Starting phenix.real_space_refine on Fri Feb 16 03:20:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/02_2024/3jcf_6551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/02_2024/3jcf_6551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/02_2024/3jcf_6551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/02_2024/3jcf_6551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/02_2024/3jcf_6551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/02_2024/3jcf_6551.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 13 5.21 5 S 40 5.16 5 C 9250 2.51 5 N 2305 2.21 5 O 2620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 165": "NH1" <-> "NH2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 269": "NH1" <-> "NH2" Residue "E TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14228 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.39, per 1000 atoms: 0.52 Number of scatterers: 14228 At special positions: 0 Unit cell: (116.025, 113.475, 124.95, 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 40 16.00 Mg 13 11.99 O 2620 8.00 N 2305 7.00 C 9250 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: 4.98 Conformation dependent library (CDL) restraints added in 2.2 seconds 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 57.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 50 through 56 removed outlier: 3.576A pdb=" N PHE A 53 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.527A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 159 through 163 removed outlier: 4.106A pdb=" N ARG A 162 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 201 removed outlier: 3.596A pdb=" N TYR A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 237 Proline residue: A 227 - end of helix removed outlier: 4.170A pdb=" N GLU A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 299 removed outlier: 3.929A pdb=" N TYR A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 325 through 345 removed outlier: 3.566A pdb=" N VAL A 329 " --> pdb=" O TRP A 325 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.575A pdb=" N PHE B 53 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.527A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 159 through 163 removed outlier: 4.105A pdb=" N ARG B 162 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 201 removed outlier: 3.598A pdb=" N TYR B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 237 Proline residue: B 227 - end of helix removed outlier: 4.169A pdb=" N GLU B 230 " --> pdb=" O TRP B 226 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 299 removed outlier: 3.928A pdb=" N TYR B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 259 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 325 through 345 removed outlier: 3.568A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 56 removed outlier: 3.576A pdb=" N PHE C 53 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 55 " --> pdb=" O PRO C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.527A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 159 through 163 removed outlier: 4.104A pdb=" N ARG C 162 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 201 removed outlier: 3.596A pdb=" N TYR C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 237 Proline residue: C 227 - end of helix removed outlier: 4.170A pdb=" N GLU C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 299 removed outlier: 3.928A pdb=" N TYR C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 325 through 345 removed outlier: 3.563A pdb=" N VAL C 329 " --> pdb=" O TRP C 325 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 removed outlier: 3.575A pdb=" N PHE D 53 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.526A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 159 through 163 removed outlier: 4.106A