Starting phenix.real_space_refine on Wed Aug 7 13:59:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b68_44249/08_2024/9b68_44249.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b68_44249/08_2024/9b68_44249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b68_44249/08_2024/9b68_44249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b68_44249/08_2024/9b68_44249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b68_44249/08_2024/9b68_44249.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b68_44249/08_2024/9b68_44249.cif" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10696 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7261 2.51 5 N 1872 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 25": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 116": "OD1" <-> "OD2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 231": "OD1" <-> "OD2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 362": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11364 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2763 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 9, 'ARG:plan': 11, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2774 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 13, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2814 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 146 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2865 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.03, per 1000 atoms: 0.62 Number of scatterers: 11364 At special positions: 0 Unit cell: (143.5, 124.64, 89.38, 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 36 16.00 O 2195 8.00 N 1872 7.00 C 7261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 901 " - " ASN B 355 " " NAG E 1 " - " ASN C 241 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN B 241 " " NAG H 1 " - " ASN D 241 " Time building additional restraints: 4.57 Conformation dependent library (CDL) restraints added in 1.9 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 40.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.585A pdb=" N ILE C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 172 through 187 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 252 through 265 removed outlier: 3.703A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.888A pdb=" N TYR A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.650A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.673A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 37 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 139 through 142 removed outlier: 3.615A pdb=" N GLY B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.625A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 301 Processing helix chain 'B' and resid 324 through 334 removed outlier: 4.100A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.993A pdb=" N TYR D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.538A pdb=" N ILE D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 172 through 188 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.937A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.961A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.464A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.607A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR C 220 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N PHE C 245 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE C 222 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 358 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR C 373 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 360 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR C 373 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 337 through 340 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 50 removed outlier: 7.414A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.136A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.719A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 47 removed outlier: 4.335A pdb=" N ALA B 72 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.035A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS B 364 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 340 Processing sheet with id=AB1, first strand: chain 'D' and resid 42 through 50 removed outlier: 6.231A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 72 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.442A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 339 551 hydrogen bonds defined for protein. 