Starting phenix.real_space_refine on Wed Feb 14 14:33:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5v_33016/02_2024/7x5v_33016_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5v_33016/02_2024/7x5v_33016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5v_33016/02_2024/7x5v_33016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5v_33016/02_2024/7x5v_33016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5v_33016/02_2024/7x5v_33016_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5v_33016/02_2024/7x5v_33016_neut.pdb" } resolution = 2.83 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= 0.006 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6263 2.51 5 N 1510 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B ASP 357": "OD1" <-> "OD2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C ASP 357": "OD1" <-> "OD2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D ASP 250": "OD1" <-> "OD2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D ASP 357": "OD1" <-> "OD2" Residue "E GLU 14": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9504 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Time building chain proxies: 5.47, per 1000 atoms: 0.58 Number of scatterers: 9504 At special positions: 0 Unit cell: (107.12, 108.16, 91.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1675 8.00 N 1510 7.00 C 6263 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: 3.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 4 sheets defined 79.2% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.832A pdb=" N VAL A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 140 removed outlier: 3.937A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.998A pdb=" N GLY A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.583A pdb=" N MET A 179 " --> pdb=" O PRO A 176 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 4.129A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 237 Proline residue: A 212 - end of helix removed outlier: 4.378A pdb=" N ASN A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.754A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 311 through 319 removed outlier: 4.068A pdb=" N ALA A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 338 through 358 Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 140 removed outlier: 3.937A pdb=" N TRP B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 removed outlier: 3.999A pdb=" N GLY B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 removed outlier: 3.584A pdb=" N MET B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 180 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 181 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 186 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 187 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 4.128A pdb=" N ARG B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 237 Proline residue: B 212 - end of helix removed outlier: 4.378A pdb=" N ASN B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 265 removed outlier: 3.753A pdb=" N VAL B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 290 through 303 Processing helix chain 'B' and resid 311 through 319 removed outlier: 4.067A pdb=" N ALA B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 338 through 358 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 107 Processing helix chain 'C' and resid 114 through 140 removed outlier: 3.938A pdb=" N TRP C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 172 removed outlier: 3.999A pdb=" N GLY C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 removed outlier: 3.584A pdb=" N MET C 179 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 181 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 184 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 186 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 187 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 4.129A pdb=" N ARG C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 237 Proline residue: C 212 - end of helix removed outlier: 4.378A pdb=" N ASN C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 258 through 265 removed outlier: 3.753A pdb=" N VAL C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 290 through 303 Processing helix chain 'C' and resid 311 through 319 removed outlier: 4.068A pdb=" N ALA C 315 