) cc_final: 0.5822 (ttmm) REVERT: P 152 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5396 (mp0) REVERT: P 156 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8196 (mm110) REVERT: P 176 ASP cc_start: 0.5936 (m-30) cc_final: 0.5696 (m-30) REVERT: P 258 LYS cc_start: 0.6604 (mtpp) cc_final: 0.5993 (mttm) REVERT: P 389 ARG cc_start: 0.6723 (mmm-85) cc_final: 0.5500 (mtm110) REVERT: P 402 MET cc_start: 0.7126 (ttt) cc_final: 0.6922 (ttt) REVERT: Q 12 ASP cc_start: 0.6978 (m-30) cc_final: 0.6763 (m-30) REVERT: Q 15 GLU cc_start: 0.6822 (tt0) cc_final: 0.6418 (mt-10) REVERT: Q 21 ASP cc_start: 0.7072 (t70) cc_final: 0.6223 (p0) REVERT: Q 26 ARG cc_start: 0.6434 (mtt-85) cc_final: 0.6194 (mtp85) REVERT: Q 44 GLU cc_start: 0.7794 (mp0) cc_final: 0.7376 (mp0) REVERT: Q 47 GLU cc_start: 0.7082 (tt0) cc_final: 0.6859 (tp30) REVERT: Q 203 ARG cc_start: 0.6431 (mtp-110) cc_final: 0.5855 (mmm-85) REVERT: Q 226 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: Q 389 ARG cc_start: 0.6728 (mmm-85) cc_final: 0.5576 (mtm110) REVERT: V 15 GLU cc_start: 0.6909 (tt0) cc_final: 0.6692 (mt-10) REVERT: V 18 LYS cc_start: 0.6822 (ttpt) cc_final: 0.6295 (mptp) REVERT: V 20 ARG cc_start: 0.6768 (mtt-85) cc_final: 0.6355 (mtm-85) REVERT: V 21 ASP cc_start: 0.7465 (t70) cc_final: 0.6622 (p0) REVERT: V 62 GLN cc_start: 0.5716 (OUTLIER) cc_final: 0.5506 (mp10) REVERT: V 104 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6737 (p0) REVERT: V 152 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5327 (mp0) REVERT: V 156 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8216 (mm110) REVERT: V 203 ARG cc_start: 0.7116 (ttt-90) cc_final: 0.6171 (tpt-90) REVERT: X 15 GLU cc_start: 0.7084 (tt0) cc_final: 0.6815 (mt-10) REVERT: X 26 ARG cc_start: 0.6269 (ttm-80) cc_final: 0.5608 (ttt90) REVERT: X 72 MET cc_start: 0.6693 (mtt) cc_final: 0.6468 (mtt) REVERT: X 73 LYS cc_start: 0.6256 (ttpp) cc_final: 0.5676 (ttpt) REVERT: X 104 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6977 (p0) REVERT: X 152 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5583 (mp0) REVERT: X 156 GLN cc_start: 0.8106 (mp10) cc_final: 0.7711 (mm110) REVERT: X 203 ARG cc_start: 0.6564 (ttt90) cc_final: 0.5803 (tpt-90) REVERT: X 402 MET cc_start: 0.6971 (ttt) cc_final: 0.6648 (ttt) REVERT: Y 15 GLU cc_start: 0.7008 (tt0) cc_final: 0.6689 (mt-10) REVERT: Y 26 ARG cc_start: 0.6206 (ttm-80) cc_final: 0.5955 (mtp180) REVERT: Y 152 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5496 (mp0) REVERT: Y 203 ARG cc_start: 0.6672 (ttt90) cc_final: 0.5918 (tpt-90) REVERT: Y 226 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.6096 (m-80) REVERT: Y 358 LEU cc_start: 0.6636 (mt) cc_final: 0.6433 (mt) outliers start: 77 outliers final: 19 residues processed: 476 average time/residue: 1.4151 time to fit residues: 806.6662 Evaluate side-chains 426 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 387 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 226 TYR Chi-restraints excluded: chain L residue 355 ARG Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 226 TYR Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 104 ASP Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 226 TYR Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 362 LYS Chi-restraints excluded: chain X residue 104 ASP Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain X residue 226 TYR Chi-restraints excluded: chain Y residue 104 ASP Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 226 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 7 optimal weight: 0.0270 chunk 380 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 435 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 458 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 156 GLN A 185 GLN A 227 HIS C 156 GLN C 227 HIS ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 317 GLN L 185 GLN O 148 ASN O 156 GLN O 185 GLN P 227 HIS ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 GLN Q 185 GLN Q 227 HIS V 185 GLN V 227 HIS X 243 ASN Y 156 GLN Y 185 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 43112 Z= 0.369 Angle : 0.529 5.924 58386 Z= 0.279 Chirality : 0.045 0.169 6239 Planarity : 0.004 0.035 7631 Dihedral : 4.238 19.325 5784 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.41 % Allowed : 9.45 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.12), residues: 5292 helix: 2.07 (0.11), residues: 2040 sheet: -0.70 (0.17), residues: 924 loop : 0.10 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 438 HIS 0.008 0.001 HIS O 227 PHE 0.027 0.002 PHE C 64 TYR 0.020 0.002 TYR L 219 ARG 0.003 0.000 ARG L 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 361 time to evaluate : 3.830 Fit side-chains REVERT: A 12 ASP cc_start: 0.6826 (m-30) cc_final: 0.6605 (m-30) REVERT: A 15 GLU cc_start: 0.6782 (tt0) cc_final: 0.6349 (mt-10) REVERT: A 47 GLU cc_start: 0.7265 (tt0) cc_final: 0.7008 (tp30) REVERT: A 152 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5443 (mp0) REVERT: A 203 ARG cc_start: 0.6432 (mtp-110) cc_final: 0.5870 (mmm-85) REVERT: A 226 TYR cc_start: 0.6508 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: A 389 ARG cc_start: 0.6526 (mmm-85) cc_final: 0.5286 (mtm110) REVERT: B 15 GLU cc_start: 0.6911 (tt0) cc_final: 0.6366 (mt-10) REVERT: B 44 GLU cc_start: 0.7747 (mp0) cc_final: 0.6992 (mp0) REVERT: B 73 LYS cc_start: 0.6253 (ttpp) cc_final: 0.5647 (ttpt) REVERT: B 121 LYS cc_start: 0.6441 (mttp) cc_final: 0.6181 (ttpp) REVERT: B 167 ARG cc_start: 0.6098 (ttp-110) cc_final: 0.5141 (mmt90) REVERT: B 185 GLN cc_start: 0.7952 (mt0) cc_final: 0.7661 (mt0) REVERT: B 203 ARG cc_start: 0.6804 (ttt-90) cc_final: 0.5952 (tpt-90) REVERT: B 402 MET cc_start: 0.6880 (ttt) cc_final: 0.6495 (ttt) REVERT: C 15 GLU cc_start: 0.6950 (tt0) cc_final: 0.6711 (mt-10) REVERT: C 18 LYS cc_start: 0.6743 (tttt) cc_final: 0.6199 (mptp) REVERT: C 21 ASP cc_start: 0.7451 (t70) cc_final: 0.6559 (p0) REVERT: C 44 GLU cc_start: 0.7699 (mp0) cc_final: 0.7306 (mp0) REVERT: C 47 GLU cc_start: 0.7290 (tt0) cc_final: 0.7001 (tp30) REVERT: C 104 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7167 (p0) REVERT: C 152 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5449 (mp0) REVERT: C 389 ARG cc_start: 0.6632 (mmm-85) cc_final: 0.5418 (mtm110) REVERT: D 15 GLU cc_start: 0.6762 (tt0) cc_final: 0.6557 (mt-10) REVERT: D 18 LYS cc_start: 0.6929 (ttpt) cc_final: 0.6313 (mptp) REVERT: D 21 ASP cc_start: 0.7487 (t70) cc_final: 0.6539 (p0) REVERT: D 44 GLU cc_start: 0.7790 (mp0) cc_final: 0.7405 (mp0) REVERT: D 82 ARG cc_start: 0.6190 (OUTLIER) cc_final: 0.5782 (ttm-80) REVERT: D 152 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5546 (mp0) REVERT: D 156 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8190 (mm110) REVERT: L 15 GLU cc_start: 0.6830 (tt0) cc_final: 0.6320 (mt-10) REVERT: L 20 ARG cc_start: 0.7004 (mtp85) cc_final: 0.6225 (mtm-85) REVERT: L 62 GLN cc_start: 0.5985 (OUTLIER) cc_final: 0.5724 (mp10) REVERT: L 72 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6949 (mtt) REVERT: L 130 MET cc_start: 0.8136 (ttp) cc_final: 0.7918 (ttp) REVERT: L 152 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5623 (mp0) REVERT: L 156 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: L 203 ARG cc_start: 0.6333 (mtp-110) cc_final: 0.6015 (mmm-85) REVERT: L 389 ARG cc_start: 0.6521 (mmm-85) cc_final: 0.5271 (mtm-85) REVERT: L 402 MET cc_start: 0.6858 (ttt) cc_final: 0.6570 (ttt) REVERT: M 20 ARG cc_start: 0.6923 (mtp85) cc_final: 0.6169 (mtm-85) REVERT: M 44 GLU cc_start: 0.7886 (mp0) cc_final: 0.7396 (mp0) REVERT: M 47 GLU cc_start: 0.7301 (tt0) cc_final: 0.6955 (tp30) REVERT: M 152 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5454 (mp0) REVERT: M 156 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7619 (mt0) REVERT: M 167 ARG cc_start: 0.5958 (ttp-110) cc_final: 0.5026 (mmt90) REVERT: M 185 GLN cc_start: 0.8030 (mt0) cc_final: 0.7701 (mt0) REVERT: M 203 ARG cc_start: 0.6616 (ttt-90) cc_final: 0.5818 (mmm-85) REVERT: M 374 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7143 (t0) REVERT: M 389 ARG cc_start: 0.6658 (mmm-85) cc_final: 0.5310 (mtm-85) REVERT: O 12 ASP cc_start: 0.6814 (m-30) cc_final: 0.6592 (m-30) REVERT: O 15 GLU cc_start: 0.6911 (tt0) cc_final: 0.6374 (mt-10) REVERT: O 26 ARG cc_start: 0.6029 (mmt90) cc_final: 0.5642 (mtp180) REVERT: O 48 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6754 (mt-10) REVERT: O 152 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5467 (mp0) REVERT: O 203 ARG cc_start: 0.6719 (ptm160) cc_final: 0.6127 (ptt90) REVERT: O 209 CYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5655 (m) REVERT: O 258 LYS cc_start: 0.6681 (mtpp) cc_final: 0.6182 (mttm) REVERT: P 12 ASP cc_start: 0.6851 (m-30) cc_final: 0.6631 (m-30) REVERT: P 15 GLU cc_start: 0.6983 (tt0) cc_final: 0.6551 (mt-10) REVERT: P 18 LYS cc_start: 0.6947 (tttt) cc_final: 0.6359 (mptp) REVERT: P 20 ARG cc_start: 0.7212 (mtt-85) cc_final: 0.6917 (mtt-85) REVERT: P 21 ASP cc_start: 0.7303 (t70) cc_final: 0.6484 (p0) REVERT: P 26 ARG cc_start: 0.6171 (mmt90) cc_final: 0.5962 (mmt180) REVERT: P 48 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6278 (pt0) REVERT: P 104 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6928 (p0) REVERT: P 152 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: P 258 LYS cc_start: 0.6520 (mtpp) cc_final: 0.5938 (mttm) REVERT: P 266 THR cc_start: 0.6745 (m) cc_final: 0.6059 (p) REVERT: P 402 MET cc_start: 0.7101 (ttt) cc_final: 0.6890 (ttt) REVERT: Q 12 ASP cc_start: 0.6924 (m-30) cc_final: 0.6653 (m-30) REVERT: Q 15 GLU cc_start: 0.6798 (tt0) cc_final: 0.6401 (mt-10) REVERT: Q 18 LYS cc_start: 0.6718 (ttpt) cc_final: 0.6426 (tptm) REVERT: Q 26 ARG cc_start: 0.6431 (mtt-85) cc_final: 0.6168 (mtp85) REVERT: Q 47 GLU cc_start: 0.7211 (tt0) cc_final: 0.6845 (tp30) REVERT: Q 152 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5435 (mp0) REVERT: Q 203 ARG cc_start: 0.6532 (mtp-110) cc_final: 0.5925 (mmm-85) REVERT: Q 209 CYS cc_start: 0.5886 (OUTLIER) cc_final: 0.5632 (m) REVERT: Q 226 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5979 (m-80) REVERT: Q 389 ARG cc_start: 0.6630 (mmm-85) cc_final: 0.5493 (mtm110) REVERT: V 18 LYS cc_start: 0.6944 (ttpt) cc_final: 0.6388 (mptp) REVERT: V 20 ARG cc_start: 0.6812 (mtt-85) cc_final: 0.6402 (mtt-85) REVERT: V 21 ASP cc_start: 0.7340 (t70) cc_final: 0.6517 (p0) REVERT: V 62 GLN cc_start: 0.5891 (OUTLIER) cc_final: 0.5463 (mp10) REVERT: V 104 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6893 (p0) REVERT: V 121 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.6227 (ttpp) REVERT: V 152 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5294 (mp0) REVERT: V 156 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8074 (mm110) REVERT: V 167 ARG cc_start: 0.6222 (ptm-80) cc_final: 0.6014 (ptt90) REVERT: V 203 ARG cc_start: 0.7119 (ttt-90) cc_final: 0.6180 (tpt-90) REVERT: X 15 GLU cc_start: 0.7094 (tt0) cc_final: 0.6828 (mt-10) REVERT: X 26 ARG cc_start: 0.6205 (ttm-80) cc_final: 0.5590 (ttt90) REVERT: X 73 LYS cc_start: 0.6289 (ttpp) cc_final: 0.5712 (ttpt) REVERT: X 152 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5560 (mp0) REVERT: X 156 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7602 (mt0) REVERT: X 203 ARG cc_start: 0.6536 (ttt90) cc_final: 0.5745 (tpt-90) REVERT: X 402 MET cc_start: 0.6849 (ttt) cc_final: 0.6516 (ttt) REVERT: Y 15 GLU cc_start: 0.6964 (tt0) cc_final: 0.6601 (mt-10) REVERT: Y 26 ARG cc_start: 0.6310 (ttm-80) cc_final: 0.6086 (mtp85) REVERT: Y 152 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5480 (mp0) REVERT: Y 185 GLN cc_start: 0.8282 (mt0) cc_final: 0.8062 (mt0) REVERT: Y 203 ARG cc_start: 0.6653 (ttt90) cc_final: 0.5978 (tpt-90) REVERT: Y 226 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5981 (m-80) outliers start: 108 outliers final: 44 residues processed: 444 average time/residue: 1.4743 time to fit residues: 780.0261 Evaluate side-chains 420 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 347 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 182 MET Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 226 TYR Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 204 PHE Chi-restraints excluded: chain M residue 226 TYR Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 268 THR Chi-restraints excluded: chain M residue 374 ASN Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 104 ASP Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain O residue 209 CYS Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain P residue 48 GLU Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 104 ASP Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 204 PHE Chi-restraints excluded: chain P residue 226 TYR Chi-restraints excluded: chain P residue 268 THR Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 209 CYS Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain V residue 12 ASP Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 121 LYS Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 268 THR Chi-restraints excluded: chain V residue 362 LYS Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain X residue 226 TYR Chi-restraints excluded: chain X residue 268 THR Chi-restraints excluded: chain Y residue 104 ASP Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 226 TYR Chi-restraints excluded: chain Y residue 268 THR Chi-restraints excluded: chain Y residue 373 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 6.9990 chunk 459 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 510 optimal weight: 8.9990 chunk 424 optimal weight: 0.4980 chunk 236 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 168 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 156 GLN A 185 GLN A 227 HIS C 156 GLN C 227 HIS ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS L 185 GLN O 62 GLN O 156 GLN O 185 GLN P 156 GLN P 227 HIS ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 GLN Q 227 HIS V 185 GLN V 227 HIS Y 62 GLN Y 156 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 43112 Z= 0.150 Angle : 0.434 5.698 58386 Z= 0.229 Chirality : 0.041 0.153 6239 Planarity : 0.003 0.031 7631 Dihedral : 3.897 19.188 5784 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.88 % Allowed : 10.32 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.12), residues: 5292 helix: 2.34 (0.11), residues: 2040 sheet: -0.70 (0.17), residues: 972 loop : 0.01 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 39 HIS 0.003 0.001 HIS O 227 PHE 0.024 0.001 PHE V 64 TYR 0.015 