1620 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: 3.78 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3708 1.35 - 1.46: 2968 1.46 - 1.58: 4879 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 11611 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" CB ASP B 231 " pdb=" CG ASP B 231 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.76e+00 bond pdb=" CB GLU C 294 " pdb=" CG GLU C 294 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.71e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.70e+00 ... (remaining 11606 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.60: 212 106.60 - 113.45: 6378 113.45 - 120.30: 4077 120.30 - 127.15: 5086 127.15 - 134.01: 93 Bond angle restraints: 15846 Sorted by residual: angle pdb=" N ILE D 306 " pdb=" CA ILE D 306 " pdb=" C ILE D 306 " ideal model delta sigma weight residual 112.29 107.84 4.45 9.40e-01 1.13e+00 2.24e+01 angle pdb=" N THR C 228 " pdb=" CA THR C 228 " pdb=" C THR C 228 " ideal model delta sigma weight residual 114.75 109.33 5.42 1.26e+00 6.30e-01 1.85e+01 angle pdb=" CA CYS B 63 " pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " ideal model delta sigma weight residual 114.40 122.22 -7.82 2.30e+00 1.89e-01 1.16e+01 angle pdb=" C MET A 113 " pdb=" N ARG A 114 " pdb=" CA ARG A 114 " ideal model delta sigma weight residual 121.61 116.90 4.71 1.39e+00 5.18e-01 1.15e+01 angle pdb=" N VAL A 165 " pdb=" CA VAL A 165 " pdb=" C VAL A 165 " ideal model delta sigma weight residual 113.47 110.09 3.38 1.01e+00 9.80e-01 1.12e+01 ... (remaining 15841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 6323 21.82 - 43.64: 434 43.64 - 65.46: 69 65.46 - 87.28: 27 87.28 - 109.11: 9 Dihedral angle restraints: 6862 sinusoidal: 2538 harmonic: 4324 Sorted by residual: dihedral pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " pdb=" SG CYS B 315 " pdb=" CB CYS B 315 " ideal model delta sinusoidal sigma weight residual 93.00 18.39 74.61 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS D 63 " pdb=" SG CYS D 63 " pdb=" SG CYS D 315 " pdb=" CB CYS D 315 " ideal model delta sinusoidal sigma weight residual -86.00 -28.20 -57.80 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CA TRP C 323 " pdb=" C TRP C 323 " pdb=" N GLY C 324 " pdb=" CA GLY C 324 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 6859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1543 0.054 - 0.108: 271 0.108 - 0.162: 37 0.162 - 0.216: 3 0.216 - 0.269: 2 Chirality restraints: 1856 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 241 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1853 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 231 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C ASP B 231 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP B 231 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 232 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 56 " 0.016 2.00e-02 2.50e+03 1.80e-02 5.65e+00 pdb=" CG PHE B 56 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 56 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 56 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 56 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 56 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 56 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 323 " 0.016 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" CG TRP C 323 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 323 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 323 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 323 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 323 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 323 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 323 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 323 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 323 " 0.000 2.00e-02 2.50e+03 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1065 2.74 - 3.28: 11498 3.28 - 3.82: 19459 3.82 - 4.36: 21977 4.36 - 4.90: 38856 Nonbonded interactions: 92855 Sorted by model distance: nonbonded pdb=" OD1 ASP C 116 " pdb=" OH TYR C 356 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 228 " pdb=" NE2 GLN C 246 " model vdw 2.223 3.120 nonbonded pdb=" N GLU D 376 " pdb=" OE1 GLU D 376 " model vdw 2.285 3.120 nonbonded pdb=" OE1 GLU B 185 " pdb=" NH2 ARG B 190 " model vdw 2.312 