pdb=" N ARG D 162 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 201 removed outlier: 3.597A pdb=" N TYR D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 237 Proline residue: D 227 - end of helix removed outlier: 4.169A pdb=" N GLU D 230 " --> pdb=" O TRP D 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 299 removed outlier: 3.928A pdb=" N TYR D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 259 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 325 through 345 removed outlier: 3.567A pdb=" N VAL D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 56 removed outlier: 3.574A pdb=" N PHE E 53 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.526A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 159 through 163 removed outlier: 4.105A pdb=" N ARG E 162 " --> pdb=" O GLY E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 201 removed outlier: 3.597A pdb=" N TYR E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 237 Proline residue: E 227 - end of helix removed outlier: 4.170A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 235 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 299 removed outlier: 3.927A pdb=" N TYR E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 259 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 313 Processing helix chain 'E' and resid 325 through 345 removed outlier: 3.566A pdb=" N VAL E 329 " --> pdb=" O TRP E 325 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 44 Processing sheet with id= B, first strand: chain 'B' and resid 39 through 44 Processing sheet with id= C, first strand: chain 'C' and resid 39 through 44 Processing sheet with id= D, first strand: chain 'D' and resid 39 through 44 Processing sheet with id= E, first strand: chain 'E' and resid 39 through 44 880 hydrogen bonds defined for protein. 2565 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: 3.85 Time building geometry restraints manager: 5.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4471 1.34 - 1.46: 1966 1.46 - 1.57: 8013 1.57 - 1.69: 0 1.69 - 1.80: 75 Bond restraints: 14525 Sorted by residual: bond pdb=" CA PRO C 240 " pdb=" C PRO C 240 " ideal model delta sigma weight residual 1.517 1.546 -0.028 9.30e-03 1.16e+04 9.35e+00 bond pdb=" CA PRO E 240 " pdb=" C PRO E 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.11e+00 bond pdb=" CA PRO A 240 " pdb=" C PRO A 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.95e+00 bond pdb=" CA PRO B 240 " pdb=" C PRO B 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.92e+00 bond pdb=" CA PRO D 240 " pdb=" C PRO D 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.78e+00 ... (remaining 14520 not shown) Histogram of bond angle deviations from ideal: 100.71 - 107.60: 440 107.60 - 114.48: 8668 114.48 - 121.37: 6666 121.37 - 128.26: 3856 128.26 - 135.14: 100 Bond angle restraints: 19730 Sorted by residual: angle pdb=" C PRO C 240 " pdb=" N PRO C 241 " pdb=" CA PRO C 241 " ideal model delta sigma weight residual 119.84 113.54 6.30 1.25e+00 6.40e-01 2.54e+01 angle pdb=" C PRO B 240 " pdb=" N PRO B 241 " pdb=" CA PRO B 241 " ideal model delta sigma weight residual 119.84 113.59 6.25 1.25e+00 6.40e-01 2.50e+01 angle pdb=" C PRO D 240 " pdb=" N PRO D 241 " pdb=" CA PRO D 241 " ideal model delta sigma weight residual 119.84 113.59 6.25 1.25e+00 6.40e-01 2.50e+01 angle pdb=" C PRO E 240 " pdb=" N PRO E 241 " pdb=" CA PRO E 241 " ideal model delta sigma weight residual 119.84 113.60 6.24 1.25e+00 6.40e-01 2.49e+01 angle pdb=" C PRO A 240 " pdb=" N PRO A 241 " pdb=" CA PRO A 241 " ideal model delta sigma weight residual 119.84 113.62 6.22 1.25e+00 6.40e-01 2.48e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.97: 7974 7.97 - 15.93: 576 15.93 - 23.90: 118 23.90 - 31.86: 59 31.86 - 39.83: 28 Dihedral angle restraints: 8755 