Starting phenix.real_space_refine on Wed Jun 11 08:02:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxe_16316/06_2025/8bxe_16316.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxe_16316/06_2025/8bxe_16316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bxe_16316/06_2025/8bxe_16316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxe_16316/06_2025/8bxe_16316.map" model { file = "/net/cci-nas-00/data/ceres_data/8bxe_16316/06_2025/8bxe_16316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxe_16316/06_2025/8bxe_16316.cif" } resolution = 3.9 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= 0.002 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 8319 2.51 5 N 2032 2.21 5 O 2123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12550 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2499 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2502 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "D" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2489 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "E" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "A" 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 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.29, per 1000 atoms: 0.66 Number of scatterers: 12550 At special positions: 0 Unit cell: (89.6328, 91.152, 124.574, 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 76 16.00 O 2123 8.00 N 2032 7.00 C 8319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 20 sheets defined 38.4% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 219 through 238 removed outlier: 4.490A pdb=" N MET A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.774A pdb=" N LYS A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 307 Processing helix chain 'A' and resid 416 through 441 removed outlier: 3.669A pdb=" N ILE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 219 through 239 removed outlier: 4.589A pdb=" N MET B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.679A pdb=" N LYS B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.716A pdb=" N MET B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 441 removed outlier: 3.576A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 219 through 238 removed outlier: 4.311A pdb=" N MET C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.797A pdb=" N LYS C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 307 Processing helix chain 'C' and resid 416 through 441 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.993A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 219 through 238 removed outlier: 4.626A pdb=" N MET D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) Proline residue: D 228 - end of helix Processing helix chain 'D' and resid 239 through 242 removed outlier: 3.544A pdb=" N ILE D 242 " --> pdb=" O MET D 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.801A pdb=" N LYS D 247 " --> pdb=" O PRO D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 307 removed outlier: 3.566A pdb=" N MET D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 441 removed outlier: 3.539A pdb=" N ILE D 420 " --> pdb=" O LEU D 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.755A pdb=" N ASP E 81 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 219 through 238 removed outlier: 4.374A pdb=" N MET E 227 " --> pdb=" O TYR E 223 " (cutoff:3.500A) Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 239 through 242 Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.794A pdb=" N LYS E 247 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 307 removed outlier: 3.588A pdb=" N MET E 307 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 441 removed outlier: 3.685A pdb=" N ILE E 420 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.549A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.549A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A 59 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 52 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR A 61 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN A 63 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 69 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.617A pdb=" N ILE A 88 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.747A pdb=" N GLY A 207 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 194 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 209 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY A 211 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.620A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.620A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 59 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP B 52 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR B 61 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN B 63 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 69 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.751A pdb=" N ILE B 88 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.759A pdb=" N GLY B 207 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE B 209 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY B 211 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.600A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.600A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 69 " --> pdb=" O ALA C 42 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 88 through 90 