0.001 TYR L 219 ARG 0.003 0.000 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 392 time to evaluate : 3.902 Fit side-chains REVERT: A 12 ASP cc_start: 0.6761 (m-30) cc_final: 0.6540 (m-30) REVERT: A 15 GLU cc_start: 0.6779 (tt0) cc_final: 0.6347 (mt-10) REVERT: A 21 ASP cc_start: 0.6951 (t70) cc_final: 0.6222 (p0) REVERT: A 47 GLU cc_start: 0.7143 (tt0) cc_final: 0.6933 (tp30) REVERT: A 152 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5515 (mp0) REVERT: A 176 ASP cc_start: 0.5619 (m-30) cc_final: 0.5392 (m-30) REVERT: A 203 ARG cc_start: 0.6391 (mtp-110) cc_final: 0.5839 (mmm-85) REVERT: A 226 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.6159 (m-80) REVERT: A 389 ARG cc_start: 0.6489 (mmm-85) cc_final: 0.5245 (mtm110) REVERT: B 15 GLU cc_start: 0.6902 (tt0) cc_final: 0.6378 (mt-10) REVERT: B 73 LYS cc_start: 0.6223 (ttpp) cc_final: 0.5665 (ttpt) REVERT: B 121 LYS cc_start: 0.6411 (mttp) cc_final: 0.6180 (ttpp) REVERT: B 156 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7787 (mm110) REVERT: B 185 GLN cc_start: 0.7902 (mt0) cc_final: 0.7654 (mt0) REVERT: B 203 ARG cc_start: 0.6790 (ttt-90) cc_final: 0.5880 (tpt-90) REVERT: B 402 MET cc_start: 0.6946 (ttt) cc_final: 0.6548 (ttt) REVERT: C 15 GLU cc_start: 0.7001 (tt0) cc_final: 0.6784 (mt-10) REVERT: C 21 ASP cc_start: 0.7524 (t70) cc_final: 0.6681 (p0) REVERT: C 47 GLU cc_start: 0.7214 (tt0) cc_final: 0.6944 (tp30) REVERT: C 104 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6948 (p0) REVERT: C 152 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5339 (mp0) REVERT: C 176 ASP cc_start: 0.6159 (m-30) cc_final: 0.5758 (m-30) REVERT: C 389 ARG cc_start: 0.6647 (mmm-85) cc_final: 0.5407 (mtm110) REVERT: D 18 LYS cc_start: 0.6806 (ttpt) cc_final: 0.6222 (mptp) REVERT: D 21 ASP cc_start: 0.7595 (t70) cc_final: 0.6700 (p0) REVERT: D 104 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6881 (p0) REVERT: D 152 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5358 (mp0) REVERT: D 156 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8223 (mm110) REVERT: D 181 HIS cc_start: 0.6846 (t70) cc_final: 0.6108 (t70) REVERT: L 15 GLU cc_start: 0.6804 (tt0) cc_final: 0.6309 (mt-10) REVERT: L 21 ASP cc_start: 0.7468 (t70) cc_final: 0.6566 (p0) REVERT: L 62 GLN cc_start: 0.5908 (OUTLIER) cc_final: 0.5689 (mp10) REVERT: L 72 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.7096 (mtt) REVERT: L 73 LYS cc_start: 0.6123 (ttpp) cc_final: 0.5583 (ttpt) REVERT: L 152 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5704 (mp0) REVERT: L 156 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7716 (mm110) REVERT: L 203 ARG cc_start: 0.6350 (mtp-110) cc_final: 0.6025 (mmm-85) REVERT: L 389 ARG cc_start: 0.6442 (mmm-85) cc_final: 0.5204 (mtm-85) REVERT: L 402 MET cc_start: 0.6832 (ttt) cc_final: 0.6540 (ttt) REVERT: M 20 ARG cc_start: 0.6921 (mtp85) cc_final: 0.6197 (mtm-85) REVERT: M 44 GLU cc_start: 0.7863 (mp0) cc_final: 0.7332 (mp0) REVERT: M 47 GLU cc_start: 0.7145 (tt0) cc_final: 0.6739 (tp30) REVERT: M 152 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5523 (mp0) REVERT: M 156 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7653 (mt0) REVERT: M 185 GLN cc_start: 0.7989 (mt0) cc_final: 0.7660 (mt0) REVERT: M 203 ARG cc_start: 0.6624 (ttt-90) cc_final: 0.5830 (mmm-85) REVERT: M 389 ARG cc_start: 0.6655 (mmm-85) cc_final: 0.5271 (mtm-85) REVERT: O 12 ASP cc_start: 0.6797 (m-30) cc_final: 0.6577 (m-30) REVERT: O 15 GLU cc_start: 0.6906 (tt0) cc_final: 0.6355 (mt-10) REVERT: O 26 ARG cc_start: 0.5983 (mmt90) cc_final: 0.5610 (mtp180) REVERT: O 55 MET cc_start: 0.7712 (mmm) cc_final: 0.7437 (mmt) REVERT: O 152 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5550 (mp0) REVERT: O 203 ARG cc_start: 0.6776 (ptm160) cc_final: 0.6170 (ptt90) REVERT: O 258 LYS cc_start: 0.6767 (mtpp) cc_final: 0.6256 (mttm) REVERT: P 12 ASP cc_start: 0.6832 (m-30) cc_final: 0.6630 (m-30) REVERT: P 15 GLU cc_start: 0.6990 (tt0) cc_final: 0.6582 (mt-10) REVERT: P 18 LYS cc_start: 0.6841 (tttt) cc_final: 0.6296 (mptp) REVERT: P 21 ASP cc_start: 0.7401 (t70) cc_final: 0.6565 (p0) REVERT: P 26 ARG cc_start: 0.6136 (mmt90) cc_final: 0.5921 (mmm160) REVERT: P 82 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.5663 (ttm-80) REVERT: P 104 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6825 (p0) REVERT: P 152 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5362 (mp0) REVERT: P 176 ASP cc_start: 0.5990 (m-30) cc_final: 0.5740 (m-30) REVERT: P 258 LYS cc_start: 0.6644 (mtpp) cc_final: 0.6042 (mttm) REVERT: P 266 THR cc_start: 0.6518 (m) cc_final: 0.5860 (p) REVERT: P 402 MET cc_start: 0.7100 (ttt) cc_final: 0.6860 (ttt) REVERT: Q 12 ASP cc_start: 0.6878 (m-30) cc_final: 0.6641 (m-30) REVERT: Q 15 GLU cc_start: 0.6790 (tt0) cc_final: 0.6405 (mt-10) REVERT: Q 21 ASP cc_start: 0.7079 (t70) cc_final: 0.6259 (p0) REVERT: Q 47 GLU cc_start: 0.7138 (tt0) cc_final: 0.6887 (tp30) REVERT: Q 152 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5500 (mp0) REVERT: Q 203 ARG cc_start: 0.6546 (mtp-110) cc_final: 0.6070 (mmm-85) REVERT: Q 226 TYR cc_start: 0.6481 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: Q 389 ARG cc_start: 0.6614 (mmm-85) cc_final: 0.5439 (mtm110) REVERT: V 18 LYS cc_start: 0.6834 (ttpt) cc_final: 0.6306 (mptp) REVERT: V 20 ARG cc_start: 0.6851 (mtt-85) cc_final: 0.6502 (mtt-85) REVERT: V 21 ASP cc_start: 0.7316 (t70) cc_final: 0.6515 (p0) REVERT: V 62 GLN cc_start: 0.5963 (OUTLIER) cc_final: 0.5547 (mp10) REVERT: V 104 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6824 (p0) REVERT: V 152 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5342 (mp0) REVERT: V 156 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8186 (mm110) REVERT: V 176 ASP cc_start: 0.5622 (m-30) cc_final: 0.5300 (m-30) REVERT: V 203 ARG cc_start: 0.6989 (ttt-90) cc_final: 0.6173 (tpt-90) REVERT: X 15 GLU cc_start: 0.7077 (tt0) cc_final: 0.6812 (mt-10) REVERT: X 26 ARG cc_start: 0.6190 (ttm-80) cc_final: 0.5610 (ttt90) REVERT: X 73 LYS cc_start: 0.6246 (ttpp) cc_final: 0.5654 (ttpt) REVERT: X 152 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5467 (mp0) REVERT: X 156 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7757 (mm110) REVERT: X 203 ARG cc_start: 0.6545 (ttt90) cc_final: 0.5785 (tpt-90) REVERT: X 402 MET cc_start: 0.7005 (ttt) cc_final: 0.6674 (ttt) REVERT: Y 15 GLU cc_start: 0.7000 (tt0) cc_final: 0.6688 (mt-10) REVERT: Y 26 ARG cc_start: 0.6305 (ttm-80) cc_final: 0.6097 (mtp180) REVERT: Y 152 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5461 (mp0) REVERT: Y 203 ARG cc_start: 0.6644 (ttt90) cc_final: 0.5934 (tpt-90) REVERT: Y 226 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.6044 (m-80) outliers start: 84 outliers final: 29 residues processed: 448 average time/residue: 1.4576 time to fit residues: 788.2143 Evaluate side-chains 425 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 370 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 226 TYR Chi-restraints excluded: chain L residue 268 THR Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 204 PHE Chi-restraints excluded: chain M residue 226 TYR Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 104 ASP Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 204 PHE Chi-restraints