3.120 nonbonded pdb=" N ASN A 355 " pdb=" OE2 GLU A 376 " model vdw 2.324 3.120 ... (remaining 92850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 78 or (resid 79 throu \ gh 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 through 140 or (resid 141 and (name N or name CA or name C or name O \ or name CB )) or resid 142 through 155 or (resid 156 through 157 and (name N or \ name CA or name C or name O or name CB )) or resid 158 through 183 or (resid 184 \ through 190 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 91 through 199 or (resid 200 and (name N or name CA or name C or name O or name \ CB )) or resid 201 through 230 or (resid 231 through 232 and (name N or name CA \ or name C or name O or name CB )) or resid 233 or (resid 234 through 236 and (na \ me N or name CA or name C or name O or name CB )) or resid 237 through 256 or (r \ esid 257 and (name N or name CA or name C or name O or name CB )) or resid 258 t \ hrough 265 or (resid 266 through 269 and (name N or name CA or name C or name O \ or name CB )) or resid 270 through 273 or (resid 274 and (name N or name CA or n \ ame C or name O or name CB )) or resid 275 through 278 or (resid 279 and (name N \ or name CA or name C or name O or name CB )) or resid 280 through 296 or (resid \ 297 and (name N or name CA or name C or name O or name CB )) or resid 298 throu \ gh 301 or (resid 302 through 303 and (name N or name CA or name C or name O or n \ ame CB )) or resid 304 through 333 or (resid 334 through 335 and (name N or name \ CA or name C or name O or name CB )) or resid 336 through 345 or (resid 346 and \ (name N or name CA or name C or name O or name CB )) or resid 347 through 351 o \ r (resid 352 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 53 through 383)) selection = (chain 'B' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 43 or (resid 44 and ( \ name N or name CA or name C or name O or name CB )) or resid 45 through 47 or (r \ esid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thr \ ough 103 or (resid 104 and (name N or name CA or name C or name O or name CB )) \ or resid 105 through 115 or (resid 116 and (name N or name CA or name C or name \ O or name CB )) or resid 117 through 139 or (resid 140 through 141 and (name N o \ r name CA or name C or name O or name CB )) or resid 142 through 155 or (resid 1 \ 56 through 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 169 or (resid 170 and (name N or name CA or name C or name O or nam \ e CB )) or resid 171 through 177 or (resid 178 and (name N or name CA or name C \ or name O or name CB )) or resid 179 through 183 or (resid 184 through 190 and ( \ name N or name CA or name C or name O or name CB )) or resid 191 through 199 or \ (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 201 \ through 205 or (resid 206 and (name N or name CA or name C or name O or name CB \ )) or resid 207 through 212 or (resid 213 and (name N or name CA or name C or n \ ame O or name CB )) or resid 214 through 215 or (resid 216 and (name N or name C \ A or name C or name O or name CB )) or resid 217 through 230 or (resid 231 throu \ gh 232 and (name N or name CA or name C or name O or name CB )) or resid 233 or \ (resid 234 through 236 and (name N or name CA or name C or name O or name CB )) \ or resid 237 through 273 or (resid 274 and (name N or name CA or name C or name \ O or name CB )) or resid 275 through 278 or (resid 279 and (name N or name CA or \ name C or name O or name CB )) or resid 280 through 293 or (resid 294 through 2 \ 95 and (name N or name CA or name C or name O or name CB )) or resid 296 through \ 298 or (resid 299 through 303 and (name N or name CA or name C or name O or nam \ e CB )) or resid 304 through 305 or (resid 306 and (name N or name CA or name C \ or name O or name CB )) or resid 307 through 333 or (resid 334 through 335 and ( \ name N or name CA or name C or name O or name CB )) or resid 336 through 361 or \ (resid 362 and (name N or name CA or name C or name O or name CB )) or resid 363 \ through 368 or (resid 369 through 370 and (name N or name CA or name C or name \ O or name CB )) or resid 371 through 383)) selection = (chain 'C' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 36 or (resid 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 through 47 or (r \ esid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thr \ ough 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or \ resid 55 through 103 or (resid 104 and (name N or name CA or name C or name O o \ r name CB )) or resid 105 through 115 or (resid 116 and (name N or name CA or na \ me C or name O or name CB )) or resid 117 through 139 or (resid 140 through 141 \ and (name N or name CA or name C or name O or name CB )) or resid 142 through 16 \ 9 or (resid 170 and (name N or name CA or name C or name O or name CB )) or resi \ d 171 through 184 or (resid 185 through 190 and (name N or name CA or name C or \ name O or name CB )) or resid 191 through 205 or (resid 206 and (name N or name \ CA or name C or name O or name CB )) or resid 207 through 212 or (resid 213 and \ (name N or name CA or name C or name O or name CB )) or resid 214 through 215 or \ (resid 216 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 7 through 265 or (resid 266 through 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 through 293 or (resid 294 through \ 295 and (name N or name CA or name C or name O or name CB )) or resid 296 or (re \ sid 297 and (name N or name CA or name C or name O or name CB )) or resid 298 or \ (resid 299 through 303 and (name N or name CA or name C or name O or name CB )) \ or resid 304 through 305 or (resid 306 and (name N or name CA or name C or name \ O or name CB )) or resid 307 through 351 or (resid 352 and (name N or name CA o \ r name C or name O or name CB )) or resid 353 through 383)) selection = (chain 'D' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 19 or (resid 20 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 21 through 23 and (name N or na \ me CA or name C or name O or name CB )) or resid 24 through 36 or (resid 37 and \ (name N or name CA or name C or name O or name CB )) or resid 38 through 43 or ( \ resid 44 and (name N or name CA or name C or name O or name CB )) or resid 45 th \ rough 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) o \ r resid 55 through 79 or (resid 80 and (name N or name CA or name C or name O or \ name CB )) or resid 81 through 115 or (resid 116 and (name N or name CA or name \ C or name O or name CB )) or resid 117 or (resid 118 and (name N or name CA or \ name C or name O or name CB )) or resid 119 through 139 or (resid 140 through 14 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 142 through \ 155 or (resid 156 through 157 and (name N or name CA or name C or name O or name \ CB )) or resid 158 through 169 or (resid 170 and (name N or name CA or name C o \ r name O or name CB )) or resid 171 through 172 or (resid 173 and (name N or nam \ e CA or name C or name O or name CB )) or resid 174 through 177 or (resid 178 an \ d (name N or name CA or name C or name O or name CB )) or resid 179 through 181 \ or (resid 182 and (name N or name CA or name C or name O or name CB )) or resid \ 183 or (resid 184 through 190 and (name N or name CA or name C or name O or name \ CB )) or resid 191 through 196 or (resid 197 and (name N or name CA or name C o \ r name O or name CB )) or resid 198 through 199 or (resid 200 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 205 or (resid 206 an \ d (name N or name CA or name C or name O or name CB )) or resid 207 through 212 \ or (resid 213 and (name N or name CA or name C or name O or name CB )) or resid \ 214 through 215 or (resid 216 and (name N or name CA or name C or name O or name \ CB )) or resid 217 through 230 or (resid 231 through 232 and (name N or name CA \ or name C or name O or name CB )) or resid 233 or (resid 234 through 236 and (n \ ame N or name CA or name C or name O or name CB )) or resid 237 through 260 or ( \ resid 261 and (name N or name CA or name C or name O or name CB )) or resid 262 \ through 265 or (resid 266 through 269 and (name N or name CA or name C or name O \ or name CB )) or resid 270 through 278 or (resid 279 and (name N or name CA or \ name C or name O or name CB )) or resid 280 through 296 or (resid 297 and (name \ N or name CA or name C or name O or name CB )) or resid 298 or (resid 299 throug \ h 303 and (name N or name CA or name C or name O or name CB )) or resid 304 thro \ ugh 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) o \ r resid 307 or (resid 308 through 309 and (name N or name CA or name C or name O \ or name CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or \ name C or name O or name CB )) or resid 326 through 330 or (resid 331 through 33 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 333 or (resi \ d 334 through 335 and (name N or name CA or name C or name O or name CB )) or re \ sid 336 through 345 or (resid 346 and (name N or name CA or name C or name O or \ name CB )) or resid 347 through 351 or (resid 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 through 361 or (resid 362 and (name N or \ name CA or name C or name O or name CB )) or resid 363 through 369 or (resid 37 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 371 through \ 383)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.060 Find NCS groups from input model: 0.580 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11611 Z= 0.218 Angle : 0.609 9.691 15846 Z= 0.345 Chirality : 0.043 0.269 1856 Planarity : 0.004 0.043 2039 Dihedral : 16.031 109.106 4082 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.27 % Allowed : 18.76 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.07 (0.22), residues: 1488 helix: 1.48 (0.21), residues: 628 sheet: -0.82 (0.34), residues: 244 loop : -1.33 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 323 HIS 0.007 0.001 HIS C 46 PHE 0.041 0.001 PHE B 56 TYR 0.023 0.001 TYR B 26 ARG 0.004 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.268 Fit side-chains REVERT: C 117 LEU cc_start: 0.8302 (tp) cc_final: 0.7781 (tt) REVERT: C 329 ILE cc_start: 0.9144 (mm) cc_final: 0.8805 (mm) REVERT: A 33 MET cc_start: 0.8050 (mmm) cc_final: 0.7808 (mmm) REVERT: B 376 GLU cc_start: 0.6813 (pm20) cc_final: 0.6586 (tp30) REVERT: D 316 LEU cc_start: 0.7475 (pp) cc_final: 0.7240 (mt) outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.2477 time to fit residues: 57.0642 Evaluate side-chains 149 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11611 Z= 0.253 Angle : 0.512 7.605 15846 Z= 0.270 Chirality : 0.042 0.198 1856 Planarity : 0.004 0.046 2039 Dihedral : 8.392 69.059 1826 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.87 % Allowed : 16.80 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.09 (0.22), residues: 1488 helix: 1.72 (0.21), residues: 596 sheet: -0.78 (0.34), residues: 244 loop : -1.19 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 323 HIS 0.005 0.001 HIS C 46 PHE 0.010 0.001 PHE B 41 TYR 0.016 0.002 TYR B 286 ARG 0.007 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 117 LEU cc_start: 0.8379 (tp) cc_final: 0.7825 (tt) REVERT: C 329 ILE cc_start: 0.9201 (mm) cc_final: 0.8726 (mm) REVERT: B 234 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8238 (mtmm) REVERT: D 316 LEU cc_start: 0.7469 (pp) cc_final: 0.7212 (mt) outliers start: 21 outliers final: 15 residues processed: 178 average time/residue: 0.2283 time to fit residues: 58.8553 Evaluate side-chains 165 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11611 Z= 0.333 Angle : 0.555 7.946 15846 Z= 0.292 Chirality : 0.044 0.209 1856 Planarity : 0.004 0.051 2039 Dihedral : 6.874 56.337 1826 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.91 % Allowed : 16.18 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.15 (0.22), residues: 1488 helix: 1.41 (0.21), residues: 604 sheet: -0.99 (0.33), residues: 244 loop : -1.19 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 323 HIS 0.008 0.002 HIS C 46 PHE 0.010 0.001 PHE B 41 TYR 0.025 0.002 TYR D 270 ARG 0.006 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 138 time to evaluate : 1.332 Fit side-chains REVERT: C 297 ARG cc_start: 0.6984 (mtp85) cc_final: 0.6497 (mtm-85) REVERT: A 50 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8128 (pp) REVERT: A 329 ILE cc_start: 0.8866 (mm) cc_final: 0.8285 (mp) REVERT: A 339 GLU cc_start: 0.6748 (tp30) cc_final: 0.6331 (mm-30) REVERT: A 380 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.6944 (ttp) REVERT: B 47 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8460 (mt) REVERT: B 360 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8811 (mp) REVERT: B 380 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8019 (tpp) outliers start: 44 outliers final: 30 residues processed: 170 average time/residue: 0.2387 time to fit residues: 58.3337 Evaluate side-chains 162 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11611 Z= 0.216 Angle : 0.499 8.919 15846 Z= 0.262 Chirality : 0.042 0.207 1856 Planarity : 0.004 0.051 2039 Dihedral : 6.097 56.236 1826 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.47 % Allowed : 17.78 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.05 (0.22), residues: 1488 helix: 1.52 (0.21), residues: 604 