sinusoidal: 3570 harmonic: 5185 Sorted by residual: dihedral pdb=" CA LEU C 131 " pdb=" CB LEU C 131 " pdb=" CG LEU C 131 " pdb=" CD1 LEU C 131 " ideal model delta sinusoidal sigma weight residual 180.00 140.17 39.83 3 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CA LEU A 131 " pdb=" CB LEU A 131 " pdb=" CG LEU A 131 " pdb=" CD1 LEU A 131 " ideal model delta sinusoidal sigma weight residual 180.00 140.19 39.81 3 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CA LEU B 131 " pdb=" CB LEU B 131 " pdb=" CG LEU B 131 " pdb=" CD1 LEU B 131 " ideal model delta sinusoidal sigma weight residual 180.00 140.22 39.78 3 1.50e+01 4.44e-03 7.06e+00 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1630 0.024 - 0.047: 245 0.047 - 0.071: 109 0.071 - 0.095: 178 0.095 - 0.119: 128 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA ILE C 160 " pdb=" N ILE C 160 " pdb=" C ILE C 160 " pdb=" CB ILE C 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE B 160 " pdb=" N ILE B 160 " pdb=" C ILE B 160 " pdb=" CB ILE B 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE B 143 " pdb=" N ILE B 143 " pdb=" C ILE B 143 " pdb=" CB ILE B 143 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 2287 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 239 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO E 240 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 240 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 240 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 239 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO C 240 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 239 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO B 240 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 240 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 240 " 0.021 5.00e-02 4.00e+02 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 181 2.63 - 3.19: 13699 3.19 - 3.76: 22099 3.76 - 4.33: 30360 4.33 - 4.90: 49384 Nonbonded interactions: 115723 Sorted by model distance: nonbonded pdb=" OD1 ASP C 253 " pdb="MG MG D 402 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP B 253 " pdb="MG MG C 402 " model vdw 2.058 2.170 nonbonded pdb=" OD1 ASP D 253 " pdb="MG MG E 402 " model vdw 2.059 2.170 nonbonded pdb=" OD1 ASP A 253 " pdb="MG MG B 402 " model vdw 2.059 2.170 nonbonded pdb=" OD1 ASP E 253 " pdb="MG MG A 402 " model vdw 2.062 2.170 ... (remaining 115718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 3 through 351 or resid 402 through 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.350 Check model and map are aligned: 0.190 Set scattering table: 0.170 Process input model: 35.420 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.004 0.028 14525 Z= 0.247 Angle : 1.028 10.141 19730 Z= 0.718 Chirality : 0.039 0.119 2290 Planarity : 0.003 0.036 2490 Dihedral : 6.812 39.830 5395 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 1735 helix: -0.43 (0.14), residues: 910 sheet: -1.06 (0.32), residues: 240 loop : -1.96 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 61 HIS 0.001 0.000 HIS A 83 PHE 0.005 0.001 PHE A 345 TYR 0.007 0.001 TYR D 317 ARG 0.001 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8092 (mtp) cc_final: 0.7527 (mtm) REVERT: A 74 GLN cc_start: 0.8920 (tt0) cc_final: 0.8652 (tp-100) REVERT: A 140 GLN cc_start: 0.8565 (mt0) cc_final: 0.8356 (mt0) REVERT: A 152 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8752 (mt-10) REVERT: A 209 GLN cc_start: 0.9136 (tt0) cc_final: 0.8909 (tm-30) REVERT: A 288 ASN cc_start: 0.8986 (t0) cc_final: 0.8757 (t0) REVERT: B 28 GLU cc_start: 0.7954 (tt0) cc_final: 0.7633 (tm-30) REVERT: B 32 MET cc_start: 0.8429 (mtp) cc_final: 0.7998 (mtt) REVERT: B 74 GLN cc_start: 0.9130 (tt0) cc_final: 0.8741 (tp-100) REVERT: B 138 MET cc_start: 0.8479 (ttp) cc_final: 0.8007 (tmm) REVERT: B 140 GLN cc_start: 0.8738 (mt0) cc_final: 0.8530 (mt0) REVERT: B 152 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8755 (mt-10) REVERT: B 213 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8648 (tp40) REVERT: C 32 MET cc_start: 0.8150 (mtp) cc_final: 0.7678 (mtt) REVERT: C 74 GLN cc_start: 0.9003 (tt0) cc_final: 0.8561 (tp-100) REVERT: D 32 MET cc_start: 0.8199 (mtp) cc_final: 0.7330 (mtm) REVERT: D 61 TRP cc_start: 0.8533 (t60) cc_final: 0.8278 (t60) REVERT: D 74 GLN cc_start: 0.9032 (tt0) cc_final: 0.8549 (tp-100) REVERT: D 112 MET cc_start: 0.8932 (mtm) cc_final: 0.8599 (mtt) REVERT: D 209 GLN cc_start: 0.9249 (tt0) cc_final: 0.9044 (tm-30) REVERT: D 213 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8537 (tp40) REVERT: D 217 ASN cc_start: 0.8839 (m-40) cc_final: 0.8573 (m110) REVERT: D 296 ILE cc_start: 0.7743 (pt) cc_final: 0.7499 (pt) REVERT: E 32 MET cc_start: 0.7933 (mtp) cc_final: 0.7266 (mtt) REVERT: E 61 TRP cc_start: 0.8523 (t60) cc_final: 0.8143 (t60) REVERT: E 74 GLN cc_start: 0.8885 (tt0) cc_final: 0.8505 (tp-100) REVERT: E 152 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8655 (mt-10) REVERT: E 209 GLN cc_start: 0.9252 (tt0) cc_final: 0.8987 (tm-30) REVERT: E 213 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8635 (tp40) REVERT: E 277 ASP cc_start: 0.9019 (m-30) cc_final: 0.8755 (t70) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2701 time to fit residues: 130.2231 Evaluate side-chains 164 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 140 GLN A 314 ASN B 94 HIS B 95 GLN B 140 GLN B 260 GLN B 314 ASN C 95 GLN C 140 GLN C 314 ASN D 94 HIS D 126 GLN D 314 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS E 95 GLN E 140 GLN E 314 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14525 Z= 0.219 Angle : 0.651 7.649 19730 Z= 0.345 Chirality : 0.042 0.176 2290 Planarity : 0.004 0.047 2490 Dihedral : 3.962 13.684 1925 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.36 % Allowed : 6.50 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1735 helix: 1.69 (0.17), residues: 940 sheet: -0.73 (0.30), residues: 250 loop : -1.75 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.002 0.000 HIS B 83 PHE 0.010 0.001 PHE D 306 TYR 0.014 0.001 TYR A 327 ARG 0.006 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8500 (tmm) cc_final: 0.7259 (tmm) REVERT: A 152 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8852 (tt0) REVERT: A 299 THR cc_start: 0.7346 (p) cc_final: 0.7095 (p) REVERT: B 74 GLN cc_start: 0.9244 (tt0) cc_final: 0.8877 (tp-100) REVERT: B 100 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8246 (mm-30) REVERT: B 134 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7965 (m-40) REVERT: B 138 MET cc_start: 0.8695 (ttp) cc_final: 0.8007 (tmm) REVERT: B 140 GLN cc_start: 0.8756 (mt0) cc_final: 0.8482 (mt0) REVERT: C 74 GLN cc_start: 0.9002 (tt0) cc_final: 0.8595 (tp-100) REVERT: C 112 MET cc_start: 0.7906 (mtt) cc_final: 0.7627 (mtm) REVERT: C 138 MET cc_start: 0.8340 (ttp) cc_final: 0.8036 (tmm) REVERT: D 32 MET cc_start: 0.8249 (mtp) cc_final: 0.7911 (mtm) REVERT: D 74 GLN cc_start: 0.9106 (tt0) cc_final: 0.8733 (tp-100) REVERT: D 91 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8915 (mt) REVERT: D 112 MET cc_start: 0.8777 (mtm) cc_final: 0.8484 (mtt) REVERT: D 152 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8644 (tt0) REVERT: D 173 LEU cc_start: 0.9398 (mt) cc_final: 0.9091 (mp) REVERT: D 213 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8756 (tp40) REVERT: E 32 MET cc_start: 0.8068 (mtp) cc_final: 0.7557 (mtt) REVERT: E 61 TRP cc_start: 0.8596 (t60) cc_final: 0.8334 (t60) REVERT: E 74 GLN cc_start: 0.9025 (tt0) cc_final: 0.8737 (tp-100) REVERT: E 209 GLN cc_start: 0.9310 (tt0) cc_final: 0.9030 (tm-30) outliers start: 