excluded: chain P residue 226 TYR Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 362 LYS Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain X residue 226 TYR Chi-restraints excluded: chain Y residue 104 ASP Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 226 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 373 optimal weight: 0.9990 chunk 289 optimal weight: 0.0870 chunk 430 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 508 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 156 GLN A 185 GLN A 227 HIS B 62 GLN C 156 GLN C 227 HIS ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS L 185 GLN O 156 GLN O 185 GLN P 156 GLN P 227 HIS Q 52 ASN Q 156 GLN Q 227 HIS V 185 GLN V 227 HIS Y 156 GLN Y 185 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43112 Z= 0.179 Angle : 0.442 5.786 58386 Z= 0.233 Chirality : 0.041 0.157 6239 Planarity : 0.004 0.031 7631 Dihedral : 3.839 18.759 5784 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.97 % Allowed : 10.70 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.12), residues: 5292 helix: 2.39 (0.11), residues: 2040 sheet: -0.69 (0.17), residues: 972 loop : 0.01 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 39 HIS 0.004 0.001 HIS X 227 PHE 0.031 0.001 PHE A 64 TYR 0.017 0.001 TYR X 219 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 382 time to evaluate : 4.010 Fit side-chains REVERT: A 12 ASP cc_start: 0.6809 (m-30) cc_final: 0.6596 (m-30) REVERT: A 15 GLU cc_start: 0.6813 (tt0) cc_final: 0.6369 (mt-10) REVERT: A 21 ASP cc_start: 0.6966 (t70) cc_final: 0.6244 (p0) REVERT: A 47 GLU cc_start: 0.7151 (tt0) cc_final: 0.6938 (tp30) REVERT: A 152 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5509 (mp0) REVERT: A 176 ASP cc_start: 0.5586 (m-30) cc_final: 0.5381 (m-30) REVERT: A 203 ARG cc_start: 0.6428 (mtp-110) cc_final: 0.5860 (mmm-85) REVERT: A 226 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: A 389 ARG cc_start: 0.6489 (mmm-85) cc_final: 0.5241 (mtm110) REVERT: B 15 GLU cc_start: 0.6929 (tt0) cc_final: 0.6411 (mt-10) REVERT: B 73 LYS cc_start: 0.6212 (ttpp) cc_final: 0.5675 (ttpt) REVERT: B 121 LYS cc_start: 0.6409 (mttp) cc_final: 0.6187 (ttpp) REVERT: B 156 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7780 (mm110) REVERT: B 185 GLN cc_start: 0.7902 (mt0) cc_final: 0.7667 (mt0) REVERT: B 203 ARG cc_start: 0.6812 (ttt-90) cc_final: 0.5892 (tpt-90) REVERT: B 402 MET cc_start: 0.6959 (ttt) cc_final: 0.6579 (ttt) REVERT: C 15 GLU cc_start: 0.6972 (tt0) cc_final: 0.6744 (mt-10) REVERT: C 21 ASP cc_start: 0.7491 (t70) cc_final: 0.6706 (p0) REVERT: C 47 GLU cc_start: 0.7284 (tt0) cc_final: 0.7003 (tp30) REVERT: C 104 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6957 (p0) REVERT: C 152 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5323 (mp0) REVERT: C 176 ASP cc_start: 0.5938 (m-30) cc_final: 0.5550 (m-30) REVERT: C 389 ARG cc_start: 0.6644 (mmm-85) cc_final: 0.5403 (mtm110) REVERT: D 18 LYS cc_start: 0.6810 (ttpt) cc_final: 0.6226 (mptp) REVERT: D 21 ASP cc_start: 0.7608 (t70) cc_final: 0.6740 (p0) REVERT: D 104 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6877 (p0) REVERT: D 152 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5346 (mp0) REVERT: D 156 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8234 (mm110) REVERT: L 15 GLU cc_start: 0.6822 (tt0) cc_final: 0.6309 (mt-10) REVERT: L 21 ASP cc_start: 0.7533 (t70) cc_final: 0.6613 (p0) REVERT: L 62 GLN cc_start: 0.5878 (OUTLIER) cc_final: 0.5676 (mp10) REVERT: L 72 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7132 (mtt) REVERT: L 73 LYS cc_start: 0.6196 (ttpp) cc_final: 0.5589 (ttmt) REVERT: L 152 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5661 (mp0) REVERT: L 156 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7643 (mt0) REVERT: L 203 ARG cc_start: 0.6349 (mtp-110) cc_final: 0.6023 (mmm-85) REVERT: L 389 ARG cc_start: 0.6431 (mmm-85) cc_final: 0.5189 (mtm-85) REVERT: L 402 MET cc_start: 0.6751 (ttt) cc_final: 0.6451 (ttt) REVERT: M 20 ARG cc_start: 0.6926 (mtp85) cc_final: 0.6232 (mtm-85) REVERT: M 44 GLU cc_start: 0.7749 (mp0) cc_final: 0.7219 (mp0) REVERT: M 62 GLN cc_start: 0.5669 (mt0) cc_final: 0.5266 (mp10) REVERT: M 152 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5703 (mp0) REVERT: M 156 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: M 185 GLN cc_start: 0.7978 (mt0) cc_final: 0.7645 (mt0) REVERT: M 203 ARG cc_start: 0.6674 (ttt-90) cc_final: 0.5856 (mmm-85) REVERT: M 389 ARG cc_start: 0.6645 (mmm-85) cc_final: 0.5252 (mtm-85) REVERT: O 12 ASP cc_start: 0.6809 (m-30) cc_final: 0.6580 (m-30) REVERT: O 15 GLU cc_start: 0.6921 (tt0) cc_final: 0.6370 (mt-10) REVERT: O 26 ARG cc_start: 0.5999 (mmt90) cc_final: 0.5668 (mtp180) REVERT: O 55 MET cc_start: 0.7718 (mmm) cc_final: 0.7423 (mmt) REVERT: O 152 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5567 (mp0) REVERT: O 203 ARG cc_start: 0.6682 (ptm160) cc_final: 0.6069 (ptt90) REVERT: O 226 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: O 258 LYS cc_start: 0.6727 (mtpp) cc_final: 0.6198 (mttm) REVERT: P 12 ASP cc_start: 0.6893 (m-30) cc_final: 0.6676 (m-30) REVERT: P 15 GLU cc_start: 0.6951 (tt0) cc_final: 0.6562 (mt-10) REVERT: P 18 LYS cc_start: 0.6845 (tttt) cc_final: 0.6267 (mptp) REVERT: P 21 ASP cc_start: 0.7382 (t70) cc_final: 0.6566 (p0) REVERT: P 82 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.5820 (ttm-80) REVERT: P 152 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5457 (mp0) REVERT: P 176 ASP cc_start: 0.5997 (m-30) cc_final: 0.5745 (m-30) REVERT: P 258 LYS cc_start: 0.6791 (mtpp) cc_final: 0.6121 (mttm) REVERT: P 266 THR cc_start: 0.6463 (m) cc_final: 0.5815 (p) REVERT: P 402 MET cc_start: 0.7077 (ttt) cc_final: 0.6850 (ttt) REVERT: Q 12 ASP cc_start: 0.6872 (m-30) cc_final: 0.6639 (m-30) REVERT: Q 15 GLU cc_start: 0.6798 (tt0) cc_final: 0.6397 (mt-10) REVERT: Q 21 ASP cc_start: 0.6989 (t70) cc_final: 0.6212 (p0) REVERT: Q 47 GLU cc_start: 0.7181 (tt0) cc_final: 0.6826 (tp30) REVERT: Q 82 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6297 (ttm-80) REVERT: Q 152 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5472 (mp0) REVERT: Q 203 ARG cc_start: 0.6537 (mtp-110) cc_final: 0.6062 (mmm-85) REVERT: Q 226 TYR cc_start: 0.6509 (OUTLIER) cc_final: 0.6059 (m-80) REVERT: Q 389 ARG cc_start: 0.6601 (mmm-85) cc_final: 0.5422 (mtm110) REVERT: V 18 LYS cc_start: 0.6867 (ttpt) cc_final: 0.6347 (mptp) REVERT: V 20 ARG cc_start: 0.6859 (mtt-85) cc_final: 0.6507 (mtt-85) REVERT: V 21 ASP cc_start: 0.7252 (t70) cc_final: 0.6506 (p0) REVERT: V 62 GLN cc_start: 0.5835 (OUTLIER) cc_final: 0.5362 (mp10) REVERT: V 104 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6798 (p0) REVERT: V 121 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.6146 (ttpp) REVERT: V 152 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5319 (mp0) REVERT: V 156 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8186 (mm110) REVERT: V 176 ASP cc_start: 0.5795 (m-30) cc_final: 0.5453 (m-30) REVERT: V 203 ARG cc_start: 0.6961 (ttt-90) cc_final: 0.6159 (tpt-90) REVERT: X 15 GLU cc_start: 0.7088 (tt0) cc_final: 0.6817 (mt-10) REVERT: X 26 ARG cc_start: 0.6193 (ttm-80) cc_final: 0.5629 (ttt90) REVERT: X 62 GLN cc_start: 0.5638 (mt0) cc_final: 