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 337 Processing helix chain 'C' and resid 338 through 358 Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.832A pdb=" N VAL D 76 " --> pdb=" O HIS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 107 Processing helix chain 'D' and resid 114 through 140 removed outlier: 3.937A pdb=" N TRP D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 172 removed outlier: 3.998A pdb=" N GLY D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 removed outlier: 3.585A pdb=" N MET D 179 " --> pdb=" O PRO D 176 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA D 180 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU D 181 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 184 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 186 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 187 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 4.128A pdb=" N ARG D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 237 Proline residue: D 212 - end of helix removed outlier: 4.377A pdb=" N ASN D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 265 removed outlier: 3.752A pdb=" N VAL D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 Processing helix chain 'D' and resid 290 through 303 Processing helix chain 'D' and resid 311 through 319 removed outlier: 4.068A pdb=" N ALA D 315 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 337 Processing helix chain 'D' and resid 338 through 358 Processing helix chain 'E' and resid 3 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 248 Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 248 Processing sheet with id=AA3, first strand: chain 'C' and resid 244 through 248 Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 248 653 hydrogen bonds defined for protein. 1887 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: 2.47 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1489 1.31 - 1.44: 2983 1.44 - 1.56: 5208 1.56 - 1.68: 0 1.68 - 1.81: 88 Bond restraints: 9768 Sorted by residual: bond pdb=" CA THR D 244 " pdb=" C THR D 244 " ideal model delta sigma weight residual 1.520 1.474 0.047 1.22e-02 6.72e+03 1.48e+01 bond pdb=" N THR D 244 " pdb=" CA THR D 244 " ideal model delta sigma weight residual 1.455 1.416 0.039 1.25e-02 6.40e+03 9.80e+00 bond pdb=" C ASN D 251 " pdb=" O ASN D 251 " ideal model delta sigma weight residual 1.236 1.202 0.035 1.15e-02 7.56e+03 9.14e+00 bond pdb=" C ASP D 250 " pdb=" O ASP D 250 " ideal model delta sigma weight residual 1.230 1.187 0.044 1.56e-02 4.11e+03 7.84e+00 bond pdb=" CA ASN D 251 " pdb=" C ASN D 251 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.27e-02 6.20e+03 6.00e+00 ... (remaining 9763 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.76: 209 106.76 - 113.59: 5115 113.59 - 120.43: 4096 120.43 - 127.26: 3761 127.26 - 134.09: 94 Bond angle restraints: 13275 Sorted by residual: angle pdb=" N HIS A 320 " pdb=" CA HIS A 320 " pdb=" C HIS A 320 " ideal model delta sigma weight residual 111.07 119.39 -8.32 1.07e+00 8.73e-01 6.05e+01 angle pdb=" N ASP C 250 " pdb=" CA ASP C 250 " pdb=" C ASP C 250 " ideal model delta sigma weight residual 111.71 102.69 9.02 1.34e+00 5.57e-01 4.53e+01 angle pdb=" N ASN C 251 " pdb=" CA ASN C 251 " pdb=" C ASN C 251 " ideal model delta sigma weight residual 111.07 117.57 -6.50 1.07e+00 8.73e-01 3.69e+01 angle pdb=" N ASN C 249 " pdb=" CA ASN C 249 " pdb=" C ASN C 249 " ideal model delta sigma weight residual 110.53 118.35 -7.82 1.29e+00 6.01e-01 3.68e+01 angle pdb=" N ARG B 146 " pdb=" CA ARG B 146 " pdb=" C ARG B 146 " ideal model delta sigma weight residual 112.23 119.74 -7.51 1.26e+00 6.30e-01 3.55e+01 ... (remaining 13270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4957 17.13 - 34.26: 471 34.26 - 51.39: 104 51.39 - 68.53: 21 68.53 - 85.66: 8 Dihedral angle restraints: 5561 sinusoidal: 2130 harmonic: 3431 Sorted by residual: dihedral pdb=" C VAL D 252 " pdb=" N VAL D 252 " pdb=" CA VAL D 252 " pdb=" CB VAL D 252 " ideal model delta harmonic sigma weight residual -122.00 -133.38 11.38 0 2.50e+00 1.60e-01 2.07e+01 dihedral pdb=" CA TYR A 281 " pdb=" C TYR A 281 " pdb=" N THR A 282 " pdb=" CA THR A 282 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR B 281 " pdb=" C TYR B 281 " pdb=" N THR B 282 " pdb=" CA THR B 282 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1254 