37 outliers final: 22 residues processed: 210 average time/residue: 0.1958 time to fit residues: 67.6649 Evaluate side-chains 166 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 135 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 137 optimal weight: 0.0270 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 126 GLN E 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14525 Z= 0.236 Angle : 0.614 7.353 19730 Z= 0.318 Chirality : 0.042 0.140 2290 Planarity : 0.004 0.049 2490 Dihedral : 3.940 14.615 1925 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.55 % Allowed : 8.09 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1735 helix: 2.05 (0.17), residues: 945 sheet: -0.47 (0.30), residues: 285 loop : -1.61 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 61 HIS 0.003 0.001 HIS C 83 PHE 0.015 0.001 PHE D 306 TYR 0.017 0.001 TYR E 327 ARG 0.003 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.823 Fit side-chains REVERT: A 138 MET cc_start: 0.8542 (tmm) cc_final: 0.7319 (tmm) REVERT: B 74 GLN cc_start: 0.9283 (tt0) cc_final: 0.8928 (tp-100) REVERT: B 100 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8266 (mm-30) REVERT: B 134 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8135 (m-40) REVERT: B 138 MET cc_start: 0.8745 (ttp) cc_final: 0.8094 (tmm) REVERT: B 140 GLN cc_start: 0.8827 (mt0) cc_final: 0.8499 (mt0) REVERT: C 74 GLN cc_start: 0.9027 (tt0) cc_final: 0.8657 (tp-100) REVERT: D 32 MET cc_start: 0.8375 (mtp) cc_final: 0.8013 (mtm) REVERT: D 74 GLN cc_start: 0.9085 (tt0) cc_final: 0.8692 (tp-100) REVERT: D 91 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9082 (mt) REVERT: D 112 MET cc_start: 0.8766 (mtm) cc_final: 0.8539 (mtt) REVERT: D 152 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8724 (tt0) REVERT: E 74 GLN cc_start: 0.9053 (tt0) cc_final: 0.8830 (tp-100) REVERT: E 138 MET cc_start: 0.8613 (ttp) cc_final: 0.7010 (tmm) REVERT: E 209 GLN cc_start: 0.9341 (tt0) cc_final: 0.8997 (tm-30) REVERT: E 291 MET cc_start: 0.8061 (mmt) cc_final: 0.7833 (mmm) outliers start: 40 outliers final: 24 residues processed: 173 average time/residue: 0.1954 time to fit residues: 56.8796 Evaluate side-chains 146 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 334 MET Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 213 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14525 Z= 0.308 Angle : 0.631 7.214 19730 Z= 0.324 Chirality : 0.043 0.166 2290 Planarity : 0.004 0.049 2490 Dihedral : 3.954 15.643 1925 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.31 % Allowed : 9.24 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1735 helix: 2.20 (0.17), residues: 945 sheet: -0.23 (0.31), residues: 275 loop : -1.45 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 325 HIS 0.005 0.001 HIS C 83 PHE 0.018 0.001 PHE B 306 TYR 0.016 0.001 TYR A 327 ARG 0.003 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 125 time to evaluate : 1.738 Fit side-chains REVERT: A 138 MET cc_start: 0.8536 (tmm) cc_final: 0.7262 (tmm) REVERT: B 74 GLN cc_start: 0.9264 (tt0) cc_final: 0.8939 (tp-100) REVERT: B 100 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8272 (mm-30) REVERT: B 138 MET cc_start: 0.8821 (ttp) cc_final: 0.8219 (tmm) REVERT: B 140 GLN cc_start: 0.8880 (mt0) cc_final: 0.8588 (mt0) REVERT: C 74 GLN cc_start: 0.9046 (tt0) cc_final: 0.8688 (tp-100) REVERT: C 300 ILE cc_start: 0.7760 (pt) cc_final: 0.7496 (pt) REVERT: D 32 MET cc_start: 0.8399 (mtp) cc_final: 0.8050 (mtm) REVERT: D 74 GLN cc_start: 0.9079 (tt0) cc_final: 0.8680 (tp-100) REVERT: D 91 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9089 (mt) REVERT: D 112 MET cc_start: 0.8789 (mtm) cc_final: 0.8543 (mtt) REVERT: D 152 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8721 (tt0) REVERT: E 74 GLN cc_start: 0.9102 (tt0) cc_final: 0.8893 (tp-100) REVERT: E 138 MET cc_start: 0.8702 (ttp) cc_final: 0.7054 (tmm) REVERT: E 209 GLN cc_start: 0.9314 (tt0) cc_final: 0.9010 (tm-30) outliers start: 52 outliers final: 34 residues processed: 161 average time/residue: 0.1981 time to fit residues: 54.0223 Evaluate side-chains 147 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 334 MET Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 14525 Z= 0.498 Angle : 0.757 7.692 19730 Z= 0.384 Chirality : 0.046 0.184 2290 Planarity : 0.005 0.052 2490 Dihedral : 4.366 18.386 1925 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.52 % Allowed : 9.81 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1735 helix: 2.05 (0.16), residues: 950 sheet: -0.64 (0.31), residues: 270 loop : -1.41 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 325 HIS 0.010 0.002 HIS C 83 PHE 0.022 0.002 PHE B 306 TYR 0.015 0.002 TYR C 327 ARG 0.003 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 125 time to evaluate : 1.659 Fit side-chains REVERT: A 138 MET cc_start: 0.8926 (tmm) cc_final: 0.7644 (tmm) REVERT: B 74 GLN cc_start: 0.9267 (tt0) cc_final: 0.8964 (tp-100) REVERT: B 129 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8919 (pp) REVERT: B 138 MET cc_start: 0.9007 (ttp) cc_final: 0.8111 (tmm) REVERT: C 74 GLN cc_start: 0.9072 (tt0) cc_final: 0.8707 (tp-100) REVERT: C 129 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9052 (pp) REVERT: D 32 MET cc_start: 0.8478 (mtp) cc_final: 0.8097 (mtm) REVERT: D 74 GLN cc_start: 0.9098 (tt0) cc_final: 0.8718 (tp-100) REVERT: D 129 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8858 (pp) REVERT: E 138 MET cc_start: 0.8945 (ttp) cc_final: 0.8262 (tmm) REVERT: E 209 GLN cc_start: 0.9323 (tt0) cc_final: 0.9039 (tm-30) REVERT: E 260 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8759 (tm-30) outliers start: 71 outliers final: 46 residues processed: 177 average time/residue: 0.1850 time to fit residues: 55.6751 Evaluate side-chains 151 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 102 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS C 83 HIS ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14525 Z= 0.187 Angle : 0.620 8.391 19730 Z= 0.314 Chirality : 0.042 0.153 2290 Planarity : 0.004 0.047 2490 Dihedral : 4.000 16.514 1925 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.17 % Allowed : 12.68 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1735 helix: 2.50 (0.17), residues: 940 sheet: -0.11 (0.32), residues: 265 loop : -1.16 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 61 HIS 0.002 0.001 HIS D 83 PHE 0.014 0.001 PHE B 306 TYR 0.016 0.001 TYR E 327 ARG 0.003 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.789 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8715 (tmm) cc_final: 0.7596 (tmm) REVERT: B 74 GLN cc_start: 0.9238 (tt0) cc_final: 0.8928 (tp-100) REVERT: B 129 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8747 (pp) REVERT: B 138 MET cc_start: 0.8776 (ttp) cc_final: 0.8250 (tmm) REVERT: C 74 GLN cc_start: 0.9007 (tt0) cc_final: 0.8641 (tp-100) REVERT: C 291 MET cc_start: 0.8559 (tpp) cc_final: 0.8339 (mmt) REVERT: D 32 MET cc_start: 0.8384 (mtp) cc_final: 0.8018 (mtm) REVERT: D 74 GLN cc_start: 0.9106 (tt0) cc_final: 0.8740 (tp-100) REVERT: D 129 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8817 (pp) REVERT: D 295 THR cc_start: 0.8513 (t) cc_final: 0.8290 (t) REVERT: E 74 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8894 (tp-100) REVERT: E 138 MET cc_start: 0.8680 (ttp) cc_final: 0.8446 (tmm) REVERT: E 209 GLN cc_start: 0.9315 (tt0) cc_final: 0.9015 (tm-30) REVERT: E 341 MET cc_start: 0.8130 (mmp) cc_final: 0.7875 (mmm) outliers start: 34 outliers final: 20 residues processed: 153 average time/residue: 0.1826 time to fit residues: 47.3703 Evaluate