sheet: -1.04 (0.33), residues: 244 loop : -1.12 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 323 HIS 0.005 0.001 HIS A 46 PHE 0.008 0.001 PHE B 62 TYR 0.016 0.001 TYR C 373 ARG 0.006 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 1.235 Fit side-chains REVERT: C 117 LEU cc_start: 0.8356 (tp) cc_final: 0.7851 (tt) REVERT: C 198 ARG cc_start: 0.6923 (tpp-160) cc_final: 0.5273 (ttp80) REVERT: C 297 ARG cc_start: 0.6916 (mtp85) cc_final: 0.6450 (mtm-85) REVERT: A 329 ILE cc_start: 0.8844 (mm) cc_final: 0.8278 (mp) REVERT: A 339 GLU cc_start: 0.6694 (tp30) cc_final: 0.6325 (mm-30) REVERT: A 380 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6903 (ttp) REVERT: B 47 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8422 (mt) REVERT: B 95 SER cc_start: 0.8926 (m) cc_final: 0.8676 (t) REVERT: B 380 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8002 (tpp) REVERT: D 112 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: D 316 LEU cc_start: 0.7512 (pp) cc_final: 0.7204 (mt) outliers start: 39 outliers final: 25 residues processed: 168 average time/residue: 0.2359 time to fit residues: 57.3955 Evaluate side-chains 159 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 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 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11611 Z= 0.162 Angle : 0.474 8.525 15846 Z= 0.248 Chirality : 0.041 0.203 1856 Planarity : 0.003 0.048 2039 Dihedral : 5.575 55.280 1826 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.47 % Allowed : 18.04 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.23 (0.22), residues: 1488 helix: 1.84 (0.21), residues: 596 sheet: -0.94 (0.33), residues: 244 loop : -1.00 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 323 HIS 0.004 0.001 HIS B 46 PHE 0.010 0.001 PHE D 36 TYR 0.019 0.001 TYR C 373 ARG 0.005 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.248 Fit side-chains REVERT: C 117 LEU cc_start: 0.8224 (tp) cc_final: 0.7717 (tt) REVERT: C 198 ARG cc_start: 0.6890 (tpp-160) cc_final: 0.5300 (ttp80) REVERT: C 297 ARG cc_start: 0.6950 (mtp85) cc_final: 0.6483 (mtm-85) REVERT: A 329 ILE cc_start: 0.8821 (mm) cc_final: 0.8284 (mp) REVERT: A 339 GLU cc_start: 0.6581 (tp30) cc_final: 0.6285 (mm-30) REVERT: A 380 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6890 (ttt) REVERT: B 95 SER cc_start: 0.8926 (m) cc_final: 0.8622 (t) REVERT: B 104 ASP cc_start: 0.6981 (t0) cc_final: 0.6648 (m-30) REVERT: D 112 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8331 (mt0) REVERT: D 316 LEU cc_start: 0.7531 (pp) cc_final: 0.7222 (mt) outliers start: 39 outliers final: 29 residues processed: 181 average time/residue: 0.2336 time to fit residues: 60.4413 Evaluate side-chains 169 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 0.2980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11611 Z= 0.166 Angle : 0.467 10.212 15846 Z= 0.244 Chirality : 0.041 0.201 1856 Planarity : 0.003 0.047 2039 Dihedral : 5.504 55.076 1826 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.02 % Allowed : 18.22 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.31 (0.23), residues: 1488 helix: 1.90 (0.21), residues: 596 sheet: -0.92 (0.33), residues: 232 loop : -0.94 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 323 HIS 0.004 0.001 HIS C 46 PHE 0.008 0.001 PHE D 36 TYR 0.019 0.001 TYR C 373 ARG 0.004 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 1.273 Fit side-chains REVERT: C 117 LEU cc_start: 0.8227 (tp) cc_final: 0.7701 (tt) REVERT: C 198 ARG cc_start: 0.6903 (tpp-160) cc_final: 0.5291 (ttp80) REVERT: C 297 ARG cc_start: 0.6989 (mtp85) cc_final: 0.6504 (mtm-85) REVERT: A 266 GLU cc_start: 0.6891 (pm20) cc_final: 0.6662 (pt0) REVERT: A 329 ILE cc_start: 0.8810 (mm) cc_final: 0.8283 (mp) REVERT: A 339 GLU cc_start: 0.6563 (tp30) cc_final: 0.6237 (mm-30) REVERT: A 373 TYR cc_start: 0.7711 (p90) cc_final: 0.7295 (p90) REVERT: A 380 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6819 (ttp) REVERT: B 95 SER cc_start: 0.8893 (m) cc_final: 0.8643 (t) REVERT: B 104 ASP cc_start: 0.6895 (t0) cc_final: 0.6595 (m-30) REVERT: B 185 GLU cc_start: 0.8305 (tp30) cc_final: 0.8008 (tp30) REVERT: B 190 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7505 (mmp-170) REVERT: B 380 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7940 (tpp) REVERT: D 39 SER cc_start: 0.5155 (OUTLIER) cc_final: 0.4520 (p) REVERT: D 112 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: D 316 LEU cc_start: 0.7519 (pp) cc_final: 0.7215 (mt) outliers start: 34 outliers final: 28 residues processed: 171 average time/residue: 0.2178 time to fit residues: 54.6158 Evaluate side-chains 177 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11611 Z= 0.161 Angle : 0.462 9.803 15846 Z= 0.242 Chirality : 0.041 0.200 1856 Planarity : 0.003 0.046 2039 Dihedral : 5.420 54.913 1826 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.29 % Allowed : 18.40 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.37 (0.22), residues: 1488 helix: 1.95 (0.21), residues: 596 sheet: -0.98 (0.33), residues: 240 loop : -0.87 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 323 HIS 0.003 0.001 HIS B 46 PHE 0.008 0.001 PHE D 36 TYR 0.019 0.001 TYR C 373 ARG 0.007 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 1.382 Fit side-chains REVERT: C 117 LEU cc_start: 0.8217 (tp) cc_final: 0.7698 (tt) REVERT: C 198 ARG cc_start: 0.6914 (tpp-160) cc_final: 0.5285 (ttp80) REVERT: C 297 ARG cc_start: 0.6988 (mtp85) cc_final: 0.6544 (mtm-85) REVERT: A 339 GLU cc_start: 0.6541 (tp30) cc_final: 0.6210 (mm-30) REVERT: A 380 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6849 (ttp) REVERT: B 95 SER cc_start: 0.8904 (m) cc_final: 0.8633 (t) REVERT: B 104 ASP cc_start: 0.6872 (t0) cc_final: 0.6662 (m-30) REVERT: B 234 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7759 (mtmm) REVERT: B 360 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8836 (mp) REVERT: B 380 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7929 (tpp) REVERT: D 39 SER cc_start: 0.5168 (OUTLIER) cc_final: 0.4535 (p) REVERT: D 112 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: D 316 LEU cc_start: 0.7512 (pp) cc_final: 0.7226 (mt) REVERT: D 380 MET cc_start: 0.7497 (tmm) cc_final: 0.7145 (ttt) outliers start: 37 outliers final: 26 residues processed: 174 average time/residue: 0.2294 time to fit residues: 57.6891 Evaluate side-chains 172 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS D 46 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11611 Z= 0.440 Angle : 0.619 9.132 15846 Z= 0.324 Chirality : 0.046 0.230 1856 Planarity : 0.004 0.053 2039 Dihedral : 6.001 57.885 1826 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.09 % Allowed : 17.96 % Favored : 77.96 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 10.00 % 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: -0.20 (0.22), residues: 1488 helix: 1.35 (0.21), residues: 596 sheet: -1.20 (0.32), residues: 252 loop : -1.06 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 323 HIS 0.006 0.002 HIS A 46 PHE 0.014 0.002 PHE B 76 TYR 0.027 0.002 TYR B 286 ARG 0.008 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 129 time to evaluate : 1.365 Fit side-chains REVERT: C 198 ARG cc_start: 0.7019 (tpp-160) cc_final: 0.5321 (ttp80) REVERT: C 297 ARG cc_start: 0.7057 (mtp85) cc_final: 0.6595 (mtm-85) REVERT: C 374 TRP cc_start: 0.8268 (t60) cc_final: 0.7897 (t60) REVERT: A 274 HIS cc_start: 0.5575 (OUTLIER) cc_final: 0.5004 (t70) REVERT: A 329 ILE cc_start: 0.8829 (mm) cc_final: 0.8329 (mp) REVERT: A 339 GLU cc_start: 0.6658 (tp30) cc_final: 0.6249 (mm-30) REVERT: A 380 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7168 (ttt) REVERT: B 47 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8544 (mt) REVERT: B 95 SER cc_start: 0.8912 (m) cc_final: 0.8625 (t) REVERT: B 300 ARG cc_start: 0.7440 (ttp80) cc_final: 0.6970 (ptm160) REVERT: B 360 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8859 (mp) REVERT: B 380 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8070 (tpp) REVERT: D 39 SER cc_start: 0.5113 (OUTLIER) cc_final: 0.4553 (p) REVERT: D 112 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8536 (mt0) REVERT: D 316 LEU cc_start: 0.7692 (pp) cc_final: 0.7316 (mt) REVERT: D 380 MET cc_start: 0.7926 (tmm) cc_final: 0.7511 (ttt) outliers start: 46 outliers final: 31 residues processed: 162 average time/residue: 0.2260 time to fit residues: 53.2359 Evaluate side-chains 159 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 382 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11611 Z= 0.182 Angle : 0.498 9.498 15846 Z= 0.261 Chirality : 0.042 0.206 1856 Planarity : 0.003 0.051 2039 Dihedral : 5.648 57.267 1826 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.76 % Allowed : 19.47 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.15 (0.22), residues: 1488 helix: 1.72 (0.21), residues: 596 sheet: -1.14 (0.32), residues: 240 loop : -0.91 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 323 HIS 0.005 0.001 HIS A 46 PHE 0.009 0.001 PHE D 36 TYR 0.019 0.001 TYR C 373 ARG 0.005 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.392 Fit side-chains REVERT: C 117 LEU cc_start: 0.8309 (tp) cc_final: 0.7853 (tt) REVERT: C 198 ARG cc_start: 0.6931 (tpp-160) cc_final: 0.5295 (ttp80) REVERT: C 250 TYR cc_start: 0.5975 (m-80) cc_final: 0.5708 (m-80) REVERT: C 297 ARG cc_start: 0.7043 (mtp85) cc_final: 0.6609 (mtm-85) REVERT: A 329 ILE cc_start: 0.8786 (mm) cc_final: 0.8274 (mp) REVERT: A 339 GLU cc_start: 0.6550 (tp30) cc_final: 0.6203 (mm-30) REVERT: A 380 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.6887 (ttp) REVERT: B 95 SER cc_start: 0.8919 (m) cc_final: 0.8637 (t) REVERT: B 104 ASP cc_start: 0.7040 (t0) cc_final: 0.6783 (m-30) REVERT: B 300 ARG cc_start: 0.7389 (ttp80) cc_final: 0.6887 (ptm160) REVERT: B 360 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8815 (mp) REVERT: B 380 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8016 (tpp) REVERT: D 39 SER cc_start: 0.5120 (OUTLIER) cc_final: 0.4553 (p) REVERT: D 316 LEU cc_start: 0.7685 (pp) cc_final: 0.7314 (mt) outliers start: 31 outliers final: 22 residues processed: 156 average time/residue: 0.2262 time to fit residues: 51.5758 Evaluate side-chains 156 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.2980 chunk 125 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11611 Z= 0.173 Angle : 0.497 9.421 15846 Z= 0.258 Chirality : 0.042 0.199 1856 Planarity : 0.003 0.051 2039 Dihedral : 5.541 56.042 1826 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.40 % Allowed : 19.82 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.28 (0.22), residues: 1488 helix: 1.84 (0.21), residues: 596 sheet: -1.04 (0.32), residues: 240 loop : -0.86 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 323 HIS 0.005 0.001 HIS A 46 PHE 0.009 0.001 PHE D 36 TYR 0.025 0.001 TYR C 286 ARG 0.004 0.000 ARG C 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.249 Fit side-chains REVERT: C 117 LEU cc_start: 0.8273 (tp) cc_final: 0.7797 (tt) REVERT: C 198 ARG cc_start: 0.6948 (tpp-160) cc_final: 0.5314 (ttp80) REVERT: C 250 TYR cc_start: 0.5732 (m-80) cc_final: 0.5488 (m-80) REVERT: C 297 ARG cc_start: 0.7045 (mtp85) cc_final: 0.6618 (mtm-85) REVERT: A 329 ILE cc_start: 0.8772 (mm) cc_final: 0.8275 (mp) REVERT: A 380 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6915 (ttt) REVERT: B 95 SER cc_start: 0.8896 (m) cc_final: 0.8616 (t) REVERT: B 104 ASP cc_start: 0.7024 (t0) cc_final: 0.6787 (m-30) REVERT: B 190 ARG cc_start: 0.8165 (mmp80) cc_final: 0.7740 (mmp-170) REVERT: B 300 ARG cc_start: 0.7352 (ttp80) cc_final: 0.6869 (ptm160) REVERT: B 360 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8841 (mp) REVERT: B 380 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8010 (tpp) REVERT: D 39 SER cc_start: 0.5243 (OUTLIER) cc_final: 0.4678 (p) REVERT: D 316 LEU cc_start: 0.7714 (pp) cc_final: 0.7347 (mt) outliers start: 27 outliers final: 23 residues processed: 157 average time/residue: 0.2205 time to fit residues: 50.4932 Evaluate side-chains 162 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 382 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.0070 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** 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 = 0.3681 r_free = 0.3681 target = 0.142723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119349 restraints weight = 16574.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120479 restraints weight = 13513.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121353 restraints weight = 10713.315| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11611 Z= 0.143 Angle : 0.486 9.471 15846 Z= 0.253 Chirality : 0.041 0.193 1856 Planarity : 0.003 0.047 2039 Dihedral : 5.401 54.704 1826 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.40 % Allowed : 20.18 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.46 (0.23), residues: 1488 helix: 2.02 (0.22), residues: 596 sheet: -0.93 (0.33), residues: 240 loop : -0.80 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 323 HIS 0.003 0.001 HIS A 46 PHE 0.012 0.001 PHE D 36 TYR 0.021 0.001 TYR C 286 ARG 0.004 0.000 ARG B 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.45 seconds wall clock time: 40 minutes 28.80 seconds (2428.80 seconds total)