0.071 - 0.142: 171 0.142 - 0.213: 19 0.213 - 0.284: 8 0.284 - 0.355: 2 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA VAL D 252 " pdb=" N VAL D 252 " pdb=" C VAL D 252 " pdb=" CB VAL D 252 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA TYR C 248 " pdb=" N TYR C 248 " pdb=" C TYR C 248 " pdb=" CB TYR C 248 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA LYS C 198 " pdb=" N LYS C 198 " pdb=" C LYS C 198 " pdb=" CB LYS C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1451 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 338 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C GLN A 338 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN A 338 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 339 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 338 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C GLN D 338 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN D 338 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE D 339 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 338 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C GLN B 338 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN B 338 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 339 " -0.018 2.00e-02 2.50e+03 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 63 2.49 - 3.09: 7388 3.09 - 3.70: 14755 3.70 - 4.30: 21910 4.30 - 4.90: 35938 Nonbonded interactions: 80054 Sorted by model distance: nonbonded pdb=" OG1 THR A 247 " pdb=" OE1 GLN A 271 " model vdw 1.891 2.440 nonbonded pdb=" O HIS A 237 " pdb=" NH2 ARG C 254 " model vdw 1.930 2.520 nonbonded pdb=" OD1 ASN A 249 " pdb=" NE2 GLN A 271 " model vdw 1.981 2.520 nonbonded pdb=" O LEU B 328 " pdb=" OG SER B 332 " model vdw 2.155 2.440 nonbonded pdb=" O LEU D 328 " pdb=" OG SER D 332 " model vdw 2.156 2.440 ... (remaining 80049 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.000 Extract box with map and model: 3.940 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.060 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 9768 Z= 0.425 Angle : 0.867 9.017 13275 Z= 0.544 Chirality : 0.052 0.355 1454 Planarity : 0.005 0.043 1665 Dihedral : 14.746 85.658 3369 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.40 % Allowed : 15.43 % Favored : 83.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.21), residues: 1166 helix: -1.18 (0.15), residues: 786 sheet: -1.34 (0.59), residues: 48 loop : -2.03 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 106 HIS 0.005 0.002 HIS A 320 PHE 0.024 0.002 PHE D 144 TYR 0.014 0.002 TYR D 109 ARG 0.005 0.001 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 238 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 271 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: C 78 ASP cc_start: 0.7827 (m-30) cc_final: 0.7590 (m-30) REVERT: D 78 ASP cc_start: 0.7537 (m-30) cc_final: 0.7313 (m-30) REVERT: D 123 PHE cc_start: 0.6518 (t80) cc_final: 0.6189 (t80) REVERT: D 329 PHE cc_start: 0.7706 (t80) cc_final: 0.7498 (t80) outliers start: 14 outliers final: 11 residues processed: 251 average time/residue: 1.0453 time to fit residues: 282.5580 Evaluate side-chains 177 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 68 optimal weight: 0.0040 chunk 106 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 266 GLN A 343 ASN B 115 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 115 GLN C 320 HIS C 343 ASN D 73 GLN D 136 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 320 HIS D 343 ASN E 7 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9768 Z= 0.192 Angle : 0.553 5.884 13275 Z= 0.296 Chirality : 0.039 0.140 1454 Planarity : 0.004 0.024 1665 Dihedral : 5.751 57.600 1307 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.41 % Allowed : 19.34 % Favored : 76.25 % 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: 0.08 (0.25), residues: 1166 helix: 0.61 (0.18), residues: 786 sheet: -0.46 (0.66), residues: 48 loop : -1.00 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 145 HIS 0.002 0.001 HIS A 237 PHE 0.025 0.001 PHE A 144 TYR 0.014 0.001 TYR D 245 ARG 0.005 0.001 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 173 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 SER cc_start: 0.8308 (m) cc_final: 0.8038 (p) REVERT: B 143 CYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6168 (t) REVERT: B 186 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6794 (mtp180) REVERT: B 253 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7884 (tptt) REVERT: C 196 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6843 (mtt-85) REVERT: D 123 PHE cc_start: 0.6605 (t80) cc_final: 0.6324 (t80) REVERT: D 148 ASN cc_start: 0.8347 (t0) cc_final: 0.8120 (t0) REVERT: D 196 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6698 (mtt-85) REVERT: D 222 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8211 (p) REVERT: D 348 VAL cc_start: 0.8698 (p) cc_final: 0.8460 (m) REVERT: D 352 LYS cc_start: 0.8244 (tppt) cc_final: 0.7913 (mptt) outliers start: 44 outliers final: 14 residues processed: 205 average time/residue: 0.9594 time to fit residues: 213.3719 Evaluate side-chains 186 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 85 optimal weight: 0.9990 overall best weight: 1.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 266 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 136 ASN D 266 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9768 Z= 0.237 Angle : 0.540 6.267 13275 Z= 0.286 Chirality : 0.040 0.135 1454 Planarity : 0.004 0.035 1665 Dihedral : 4.370 21.300 1292 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.51 % Allowed : 19.74 % Favored : 75.75 % 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: 0.68 (0.25), residues: 1166 helix: 1.02 (0.18), residues: 786 sheet: -0.41 (0.65), residues: 48 loop : -0.63 (0.40), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 145 HIS 0.005 0.001 HIS D 320 PHE 0.024 0.002 PHE A 144 TYR 0.015 0.001 TYR D 109 ARG 0.006 0.001 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 CYS cc_start: 0.6390 (OUTLIER) cc_final: 0.5551 (t) REVERT: A 268 SER cc_start: 0.8344 (m) cc_final: 0.8099 (p) REVERT: B 122 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5525 (mp0) REVERT: B 143 CYS cc_start: 0.6383 (OUTLIER) cc_final: 0.6034 (t) REVERT: B 186 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6642 (mtp180) REVERT: B 234 GLU cc_start: 0.7065 (tp30) cc_final: 0.6860 (tp30) REVERT: B 253 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8104 (tptt) REVERT: C 143 CYS cc_start: 0.6024 (OUTLIER) cc_final: 0.5324 (t) REVERT: C 196 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6750 (mtt-85) REVERT: D 192 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7103 (mtm-85) REVERT: D 196 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7026 (mtt-85) REVERT: D 352 LYS cc_start: 0.8256 (tppt) cc_final: 0.7958 (mptt) outliers start: 45 outliers final: 17 residues processed: 195 average time/residue: 1.0478 time to fit residues: 220.6311 Evaluate side-chains 182 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 258 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN B 100 ASN B 115 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9768 Z= 0.254 Angle : 0.539 7.194 13275 Z= 0.286 Chirality : 0.040 0.147 1454 Planarity : 0.004 0.031 1665 Dihedral : 4.304 18.504 1290 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.71 % Allowed : 20.34 % Favored : 74.95 % 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: 0.97 (0.25), residues: 1166 helix: 1.19 (0.18), residues: 794 sheet: -0.40 (0.66), residues: 48 loop : -0.39 (0.40), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 106 HIS 0.007 0.002 HIS A 320 PHE 0.024 0.002 PHE A 144 TYR 0.014 0.002 TYR D 109 ARG 0.004 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 CYS cc_start: 0.6505 (OUTLIER) cc_final: 0.5713 (t) REVERT: A 238 MET cc_start: 0.8748 (tpt) cc_final: 0.8508 (tpt) REVERT: A 242 ASP cc_start: 0.7498 (t0) cc_final: 0.7175 (t0) REVERT: A 268 SER cc_start: 0.8411 (m) cc_final: 0.8187 (p) REVERT: B 132 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: B 133 LEU cc_start: 0.7985 (tp) cc_final: 0.7641 (tp) REVERT: B 137 PHE cc_start: 0.8626 (m-10) cc_final: 0.8302 (m-10) REVERT: B 143 CYS cc_start: 0.6293 (OUTLIER) cc_final: 0.5730 (t) REVERT: B 186 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7032 (ptm160) REVERT: B 234 GLU cc_start: 0.7168 (tp30) cc_final: 0.6963 (tp30) REVERT: B 253 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8088 (tttt) REVERT: C 143 CYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5398 (t) REVERT: C 196 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6737 (mtt-85) REVERT: C 267 CYS cc_start: 0.7941 (m) cc_final: 0.7707 (m) REVERT: C 342 ILE cc_start: 0.8316 (mm) cc_final: 0.8076 (mt) REVERT: D 143 CYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5257 (t) REVERT: D 192 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7035 (mtm-85) REVERT: D 196 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6960 (mtt-85) REVERT: D 352 LYS cc_start: 0.8214 (mppt) cc_final: 0.7883 (mptt) outliers start: 47 outliers final: 13 residues processed: 193 average time/residue: 0.9969 time to fit residues: 208.6122 Evaluate side-chains 180 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN B 115 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9768 Z= 0.200 Angle : 0.518 7.104 13275 Z= 0.272 Chirality : 0.038 0.138 1454 Planarity : 0.004 0.028 1665 Dihedral : 4.218 18.279 1290 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.41 % Allowed : 21.34 % Favored : 74.25 % 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: 1.19 (0.25), residues: 1166 helix: 1.35 (0.18), residues: 798 sheet: -0.16 (0.66), residues: 48 loop : -0.35 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 145 HIS 0.010 0.002 HIS A 320 PHE 0.023 0.001 PHE A 144 TYR 0.011 0.001 TYR D 109 ARG 0.003 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 165 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 CYS cc_start: 0.6441 (OUTLIER) cc_final: 0.5697 (t) REVERT: A 242 ASP cc_start: 0.7473 (t0) cc_final: 0.7165 (t0) REVERT: A 268 SER cc_start: 0.8367 (m) cc_final: 0.8146 (p) REVERT: B 143 CYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5737 (t) REVERT: B 186 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7020 (ptm160) REVERT: C 143 CYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5387 (t) REVERT: C 196 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6714 (mtt-85) REVERT: C 267 CYS cc_start: 0.7883 (m) cc_final: 0.7678 (m) REVERT: C 322 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6458 (m-30) REVERT: D 143 CYS cc_start: 0.5964 (OUTLIER) cc_final: 0.5248 (t) REVERT: D 196 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6974 (mtt-85) REVERT: D 322 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6435 (m-30) REVERT: D 352 LYS cc_start: 0.8216 (mppt) cc_final: 0.7879 (mptt) outliers start: 44 outliers final: 17 residues processed: 190 average time/residue: 1.0081 time to fit residues: 208.8299 Evaluate side-chains 183 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 136 ASN A 266 GLN B 115 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9768 Z= 0.191 Angle : 0.516 8.132 13275 Z= 0.271 Chirality : 0.038 0.138 1454 Planarity : 0.004 0.026 1665 Dihedral : 4.146 17.853 1290 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.01 % Allowed : 21.14 % Favored : 73.85 % 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: 1.29 (0.25), residues: 1166 helix: 1.44 (0.18), residues: 798 sheet: -0.07 (0.66), residues: 48 loop : -0.35 (0.40), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 149 HIS 0.004 0.001 HIS A 320 PHE 0.023 0.001 PHE D 144 TYR 0.011 0.001 TYR D 109 ARG 0.003 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 CYS cc_start: 0.6354 (OUTLIER) cc_final: 0.5631 (t) REVERT: A 242 ASP cc_start: 0.7497 (t0) cc_final: 0.7207 (t0) REVERT: A 268 SER cc_start: 0.8357 (m) cc_final: 0.8150 (p) REVERT: B 132 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: B 133 LEU cc_start: 0.7899 (tp) cc_final: 0.7691 (tp) REVERT: B 137 PHE cc_start: 0.8371 (m-10) cc_final: 0.8168 (m-10) REVERT: B 143 CYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5827 (t) REVERT: B 186 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7019 (ptm160) REVERT: B 209 LYS cc_start: 0.7700 (mtpp) cc_final: 0.7249 (mtpm) REVERT: B 322 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6434 (m-30) REVERT: C 196 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6715 (mtt-85) REVERT: C 322 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6491 (m-30) REVERT: D 196 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6985 (mtt-85) REVERT: D 322 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6495 (m-30) REVERT: D 342 ILE cc_start: 0.8306 (mm) cc_final: 0.8051 (mt) REVERT: D 352 LYS cc_start: 0.8224 (mppt) cc_final: 0.7868 (mptt) outliers start: 50 outliers final: 20 residues processed: 189 average time/residue: 