side-chains 135 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS C 95 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14525 Z= 0.322 Angle : 0.654 8.521 19730 Z= 0.328 Chirality : 0.042 0.141 2290 Planarity : 0.004 0.051 2490 Dihedral : 4.036 17.774 1925 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.68 % Allowed : 13.50 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.21), residues: 1735 helix: 2.50 (0.17), residues: 940 sheet: -0.17 (0.31), residues: 265 loop : -1.20 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 325 HIS 0.004 0.001 HIS D 83 PHE 0.020 0.001 PHE B 306 TYR 0.015 0.001 TYR A 327 ARG 0.002 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 110 time to evaluate : 1.671 Fit side-chains REVERT: A 138 MET cc_start: 0.8811 (tmm) cc_final: 0.7685 (tmm) REVERT: B 74 GLN cc_start: 0.9237 (tt0) cc_final: 0.8943 (tp-100) REVERT: B 129 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8730 (pp) REVERT: B 138 MET cc_start: 0.8914 (ttp) cc_final: 0.8296 (tmm) REVERT: C 74 GLN cc_start: 0.9027 (tt0) cc_final: 0.8680 (tp-100) REVERT: C 138 MET cc_start: 0.8726 (tmm) cc_final: 0.8316 (tmm) REVERT: D 32 MET cc_start: 0.8413 (mtp) cc_final: 0.8037 (mtm) REVERT: D 74 GLN cc_start: 0.9108 (tt0) cc_final: 0.8743 (tp-100) REVERT: D 129 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8839 (pp) REVERT: E 138 MET cc_start: 0.8768 (ttp) cc_final: 0.8464 (tmm) REVERT: E 209 GLN cc_start: 0.9318 (tt0) cc_final: 0.9011 (tm-30) outliers start: 42 outliers final: 31 residues processed: 139 average time/residue: 0.1702 time to fit residues: 40.4875 Evaluate side-chains 142 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14525 Z= 0.353 Angle : 0.673 8.911 19730 Z= 0.338 Chirality : 0.043 0.224 2290 Planarity : 0.004 0.049 2490 Dihedral : 4.099 17.809 1925 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.23 % Allowed : 13.69 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1735 helix: 2.47 (0.17), residues: 940 sheet: -0.20 (0.32), residues: 265 loop : -1.24 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 325 HIS 0.004 0.001 HIS D 83 PHE 0.032 0.002 PHE B 306 TYR 0.016 0.001 TYR C 327 ARG 0.002 0.000 ARG E 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 1.831 Fit side-chains REVERT: A 138 MET cc_start: 0.8884 (tmm) cc_final: 0.7780 (tmm) REVERT: B 74 GLN cc_start: 0.9235 (tt0) cc_final: 0.8950 (tp-100) REVERT: B 129 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8830 (pp) REVERT: B 138 MET cc_start: 0.8932 (ttp) cc_final: 0.8296 (tmm) REVERT: C 74 GLN cc_start: 0.9020 (tt0) cc_final: 0.8702 (tp-100) REVERT: C 138 MET cc_start: 0.8750 (tmm) cc_final: 0.8339 (tmm) REVERT: D 32 MET cc_start: 0.8400 (mtp) cc_final: 0.8025 (mtm) REVERT: D 74 GLN cc_start: 0.9106 (tt0) cc_final: 0.8786 (tp-100) REVERT: D 129 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8864 (pp) REVERT: E 138 MET cc_start: 0.8872 (ttp) cc_final: 0.8509 (tmm) REVERT: E 209 GLN cc_start: 0.9321 (tt0) cc_final: 0.9017 (tm-30) outliers start: 35 outliers final: 29 residues processed: 133 average time/residue: 0.1842 time to fit residues: 41.8379 Evaluate side-chains 139 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.5980 chunk 143 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 0.1980 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14525 Z= 0.225 Angle : 0.623 9.259 19730 Z= 0.312 Chirality : 0.042 0.197 2290 Planarity : 0.004 0.049 2490 Dihedral : 3.970 18.006 1925 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.10 % Allowed : 13.82 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1735 helix: 2.57 (0.17), residues: 940 sheet: 0.24 (0.33), residues: 255 loop : -1.27 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 325 HIS 0.002 0.001 HIS D 257 PHE 0.033 0.001 PHE B 306 TYR 0.016 0.001 