0.5229 (mp10) REVERT: X 73 LYS cc_start: 0.6195 (ttpp) cc_final: 0.5626 (ttpt) REVERT: X 152 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5552 (mp0) REVERT: X 156 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7734 (mm110) REVERT: X 176 ASP cc_start: 0.6234 (m-30) cc_final: 0.5882 (m-30) REVERT: X 203 ARG cc_start: 0.6527 (ttt90) cc_final: 0.5794 (tpt-90) REVERT: X 402 MET cc_start: 0.7001 (ttt) cc_final: 0.6688 (ttt) REVERT: Y 15 GLU cc_start: 0.7120 (tt0) cc_final: 0.6828 (mt-10) REVERT: Y 152 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5458 (mp0) REVERT: Y 185 GLN cc_start: 0.8330 (mt0) cc_final: 0.8117 (mt0) REVERT: Y 203 ARG cc_start: 0.6612 (ttt90) cc_final: 0.5915 (tpt-90) REVERT: Y 226 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.6058 (m-80) outliers start: 88 outliers final: 41 residues processed: 441 average time/residue: 1.3850 time to fit residues: 735.8451 Evaluate side-chains 435 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 366 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 226 TYR Chi-restraints excluded: chain L residue 268 THR Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 204 PHE Chi-restraints excluded: chain M residue 226 TYR Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 181 HIS Chi-restraints excluded: chain O residue 226 TYR Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 204 PHE Chi-restraints excluded: chain P residue 226 TYR Chi-restraints excluded: chain P residue 268 THR Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 82 ARG Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 72 MET Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 121 LYS Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 268 THR Chi-restraints excluded: chain V residue 362 LYS Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain X residue 226 TYR Chi-restraints excluded: chain X residue 268 THR Chi-restraints excluded: chain X residue 440 LEU Chi-restraints excluded: chain Y residue 104 ASP Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 226 TYR Chi-restraints excluded: chain Y residue 268 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 303 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 98 optimal weight: 0.0670 chunk 323 optimal weight: 1.9990 chunk 346 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 400 optimal weight: 0.0020 overall best weight: 0.7730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 185 GLN A 227 HIS C 156 GLN C 227 HIS ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS L 185 GLN O 156 GLN P 156 GLN P 227 HIS Q 156 GLN Q 227 HIS V 185 GLN V 227 HIS Y 156 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 43112 Z= 0.115 Angle : 0.413 5.765 58386 Z= 0.217 Chirality : 0.040 0.149 6239 Planarity : 0.003 0.030 7631 Dihedral : 3.650 18.150 5784 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.63 % Allowed : 11.35 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.12), residues: 5292 helix: 2.53 (0.11), residues: 2040 sheet: -0.52 (0.17), residues: 924 loop : 0.29 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 39 HIS 0.003 0.001 HIS C 415 PHE 0.024 0.001 PHE V 64 TYR 0.016 0.001 TYR P 219 ARG 0.002 0.000 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 410 time to evaluate : 3.935 Fit side-chains REVERT: A 12 ASP cc_start: 0.6925 (m-30) cc_final: 0.6721 (m-30) REVERT: A 15 GLU cc_start: 0.6818 (tt0) cc_final: 0.6356 (mt-10) REVERT: A 21 ASP cc_start: 0.6952 (t70) cc_final: 0.6262 (p0) REVERT: A 62 GLN cc_start: 0.5050 (mt0) cc_final: 0.4837 (mp10) REVERT: A 152 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5543 (mp0) REVERT: A 176 ASP cc_start: 0.5585 (m-30) cc_final: 0.5355 (m-30) REVERT: A 203 ARG cc_start: 0.6361 (mtp-110) cc_final: 0.5894 (mmm-85) REVERT: A 226 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: A 389 ARG cc_start: 0.6472 (mmm-85) cc_final: 0.5221 (mtm110) REVERT: B 15 GLU cc_start: 0.6919 (tt0) cc_final: 0.6400 (mt-10) REVERT: B 73 LYS cc_start: 0.6128 (ttpp) cc_final: 0.5503 (ttmt) REVERT: B 121 LYS cc_start: 0.6331 (mttp) cc_final: 0.6107 (ttpp) REVERT: B 156 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7803 (mm110) REVERT: B 176 ASP cc_start: 0.6102 (m-30) cc_final: 0.5753 (m-30) REVERT: B 185 GLN cc_start: 0.7873 (mt0) cc_final: 0.7634 (mt0) REVERT: B 203 ARG cc_start: 0.6769 (ttt-90) cc_final: 0.5882 (tpt-90) REVERT: B 402 MET cc_start: 0.6964 (ttt) cc_final: 0.6579 (ttp) REVERT: C 15 GLU cc_start: 0.6960 (tt0) cc_final: 0.6712 (mt-10) REVERT: C 21 ASP cc_start: 0.7599 (t70) cc_final: 0.6707 (p0) REVERT: C 47 GLU cc_start: 0.7269 (tt0) cc_final: 0.6992 (tp30) REVERT: C 130 MET cc_start: 0.8076 (ttt) cc_final: 0.7445 (ttt) REVERT: C 176 ASP cc_start: 0.6218 (m-30) cc_final: 0.5857 (m-30) REVERT: C 389 ARG cc_start: 0.6624 (mmm-85) cc_final: 0.5367 (mtm110) REVERT: D 18 LYS cc_start: 0.6733 (ttpt) cc_final: 0.6176 (mptp) REVERT: D 21 ASP cc_start: 0.7554 (t70) cc_final: 0.6707 (p0) REVERT: D 73 LYS cc_start: 0.6118 (ttpp) cc_final: 0.5826 (ttmm) REVERT: D 82 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5673 (ttm-80) REVERT: D 130 MET cc_start: 0.8210 (ttt) cc_final: 0.7578 (ttt) REVERT: D 156 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8222 (mm110) REVERT: D 181 HIS cc_start: 0.6831 (t70) cc_final: 0.6117 (t70) REVERT: L 15 GLU cc_start: 0.6826 (tt0) cc_final: 0.6321 (mt-10) REVERT: L 21 ASP cc_start: 0.7557 (t70) cc_final: 0.6664 (p0) REVERT: L 73 LYS cc_start: 0.6203 (ttpp) cc_final: 0.5548 (ttmt) REVERT: L 152 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5706 (mp0) REVERT: L 156 GLN cc_start: 0.8134 (mp10) cc_final: 0.7767 (mm110) REVERT: L 203 ARG cc_start: 0.6357 (mtp-110) cc_final: 0.6019 (mmm-85) REVERT: L 389 ARG cc_start: 0.6413 (mmm-85) cc_final: 0.5169 (mtm-85) REVERT: L 402 MET cc_start: 0.6786 (ttt) cc_final: 0.6470 (ttp) REVERT: L 446 MET cc_start: 0.7880 (ttm) cc_final: 0.7191 (ttm) REVERT: M 15 GLU cc_start: 0.6796 (tt0) cc_final: 0.6299 (mt-10) REVERT: M 62 GLN cc_start: 0.5575 (mt0) cc_final: 0.5205 (mp10) REVERT: M 152 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5639 (mp0) REVERT: M 156 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7778 (mm110) REVERT: M 185 GLN cc_start: 0.7938 (mt0) cc_final: 0.7556 (mt0) REVERT: M 203 ARG cc_start: 0.6673 (ttt-90) cc_final: 0.5836 (mmm-85) REVERT: M 389 ARG cc_start: 0.6628 (mmm-85) cc_final: 0.5217 (mtm-85) REVERT: O 12 ASP cc_start: 0.6792 (m-30) cc_final: 0.6589 (m-30) REVERT: O 15 GLU cc_start: 0.6904 (tt0) cc_final: 0.6332 (mt-10) REVERT: O 21 ASP cc_start: 0.6935 (t70) cc_final: 0.6093 (p0) REVERT: O 26 ARG cc_start: 0.5986 (mmt90) cc_final: 0.5684 (mtp180) REVERT: O 55 MET cc_start: 0.7753 (mmm) cc_final: 0.7460 (mmt) REVERT: O 152 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5598 (mp0) REVERT: O 203 ARG cc_start: 0.6892 (ptm160) cc_final: 0.6044 (ppp80) REVERT: O 226 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: O 258 LYS cc_start: 0.6751 (mtpp) cc_final: 0.6213 (mttm) REVERT: P 12 ASP cc_start: 0.6879 (m-30) cc_final: 0.6673 (m-30) REVERT: P 15 GLU cc_start: 0.6965 (tt0) cc_final: 0.6537 (mt-10) REVERT: P 18 LYS cc_start: 0.6799 (tttt) cc_final: 0.6245 (mptp) REVERT: P 21 ASP cc_start: 0.7392 (t70) cc_final: 0.6551 (p0) REVERT: P 152 