removed outlier: 3.592A pdb=" N ILE C 88 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY C 207 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG C 194 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 209 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY C 211 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.596A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.596A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 59 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP D 52 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR D 61 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN D 63 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 69 " --> pdb=" O ALA D 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 88 through 90 removed outlier: 3.517A pdb=" N ILE D 88 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 101 through 102 removed outlier: 5.521A pdb=" N GLY D 211 " --> pdb=" O GLN D 191 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN D 191 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS D 213 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER D 189 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LYS D 215 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL D 187 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 54 removed outlier: 3.698A pdb=" N GLU E 69 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP E 70 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 126 " --> pdb=" O TRP E 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 54 removed outlier: 3.698A pdb=" N GLU E 69 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AC2, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.751A pdb=" N GLY E 207 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG E 194 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE E 209 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY E 211 " --> pdb=" O VAL E 190 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1677 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: 3.39 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3762 1.34 - 1.46: 2547 1.46 - 1.58: 6429 1.58 - 1.70: 0 1.70 - 1.81: 133 Bond restraints: 12871 Sorted by residual: bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 ... (remaining 12866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 17220 2.01 - 4.03: 379 4.03 - 6.04: 57 6.04 - 8.05: 5 8.05 - 10.07: 2 Bond angle restraints: 17663 Sorted by residual: angle pdb=" CA LEU A 235 " pdb=" CB LEU A 235 " pdb=" CG LEU A 235 " ideal model delta sigma weight residual 116.30 126.37 -10.07 3.50e+00 8.16e-02 8.28e+00 angle pdb=" CA LYS C 125 " pdb=" CB LYS C 125 " pdb=" CG LYS C 125 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.52e+00 angle pdb=" N ALA D 28 " pdb=" CA ALA D 28 " pdb=" C ALA D 28 " ideal model delta sigma weight residual 114.56 111.19 3.37 1.27e+00 6.20e-01 7.05e+00 angle pdb=" N ALA A 28 " pdb=" CA ALA A 28 " pdb=" C ALA A 28 " ideal model delta sigma weight residual 114.56 111.26 3.30 1.27e+00 6.20e-01 6.74e+00 angle pdb=" N ALA E 28 " pdb=" CA ALA E 28 " pdb=" C ALA E 28 " ideal model delta sigma weight residual 114.56 111.42 3.14 1.27e+00 6.20e-01 6.13e+00 ... (remaining 17658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.22: 6558 12.22 - 24.44: 607 24.44 - 36.67: 275 36.67 - 48.89: 62 48.89 - 61.11: 27 Dihedral angle restraints: 7529 sinusoidal: 2684 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS E 138 " pdb=" SG CYS E 138 " pdb=" SG CYS E 152 " pdb=" CB CYS E 152 " ideal model delta sinusoidal sigma weight residual 93.00 44.33 48.67 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 45.37 47.63 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 152 " pdb=" CB CYS D 152 " ideal model delta sinusoidal sigma weight residual 93.00 45.97 47.03 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 7526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1755 0.057 - 0.115: 380 0.115 - 0.172: 38 0.172 - 0.229: 0 0.229 - 0.287: 1 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CB ILE E 180 " pdb=" CA ILE E 180 " pdb=" CG1 ILE E 180 " pdb=" CG2 ILE E 180 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 167 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 167 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 2171 not shown) Planarity restraints: 2128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 289 " -0.017 2.00e-02 2.50e+03 1.50e-02 3.96e+00 pdb=" CG PHE A 289 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 289 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 289 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 289 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 78 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO D 79 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 79 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 79 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 289 " -0.013 2.00e-02 2.50e+03 1.22e-02 2.62e+00 pdb=" CG PHE C 289 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 289 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 289 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 289 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 289 " -0.001 2.00e-02 2.50e+03 ... (remaining 2125 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1637 2.76 - 3.29: 12897 3.29 - 3.83: 21457 3.83 - 4.36: 23388 