TYR D 327 ARG 0.002 0.000 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.801 Fit side-chains REVERT: A 138 MET cc_start: 0.8806 (tmm) cc_final: 0.7690 (tmm) REVERT: B 74 GLN cc_start: 0.9218 (tt0) cc_final: 0.8924 (tp-100) REVERT: B 129 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8729 (pp) REVERT: B 138 MET cc_start: 0.8807 (ttp) cc_final: 0.8312 (tmm) REVERT: C 74 GLN cc_start: 0.8987 (tt0) cc_final: 0.8687 (tp-100) REVERT: C 138 MET cc_start: 0.8668 (tmm) cc_final: 0.8261 (tmm) REVERT: C 291 MET cc_start: 0.8479 (tpp) cc_final: 0.8267 (tpp) REVERT: D 32 MET cc_start: 0.8379 (mtp) cc_final: 0.8010 (mtm) REVERT: D 74 GLN cc_start: 0.9106 (tt0) cc_final: 0.8768 (tp-100) REVERT: D 129 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8833 (pp) REVERT: E 138 MET cc_start: 0.8769 (ttp) cc_final: 0.8501 (tmm) REVERT: E 209 GLN cc_start: 0.9324 (tt0) cc_final: 0.9023 (tm-30) outliers start: 33 outliers final: 26 residues processed: 139 average time/residue: 0.1861 time to fit residues: 43.8437 Evaluate side-chains 137 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14525 Z= 0.197 Angle : 0.621 9.498 19730 Z= 0.309 Chirality : 0.042 0.184 2290 Planarity : 0.004 0.048 2490 Dihedral : 3.903 17.721 1925 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.91 % Allowed : 14.14 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.21), residues: 1735 helix: 2.59 (0.17), residues: 940 sheet: 0.45 (0.33), residues: 255 loop : -1.27 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 325 HIS 0.001 0.000 HIS A 120 PHE 0.034 0.001 PHE B 306 TYR 0.015 0.001 TYR D 327 ARG 0.002 0.000 ARG C 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 1.797 Fit side-chains REVERT: A 138 MET cc_start: 0.8796 (tmm) cc_final: 0.7903 (tmm) REVERT: B 74 GLN cc_start: 0.9205 (tt0) cc_final: 0.8910 (tp-100) REVERT: B 129 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8703 (pp) REVERT: B 138 MET cc_start: 0.8849 (ttp) cc_final: 0.8243 (tmm) REVERT: B 260 GLN cc_start: 0.8962 (tt0) cc_final: 0.8687 (tm-30) REVERT: C 74 GLN cc_start: 0.9009 (tt0) cc_final: 0.8733 (tp-100) REVERT: C 138 MET cc_start: 0.8626 (tmm) cc_final: 0.8215 (tmm) REVERT: C 291 MET cc_start: 0.8356 (tpp) cc_final: 0.8147 (tpp) REVERT: D 32 MET cc_start: 0.8370 (mtp) cc_final: 0.7995 (mtm) REVERT: D 74 GLN cc_start: 0.9096 (tt0) cc_final: 0.8754 (tp-100) REVERT: D 129 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8811 (pp) REVERT: E 138 MET cc_start: 0.8748 (ttp) cc_final: 0.8541 (tmm) REVERT: E 209 GLN cc_start: 0.9314 (tt0) cc_final: 0.8996 (tm-30) outliers start: 30 outliers final: 27 residues processed: 133 average time/residue: 0.1887 time to fit residues: 42.7075 Evaluate side-chains 135 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 334 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0870 chunk 124 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057174 restraints weight = 46651.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.059273 restraints weight = 26486.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060753 restraints weight = 18036.374| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14525 Z= 0.212 Angle : 0.617 9.393 19730 Z= 0.307 Chirality : 0.042 0.176 2290 Planarity : 0.004 0.048 2490 Dihedral : 3.871 17.782 1925 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.23 % Allowed : 14.01 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.21), residues: 1735 helix: 2.55 (0.17), residues: 945 sheet: 0.49 (0.34), residues: 255 loop : -1.27 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 325 HIS 0.002 0.000 HIS D 257 PHE 0.022 0.001 PHE B 306 TYR 0.017 0.001 TYR D 327 ARG 0.002 0.000 ARG A 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.66 seconds wall clock time: 42 minutes 59.27 seconds (2579.27 seconds total)