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5336 (mp0) REVERT: P 176 ASP cc_start: 0.6016 (m-30) cc_final: 0.5774 (m-30) REVERT: P 258 LYS cc_start: 0.6758 (mtpp) cc_final: 0.6064 (mttm) REVERT: P 266 THR cc_start: 0.6192 (m) cc_final: 0.5587 (p) REVERT: P 389 ARG cc_start: 0.6552 (mmm-85) cc_final: 0.5324 (mtm110) REVERT: P 402 MET cc_start: 0.7077 (ttt) cc_final: 0.6869 (ttt) REVERT: Q 15 GLU cc_start: 0.6807 (tt0) cc_final: 0.6403 (mt-10) REVERT: Q 21 ASP cc_start: 0.6981 (t70) cc_final: 0.6252 (p0) REVERT: Q 47 GLU cc_start: 0.7125 (tt0) cc_final: 0.6715 (tp30) REVERT: Q 72 MET cc_start: 0.7554 (ptp) cc_final: 0.7203 (pmm) REVERT: Q 152 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5550 (mp0) REVERT: Q 203 ARG cc_start: 0.6535 (mtp-110) cc_final: 0.6051 (mmm-85) REVERT: Q 226 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: Q 389 ARG cc_start: 0.6589 (mmm-85) cc_final: 0.5392 (mtm110) REVERT: V 18 LYS cc_start: 0.6760 (ttpt) cc_final: 0.6265 (mptp) REVERT: V 20 ARG cc_start: 0.6905 (mtt-85) cc_final: 0.6598 (mtt-85) REVERT: V 21 ASP cc_start: 0.7459 (t70) cc_final: 0.6673 (p0) REVERT: V 62 GLN cc_start: 0.5906 (OUTLIER) cc_final: 0.5463 (mp10) REVERT: V 72 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7012 (mtm) REVERT: V 156 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8167 (mm110) REVERT: V 176 ASP cc_start: 0.5790 (m-30) cc_final: 0.5505 (m-30) REVERT: V 203 ARG cc_start: 0.6916 (ttt-90) cc_final: 0.6193 (tpt-90) REVERT: X 15 GLU cc_start: 0.7091 (tt0) cc_final: 0.6808 (mt-10) REVERT: X 26 ARG cc_start: 0.6204 (ttm-80) cc_final: 0.5649 (ttt90) REVERT: X 62 GLN cc_start: 0.5542 (mt0) cc_final: 0.5166 (mp10) REVERT: X 73 LYS cc_start: 0.6222 (ttpp) cc_final: 0.5625 (ttmt) REVERT: X 152 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5561 (mp0) REVERT: X 156 GLN cc_start: 0.8066 (mp10) cc_final: 0.7700 (mm110) REVERT: X 176 ASP cc_start: 0.6199 (m-30) cc_final: 0.5869 (m-30) REVERT: X 203 ARG cc_start: 0.6448 (ttt90) cc_final: 0.5706 (tpt-90) REVERT: X 402 MET cc_start: 0.7003 (ttt) cc_final: 0.6672 (ttp) REVERT: Y 15 GLU cc_start: 0.7138 (tt0) cc_final: 0.6862 (mt-10) REVERT: Y 21 ASP cc_start: 0.7019 (t0) cc_final: 0.6148 (p0) REVERT: Y 152 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5540 (mp0) REVERT: Y 185 GLN cc_start: 0.8242 (mt0) cc_final: 0.8036 (mt0) REVERT: Y 203 ARG cc_start: 0.6592 (ttt90) cc_final: 0.5885 (tpt-90) REVERT: Y 226 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.6159 (m-80) outliers start: 73 outliers final: 26 residues processed: 453 average time/residue: 1.3616 time to fit residues: 744.7816 Evaluate side-chains 433 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 390 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 268 THR Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 204 PHE Chi-restraints excluded: chain M residue 226 TYR Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 226 TYR Chi-restraints excluded: chain O residue 228 LYS Chi-restraints excluded: chain O residue 317 GLN Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 268 THR Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 72 MET Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain X residue 268 THR Chi-restraints excluded: chain X residue 440 LEU Chi-restraints excluded: chain Y residue 104 ASP Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 226 TYR Chi-restraints excluded: chain Y residue 268 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 3.9990 chunk 487 optimal weight: 10.0000 chunk 444 optimal weight: 6.9990 chunk 474 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 372 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 428 optimal weight: 4.9990 chunk 448 optimal weight: 7.9990 chunk 472 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 185 GLN A 227 HIS C 156 GLN C 227 HIS D 52 ASN D 106 ASN D 227 HIS L 185 GLN O 156 GLN O 185 GLN P 156 GLN P 227 HIS Q 156 GLN Q 227 HIS V 227 HIS X 243 ASN Y 156 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 43112 Z= 0.222 Angle : 0.461 5.827 58386 Z= 0.242 Chirality : 0.042 0.159 6239 Planarity : 0.004 0.031 7631 Dihedral : 3.856 18.491 5784 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.59 % Allowed : 11.60 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.12), residues: 5292 helix: 2.38 (0.11), residues: 2052 sheet: -0.63 (0.17), residues: 984 loop : 0.06 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 39 HIS 0.004 0.001 HIS B 227 PHE 0.026 0.002 PHE C 64 TYR 0.018 0.001 TYR B 219 ARG 0.003 0.000 ARG L 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 369 time to evaluate : 3.819 Fit side-chains REVERT: A 15 GLU cc_start: 0.6839 (tt0) cc_final: 0.6380 (mt-10) REVERT: A 21 ASP cc_start: 0.6977 (t70) cc_final: 0.6224 (p0) REVERT: A 152 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5529 (mp0) REVERT: A 176 ASP cc_start: 0.5595 (m-30) cc_final: 0.5387 (m-30) REVERT: A 203 ARG cc_start: 0.6478 (mtp-110) cc_final: 0.5828 (mmm-85) REVERT: A 226 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: A 389 ARG cc_start: 0.6470 (mmm-85) cc_final: 0.5239 (mtm110) REVERT: B 15 GLU cc_start: 0.6912 (tt0) cc_final: 0.6466 (mt-10) REVERT: B 73 LYS cc_start: 0.6218 (ttpp) cc_final: 0.5685 (ttpt) REVERT: B 121 LYS cc_start: 0.6344 (mttp) cc_final: 0.6120 (ttpp) REVERT: B 156 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7776 (mm110) REVERT: B 185 GLN cc_start: 0.7895 (mt0) cc_final: 0.7686 (mt0) REVERT: B 203 ARG cc_start: 0.6782 (ttt-90) cc_final: 0.5875 (tpt-90) REVERT: B 402 MET cc_start: 0.6963 (ttt) cc_final: 0.6607 (ttt) REVERT: C 15 GLU cc_start: 0.6954 (tt0) cc_final: 0.6705 (mt-10) REVERT: C 21 ASP cc_start: 0.7468 (t70) cc_final: 0.6657 (p0) REVERT: C 47 GLU cc_start: 0.7192 (tt0) cc_final: 0.6934 (tp30) REVERT: C 176 ASP cc_start: 0.5935 (m-30) cc_final: 0.5521 (m-30) REVERT: C 389 ARG cc_start: 0.6606 (mmm-85) cc_final: 0.5371 (mtm110) REVERT: D 18 LYS cc_start: 0.6811 (ttpt) cc_final: 0.6229 (mptp) REVERT: D 21 ASP cc_start: 0.7550 (t70) cc_final: 0.6685 (p0) REVERT: D 152 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5481 (mp0) REVERT: D 156 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8236 (mm110) REVERT: L 15 GLU cc_start: 0.6826 (tt0) cc_final: 0.6312 (mt-10) REVERT: L 20 ARG cc_start: 0.7171 (mtp85) cc_final: 0.6461 (mtm-85) REVERT: L 62 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.5654 (mp10) REVERT: L 72 MET cc_start: 0.6958 (mtt) cc_final: 0.6753 (mtt) REVERT: L 152 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5657 (mp0) REVERT: L 203 ARG cc_start: 0.6408 (mtp-110) cc_final: 0.6035 (mmm-85) REVERT: L 389 ARG cc_start: 0.6458 (mmm-85) cc_final: 0.5184 (mtm-85) REVERT: L 402 MET cc_start: 0.6756 (ttt) cc_final: 0.6476 (ttt) REVERT: M 15 GLU cc_start: 0.6812 (tt0) cc_final: 0.6312 (mt-10) REVERT: M 20 ARG cc_start: 0.6905 (mtp85) cc_final: 0.6165 (mtm-85) REVERT: M 62 GLN cc_start: 0.5646 (mt0) cc_final: 0.5235 (mp10) REVERT: M 152 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: M 156 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: M 167 ARG cc_start: 0.5987 (ttp-110) cc_final: 0.5057 (mmt90) REVERT: M 185 GLN cc_start: 0.7967 (mt0) cc_final: 0.7634 (mt0) REVERT: M 203 ARG cc_start: 0.6625 (ttt-90) cc_final: 0.5865 (mmm-85) REVERT: M 374 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7203 (t0) REVERT: M 389 ARG cc_start: 0.6639 (mmm-85) cc_final: 0.5277 (mtm-85) REVERT: O 12 ASP cc_start: 0.6798 (m-30) cc_final: 0.6584 (m-30) REVERT: O 15 GLU cc_start: 0.6871 (tt0) cc_final: 0.6296 (mt-10) REVERT: O 26 ARG cc_start: 0.6046 (mmt90) cc_final: 0.5685 (mtp180) REVERT: O 152 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5569 (mp0) REVERT: O 203 ARG cc_start: 0.6884 (ptm160) cc_final: 0.6156 (ptt90) REVERT: O 226 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: O 258 LYS cc_start: 0.6783 (mtpp) cc_final: 0.6214 (mttm) REVERT: P 12 ASP cc_start: 0.6897 (m-30) cc_final: 0.6679 (m-30) REVERT: P 15 GLU cc_start: 0.7010 (tt0) cc_final: 0.6613 (mt-10) REVERT: P 18 LYS cc_start: 0.6812 (tttt) cc_final: 0.6254 (mptp) REVERT: P 21 ASP cc_start: 0.7212 (t70) cc_final: 0.6506 (p0) REVERT: P 82 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.5532 (ttm-80) REVERT: P 152 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5472 (mp0) REVERT: P 176 ASP cc_start: 0.6012 (m-30) cc_final: 0.5764 (m-30) REVERT: P 258 LYS cc_start: 0.6801 (mtpp) cc_final: 0.6132 (mttm) REVERT: P 266 THR cc_start: 0.6340 (m) cc_final: 0.5713 (p) REVERT: P 317 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.5742 (pm20) REVERT: P 389 ARG cc_start: 0.6557 (mmm-85) cc_final: 0.5350 (mtm110) REVERT: P 402 MET cc_start: 0.7072 (ttt) cc_final: 0.6855 (ttt) REVERT: Q 15 GLU cc_start: 0.6808 (tt0) cc_final: 0.6396 (mt-10) REVERT: Q 21 ASP cc_start: 0.7006 (t70) cc_final: 0.6224 (p0) REVERT: Q 47 GLU cc_start: 0.7202 (tt0) cc_final: 0.6762 (tp30) REVERT: Q 72 MET cc_start: 0.7549 (ptp) cc_final: 0.7065 (pmm) REVERT: Q 82 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6320 (ttm-80) REVERT: Q 152 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5470 (mp0) REVERT: Q 203 ARG cc_start: 0.6660 (mtp-110) cc_final: 0.6176 (mmm-85) REVERT: Q 226 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: Q 389 ARG cc_start: 0.6594 (mmm-85) cc_final: 0.5415 (mtm110) REVERT: V 18 LYS cc_start: 0.6831 (ttpt) cc_final: 0.6315 (mptp) REVERT: V 20 ARG cc_start: 0.6937 (mtt-85) cc_final: 0.6595 (mtt-85) REVERT: V 21 ASP cc_start: 0.7255 (t70) cc_final: 0.6542 (p0) REVERT: V 62 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5384 (mp10) REVERT: V 121 LYS cc_start: 0.6466 (OUTLIER) cc_final: 0.6218 (ttpp) REVERT: V 152 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5445 (mp0) REVERT: V 156 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8186 (mm110) REVERT: V 176 ASP cc_start: 0.5797 (m-30) cc_final: 0.5443 (m-30) REVERT: V 203 ARG cc_start: 0.6851 (ttt-90) cc_final: 0.6112 (tpt-90) REVERT: X 15 GLU cc_start: 0.7097 (tt0) cc_final: 0.6820 (mt-10) REVERT: X 62 GLN cc_start: 0.5594 (mt0) cc_final: 0.5231 (mp10) REVERT: X 73 LYS cc_start: 0.6249 (ttpp) cc_final: 0.5672 (ttpt) REVERT: X 152 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5546 (mp0) REVERT: X 156 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: X 176 ASP cc_start: 0.6242 (m-30) cc_final: 0.5887 (m-30) REVERT: X 203 ARG cc_start: 0.6496 (ttt90) cc_final: 0.5772 (tpt-90) REVERT: X 402 MET cc_start: 0.7039 (ttt) cc_final: 0.6725 (ttt) REVERT: Y 15 GLU cc_start: 0.7161 (tt0) cc_final: 0.6850 (mt-10) REVERT: Y 152 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5475 (mp0) REVERT: Y 203 ARG cc_start: 0.6635 (ttt90) cc_final: 0.5947 (tpt-90) REVERT: Y 226 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.6081 (m-80) outliers start: 71 outliers final: 35 residues processed: 414 average time/residue: 1.4264 time to fit residues: 709.0082 Evaluate side-chains 419 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 360 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 226 TYR Chi-restraints excluded: chain L residue 268 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 204 PHE Chi-restraints excluded: chain M residue 226 TYR Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 268 THR Chi-restraints excluded: chain M residue 374 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 226 TYR Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain O residue 317 GLN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 204 PHE Chi-restraints excluded: chain P residue 268 THR Chi-restraints excluded: chain P residue 317 GLN Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 82 ARG Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 181 HIS Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain V residue 12 ASP Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 72 MET Chi-restraints excluded: chain V residue 121 LYS Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 268 THR Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain X residue 226 TYR Chi-restraints excluded: chain X residue 268 THR Chi-restraints excluded: chain Y residue 104 ASP Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 226 TYR Chi-restraints excluded: chain Y residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 0.0870 chunk 501 optimal weight: 9.9990 chunk 306 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 348 optimal weight: 6.9990 chunk 526 optimal weight: 5.9990 chunk 484 optimal weight: 10.0000 chunk 418 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 323 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 185 GLN A 227 HIS C 156 GLN L 185 GLN O 156 GLN P 156 GLN P 227 HIS Q 156 GLN V 227 HIS Y 156 GLN Y 185 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 43112 Z= 0.226 Angle : 0.462 5.762 58386 Z= 0.242 Chirality : 0.042 0.158 6239 Planarity : 0.004 0.031 7631 Dihedral : 3.918 18.932 5784 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.47 % Allowed : 11.84 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.12), residues: 5292 helix: 2.37 (0.11), residues: 2040 sheet: -0.67 (0.17), residues: 972 loop : -0.04 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 39 HIS 0.005 0.001 HIS O 227 PHE 0.027 0.002 PHE V 64 TYR 0.017 0.001 TYR L 219 ARG 0.002 0.000 ARG Q 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 357 time to evaluate : 3.762 Fit side-chains REVERT: A 15 GLU cc_start: 0.6730 (tt0) cc_final: 0.6369 (mt-10) REVERT: A 21 ASP cc_start: 0.6852 (t70) cc_final: 0.6148 (p0) REVERT: A 152 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5527 (mp0) REVERT: A 203 ARG cc_start: 0.6441 (mtp-110) cc_final: 0.5785 (mmm-85) REVERT: A 226 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: A 389 ARG cc_start: 0.6463 (mmm-85) cc_final: 0.5220 (mtm110) REVERT: B 15 GLU cc_start: 0.6909 (tt0) cc_final: 0.6468 (mt-10) REVERT: B 73 LYS cc_start: 0.6224 (ttpp) cc_final: 0.5679 (ttpt) REVERT: B 121 LYS cc_start: 0.6345 (mttp) cc_final: 0.6122 (ttpp) REVERT: B 156 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7773 (mm110) REVERT: B 185 GLN cc_start: 0.7891 (mt0) cc_final: 0.7660 (mt0) REVERT: B 203 ARG cc_start: 0.6798 (ttt-90) cc_final: 0.5891 (tpt-90) REVERT: B 402 MET cc_start: 0.6957 (ttt) cc_final: 0.6575 (ttt) REVERT: C 15 GLU cc_start: 0.6983 (tt0) cc_final: 0.6746 (mt-10) REVERT: C 21 ASP cc_start: 0.7460 (t70) cc_final: 0.6666 (p0) REVERT: C 47 GLU cc_start: 0.7283 (tt0) cc_final: 0.6990 (tp30) REVERT: C 176 ASP cc_start: 0.5839 (m-30) cc_final: 0.5445 (m-30) REVERT: C 389 