0.8979 time to fit residues: 185.3545 Evaluate side-chains 183 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 266 GLN B 115 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 96 ASN D 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9768 Z= 0.174 Angle : 0.515 7.168 13275 Z= 0.269 Chirality : 0.038 0.137 1454 Planarity : 0.004 0.027 1665 Dihedral : 4.104 17.789 1290 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.01 % Allowed : 22.55 % Favored : 73.45 % 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: 1.42 (0.25), residues: 1166 helix: 1.56 (0.18), residues: 798 sheet: -0.11 (0.65), residues: 48 loop : -0.36 (0.40), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 145 HIS 0.003 0.001 HIS C 320 PHE 0.023 0.001 PHE A 144 TYR 0.010 0.001 TYR A 109 ARG 0.003 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.5563 (pmm) cc_final: 0.5177 (tpp) REVERT: A 242 ASP cc_start: 0.7513 (t0) cc_final: 0.7224 (t0) REVERT: B 137 PHE cc_start: 0.8310 (m-10) cc_final: 0.8072 (m-10) REVERT: B 179 MET cc_start: 0.5204 (pmm) cc_final: 0.4803 (tpp) REVERT: B 186 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6983 (ptm160) REVERT: B 209 LYS cc_start: 0.7660 (mtpp) cc_final: 0.7234 (mtpm) REVERT: B 322 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6396 (m-30) REVERT: C 179 MET cc_start: 0.4803 (pmm) cc_final: 0.4466 (tpp) REVERT: C 196 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6740 (mtt-85) REVERT: C 322 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6513 (m-30) REVERT: C 342 ILE cc_start: 0.8295 (mm) cc_final: 0.8095 (mt) REVERT: D 135 ILE cc_start: 0.8719 (mt) cc_final: 0.8492 (mt) REVERT: D 196 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6954 (mtt-85) REVERT: D 322 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6513 (m-30) REVERT: D 342 ILE cc_start: 0.8289 (mm) cc_final: 0.8072 (mt) REVERT: D 352 LYS cc_start: 0.8234 (mppt) cc_final: 0.7932 (mptt) outliers start: 40 outliers final: 20 residues processed: 188 average time/residue: 1.0073 time to fit residues: 205.4733 Evaluate side-chains 183 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 96 ASN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9768 Z= 0.164 Angle : 0.500 7.053 13275 Z= 0.261 Chirality : 0.037 0.145 1454 Planarity : 0.004 0.028 1665 Dihedral : 4.051 17.721 1290 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.71 % Allowed : 22.75 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1166 helix: 1.69 (0.18), residues: 790 sheet: 0.04 (0.64), residues: 48 loop : -0.46 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 145 HIS 0.003 0.001 HIS C 320 PHE 0.024 0.001 PHE A 144 TYR 0.009 0.001 TYR B 109 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.5748 (pmm) cc_final: 0.5399 (tpp) REVERT: A 209 LYS cc_start: 0.7501 (mttm) cc_final: 0.7290 (mtmm) REVERT: A 242 ASP cc_start: 0.7498 (t0) cc_final: 0.7225 (t0) REVERT: B 179 MET cc_start: 0.5494 (pmm) cc_final: 0.4974 (tpp) REVERT: B 186 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6844 (mtp180) REVERT: B 209 LYS cc_start: 0.7583 (mtpp) cc_final: 0.7182 (mtpm) REVERT: B 322 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6492 (m-30) REVERT: C 179 MET cc_start: 0.5264 (pmm) cc_final: 0.4805 (tpp) REVERT: C 196 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6899 (mtt-85) REVERT: C 322 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6476 (m-30) REVERT: D 196 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7040 (mtt-85) REVERT: D 209 LYS cc_start: 0.7768 (mttp) cc_final: 0.7231 (mtpm) REVERT: D 322 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6497 (m-30) REVERT: D 342 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8132 (mt) REVERT: D 352 LYS cc_start: 0.8220 (mppt) cc_final: 0.7913 (mptt) outliers start: 37 outliers final: 23 residues processed: 189 average time/residue: 0.9536 time to fit residues: 196.2702 Evaluate side-chains 187 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 342 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0670 chunk 105 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 266 GLN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9768 Z= 0.166 Angle : 0.518 8.857 13275 Z= 0.272 Chirality : 0.037 0.143 1454 Planarity : 0.004 0.029 1665 Dihedral : 4.050 17.618 1290 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.01 % Allowed : 23.85 % Favored : 73.15 % 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: 1.51 (0.25), residues: 1166 helix: 1.69 (0.18), residues: 790 sheet: 0.15 (0.65), residues: 48 loop : -0.49 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 145 HIS 0.003 0.001 HIS A 237 PHE 0.036 0.001 PHE A 137 TYR 0.011 0.001 TYR B 109 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.5683 (pmm) cc_final: 0.5394 (tpp) REVERT: A 209 LYS cc_start: 0.7504 (mttm) cc_final: 0.7284 (mtmm) REVERT: A 242 ASP cc_start: 0.7496 (t0) cc_final: 0.7226 (t0) REVERT: B 105 GLU cc_start: 0.7835 (tp30) cc_final: 0.7444 (tp30) REVERT: B 155 ASP cc_start: 0.6941 (t0) cc_final: 0.6644 (t0) REVERT: B 179 MET cc_start: 0.5557 (pmm) cc_final: 0.4920 (tpp) REVERT: B 186 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6821 (mtp180) REVERT: B 209 LYS cc_start: 0.7568 (mtpp) cc_final: 0.7173 (mtpm) REVERT: C 179 MET cc_start: 0.5284 (pmm) cc_final: 0.5002 (tpp) REVERT: C 196 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6869 (mtt-85) REVERT: D 196 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7048 (mtt-85) REVERT: D 352 LYS cc_start: 0.8222 (mppt) cc_final: 0.7920 (mptt) outliers start: 30 outliers final: 20 residues processed: 179 average time/residue: 0.9924 time to fit residues: 192.7153 Evaluate side-chains 177 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 268 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 148 ASN A 266 GLN B 115 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 96 ASN D 266 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9768 Z= 0.185 Angle : 0.535 8.696 13275 Z= 0.278 Chirality : 0.038 0.210 1454 Planarity : 0.004 0.030 1665 Dihedral : 4.104 17.834 1290 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.81 % Allowed : 24.05 % Favored : 73.15 % 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: 1.48 (0.25), residues: 1166 helix: 1.66 (0.18), residues: 790 sheet: 0.23 (0.65), residues: 48 loop : -0.50 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 145 HIS 0.003 0.001 HIS A 237 PHE 0.030 0.002 PHE C 137 TYR 0.010 0.001 TYR B 109 ARG 0.002 0.000 ARG A 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.5743 (pmm) cc_final: 0.5514 (tpp) REVERT: A 209 LYS cc_start: 0.7491 (mttm) cc_final: 0.7278 (mtmm) REVERT: A 242 ASP cc_start: 0.7508 (t0) cc_final: 0.7231 (t0) REVERT: B 155 ASP cc_start: 0.6932 (t0) cc_final: 0.6623 (t0) REVERT: B 179 MET cc_start: 0.5689 (pmm) cc_final: 0.5094 (tpp) REVERT: B 186 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6888 (mtp180) REVERT: B 209 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7232 (mtpm) REVERT: B 322 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6516 (m-30) REVERT: C 196 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6913 (mtt-85) REVERT: C 267 CYS cc_start: 0.7764 (m) cc_final: 0.7413 (t) REVERT: C 322 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: D 196 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7083 (mtt-85) REVERT: D 352 LYS cc_start: 0.8184 (mppt) cc_final: 0.7886 (mptt) outliers start: 28 outliers final: 19 residues processed: 169 average time/residue: 1.0021 time to fit residues: 183.9848 Evaluate side-chains 173 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 196 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0370 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 266 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.176954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120639 restraints weight = 9675.763| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.79 r_work: 0.3248 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9768 Z= 0.183 Angle : 0.531 8.547 13275 Z= 0.279 Chirality : 0.038 0.141 1454 Planarity : 0.004 0.028 1665 Dihedral : 4.078 17.792 1290 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.61 % Allowed : 24.75 % Favored : 72.65 % 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: 1.46 (0.25), residues: 1166 helix: 1.63 (0.18), residues: 790 sheet: 0.29 (0.67), residues: 48 loop : -0.47 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 145 HIS 0.003 0.001 HIS C 237 PHE 0.043 0.002 PHE C 137 TYR 0.010 0.001 TYR B 109 ARG 0.002 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3843.52 seconds wall clock time: 69 minutes 25.44 seconds (4165.44 seconds total)