ARG cc_start: 0.6629 (mmm-85) cc_final: 0.5377 (mtm110) REVERT: D 18 LYS cc_start: 0.6818 (ttpt) cc_final: 0.6232 (mptp) REVERT: D 21 ASP cc_start: 0.7482 (t70) cc_final: 0.6645 (p0) REVERT: D 152 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5487 (mp0) REVERT: D 156 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8204 (mm110) REVERT: L 15 GLU cc_start: 0.6788 (tt0) cc_final: 0.6365 (mt-10) REVERT: L 72 MET cc_start: 0.6964 (mtt) cc_final: 0.6756 (mtt) REVERT: L 152 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5637 (mp0) REVERT: L 156 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: L 203 ARG cc_start: 0.6393 (mtp-110) cc_final: 0.5997 (mmm-85) REVERT: L 389 ARG cc_start: 0.6469 (mmm-85) cc_final: 0.5219 (mtm-85) REVERT: L 402 MET cc_start: 0.6854 (ttt) cc_final: 0.6560 (ttt) REVERT: L 446 MET cc_start: 0.7932 (ttm) cc_final: 0.7283 (ttm) REVERT: M 15 GLU cc_start: 0.6809 (tt0) cc_final: 0.6312 (mt-10) REVERT: M 20 ARG cc_start: 0.6910 (mtp85) cc_final: 0.6198 (mtm-85) REVERT: M 62 GLN cc_start: 0.5678 (mt0) cc_final: 0.5230 (mp10) REVERT: M 152 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5513 (mp0) REVERT: M 156 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: M 185 GLN cc_start: 0.7968 (mt0) cc_final: 0.7589 (mt0) REVERT: M 203 ARG cc_start: 0.6630 (ttt-90) cc_final: 0.5801 (mmm-85) REVERT: M 389 ARG cc_start: 0.6617 (mmm-85) cc_final: 0.5270 (mtm-85) REVERT: O 15 GLU cc_start: 0.6872 (tt0) cc_final: 0.6294 (mt-10) REVERT: O 26 ARG cc_start: 0.5974 (mmt90) cc_final: 0.5473 (mtp180) REVERT: O 152 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5520 (mp0) REVERT: O 185 GLN cc_start: 0.8224 (mt0) cc_final: 0.7995 (mt0) REVERT: O 203 ARG cc_start: 0.6771 (ptm160) cc_final: 0.6105 (ppt-90) REVERT: O 226 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: P 12 ASP cc_start: 0.6911 (m-30) cc_final: 0.6693 (m-30) REVERT: P 15 GLU cc_start: 0.7010 (tt0) cc_final: 0.6587 (mt-10) REVERT: P 18 LYS cc_start: 0.6945 (tttt) cc_final: 0.6368 (mptp) REVERT: P 21 ASP cc_start: 0.7174 (t70) cc_final: 0.6496 (p0) REVERT: P 82 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5846 (ttm-80) REVERT: P 152 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5462 (mp0) REVERT: P 176 ASP cc_start: 0.5945 (m-30) cc_final: 0.5676 (m-30) REVERT: P 266 THR cc_start: 0.6518 (m) cc_final: 0.5865 (p) REVERT: P 317 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5686 (pm20) REVERT: P 389 ARG cc_start: 0.6547 (mmm-85) cc_final: 0.5349 (mtm110) REVERT: P 402 MET cc_start: 0.7074 (ttt) cc_final: 0.6859 (ttt) REVERT: Q 15 GLU cc_start: 0.6791 (tt0) cc_final: 0.6383 (mt-10) REVERT: Q 21 ASP cc_start: 0.7003 (t70) cc_final: 0.6226 (p0) REVERT: Q 47 GLU cc_start: 0.7201 (tt0) cc_final: 0.6757 (tp30) REVERT: Q 72 MET cc_start: 0.7563 (ptp) cc_final: 0.7049 (pmm) REVERT: Q 82 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6330 (ttm-80) REVERT: Q 152 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5497 (mp0) REVERT: Q 226 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: Q 389 ARG cc_start: 0.6593 (mmm-85) cc_final: 0.5425 (mtm110) REVERT: V 18 LYS cc_start: 0.6922 (ttpt) cc_final: 0.6371 (mptp) REVERT: V 20 ARG cc_start: 0.6911 (mtt-85) cc_final: 0.6575 (mtt-85) REVERT: V 21 ASP cc_start: 0.7304 (t70) cc_final: 0.6490 (p0) REVERT: V 62 GLN cc_start: 0.5987 (OUTLIER) cc_final: 0.5595 (mp10) REVERT: V 121 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.6220 (ttpp) REVERT: V 152 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5406 (mp0) REVERT: V 156 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8186 (mm110) REVERT: V 176 ASP cc_start: 0.5747 (m-30) cc_final: 0.5376 (m-30) REVERT: V 203 ARG cc_start: 0.6805 (ttt-90) cc_final: 0.6140 (tpt-90) REVERT: X 15 GLU cc_start: 0.7104 (tt0) cc_final: 0.6818 (mt-10) REVERT: X 62 GLN cc_start: 0.5761 (mt0) cc_final: 0.5359 (mp10) REVERT: X 73 LYS cc_start: 0.6257 (ttpp) cc_final: 0.5681 (ttpt) REVERT: X 152 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5546 (mp0) REVERT: X 156 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: X 203 ARG cc_start: 0.6511 (ttt90) cc_final: 0.5808 (tpt-90) REVERT: X 402 MET cc_start: 0.6973 (ttt) cc_final: 0.6657 (ttt) REVERT: Y 15 GLU cc_start: 0.6968 (tt0) cc_final: 0.6602 (mt-10) REVERT: Y 152 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5536 (mp0) REVERT: Y 203 ARG cc_start: 0.6633 (ttt90) cc_final: 0.5943 (tpt-90) REVERT: Y 226 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.6062 (m-80) outliers start: 66 outliers final: 34 residues processed: 396 average time/residue: 1.4661 time to fit residues: 695.8566 Evaluate side-chains 404 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 347 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 166 ASP Chi-restraints excluded: chain L residue 226 TYR Chi-restraints excluded: chain L residue 268 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 204 PHE Chi-restraints excluded: chain M residue 226 TYR Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 268 THR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 226 TYR Chi-restraints excluded: chain O residue 228 LYS Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain O residue 317 GLN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 204 PHE Chi-restraints excluded: chain P residue 268 THR Chi-restraints excluded: chain P residue 317 GLN Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 82 ARG Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 181 HIS Chi-restraints excluded: chain Q residue 226 TYR Chi-restraints excluded: chain V residue 12 ASP Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 72 MET Chi-restraints excluded: chain V residue 121 LYS Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 268 THR Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain X residue 226 TYR Chi-restraints excluded: chain X residue 268 THR Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 226 TYR Chi-restraints excluded: chain Y residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 9.9990 chunk 446 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 386 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 419 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 430 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 185 GLN A 227 HIS C 156 GLN D 227 HIS L 185 GLN O 156 GLN P 156 GLN Q 156 GLN V 227 HIS Y 156 GLN Y 185 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096657 restraints weight = 53038.899| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.59 r_work: 0.2991 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 43112 Z= 0.153 Angle : 0.433 5.736 58386 Z= 0.227 Chirality : 0.041 0.153 6239 Planarity : 0.003 0.031 7631 Dihedral : 3.758 18.590 5784 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.36 % Allowed : 12.18 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.12), residues: 5292 helix: 2.49 (0.11), residues: 2040 sheet: -0.55 (0.17), residues: 924 loop : 0.22 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 39 HIS 0.003 0.001 HIS P 227 PHE 0.029 0.001 PHE A 64 TYR 0.016 0.001 TYR L 219 ARG 0.002 0.000 ARG D 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12379.56 seconds wall clock time: 216 minutes 31.85 seconds (12991.85 seconds total)