4.36 - 4.90: 40845 Nonbonded interactions: 100224 Sorted by model distance: nonbonded pdb=" OD1 ASN A 34 " pdb=" OG SER A 36 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN C 34 " pdb=" OG SER C 36 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASN D 34 " pdb=" OG SER D 36 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASN E 34 " pdb=" OG SER E 36 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASN B 34 " pdb=" OG SER B 36 " model vdw 2.247 3.040 ... (remaining 100219 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 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 234 or (resid 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 304 o \ r (resid 305 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 06 through 443 or resid 501)) selection = (chain 'B' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 234 or (resid 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE )) or resid 271 through 306 or (resid 307 and (name N or nam \ e CA or name C or name O or name CB )) or resid 414 through 443 or resid 501)) selection = (chain 'C' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 234 or (resid 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 236 through 443 or resid 501)) \ selection = chain 'D' selection = (chain 'E' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 234 or (resid 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 236 through 443 or resid 501)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.430 Find NCS groups from input model: 0.570 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 0.039 12881 Z= 0.165 Angle : 0.718 10.068 17688 Z= 0.385 Chirality : 0.045 0.287 2174 Planarity : 0.004 0.041 2123 Dihedral : 12.692 61.109 4384 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.20), residues: 1610 helix: 1.14 (0.23), residues: 530 sheet: -0.52 (0.32), residues: 310 loop : -2.17 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 77 HIS 0.002 0.001 HIS B 68 PHE 0.034 0.002 PHE A 289 TYR 0.024 0.001 TYR D 287 ARG 0.009 0.000 ARG C 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 0.71803 ( 15) hydrogen bonds : bond 0.13527 ( 586) hydrogen bonds : angle 5.95496 ( 1677) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.67929 ( 10) covalent geometry : bond 0.00346 (12871) covalent geometry : angle 0.71812 (17663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8343 (tmm) cc_final: 0.8019 (tpp) REVERT: A 234 PHE cc_start: 0.8842 (t80) cc_final: 0.8579 (t80) REVERT: A 287 TYR cc_start: 0.8255 (t80) cc_final: 0.8022 (t80) REVERT: B 23 HIS cc_start: 0.8676 (t-170) cc_final: 0.8427 (t-170) REVERT: B 129 VAL cc_start: 0.9133 (t) cc_final: 0.8932 (m) REVERT: B 227 MET cc_start: 0.8155 (tmm) cc_final: 0.7893 (tmm) REVERT: B 270 ARG cc_start: 0.7352 (mmt-90) cc_final: 0.7060 (mpt-90) REVERT: B 431 LEU cc_start: 0.8819 (pp) cc_final: 0.8537 (pp) REVERT: C 123 THR cc_start: 0.8432 (p) cc_final: 0.8178 (p) REVERT: C 127 MET cc_start: 0.8220 (mtt) cc_final: 0.7799 (mtm) REVERT: C 197 TRP cc_start: 0.4971 (t-100) cc_final: 0.4694 (t-100) REVERT: C 227 MET cc_start: 0.8478 (tmm) cc_final: 0.8071 (tpp) REVERT: C 431 LEU cc_start: 0.8861 (pp) cc_final: 0.8227 (tp) REVERT: D 77 TRP cc_start: 0.6590 (p-90) cc_final: 0.4841 (p-90) REVERT: D 123 THR cc_start: 0.8450 (p) cc_final: 0.8209 (p) REVERT: D 125 LYS cc_start: 0.8440 (tttm) cc_final: 0.8033 (tmtm) REVERT: D 215 LYS cc_start: 0.8321 (tptp) cc_final: 0.7390 (pttm) REVERT: D 440 TYR cc_start: 0.7731 (t80) cc_final: 0.7439 (t80) REVERT: E 81 ASP cc_start: 0.7087 (p0) cc_final: 0.6409 (t70) REVERT: E 151 MET cc_start: 0.8307 (ttm) cc_final: 0.8012 (ttt) REVERT: E 197 TRP cc_start: 0.5002 (t-100) cc_final: 0.4698 (t-100) REVERT: E 440 TYR cc_start: 0.7476 (t80) cc_final: 0.7098 (t80) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2010 time to fit residues: 114.5713 Evaluate side-chains 278 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.0000 chunk 121 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 0.3980 chunk 145 optimal weight: 4.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108760 restraints weight = 22366.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112406 restraints weight = 12986.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.114936 restraints weight = 9212.488| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12881 Z= 0.143 Angle : 0.687 14.014 17688 Z= 0.337 Chirality : 0.046 0.193 2174 Planarity : 0.004 0.033 2123 Dihedral : 5.154 39.577 1876 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.27 % Allowed : 11.48 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1610 helix: 1.14 (0.22), residues: 530 sheet: -0.33 (0.32), residues: 310 loop : -2.24 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 77 HIS 0.002 0.001 HIS C 161 PHE 0.027 0.002 PHE B 425 TYR 0.019 0.002 TYR B 122 ARG 0.005 0.000 ARG C 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 5) link_NAG-ASN : angle 0.47467 ( 15) hydrogen bonds : bond 0.04393 ( 586) hydrogen bonds : angle 5.02970 ( 1677) SS BOND : bond 0.00170 ( 5) SS BOND : angle 0.64648 ( 10) covalent geometry : bond 0.00321 (12871) covalent geometry : angle 0.68669 (17663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 332 time to evaluate : 1.299 Fit side-chains REVERT: A 173 GLN cc_start: 0.8313 (pm20) cc_final: 0.8010 (pm20) REVERT: A 227 MET cc_start: 0.8375 (tmm) cc_final: 0.7992 (tpp) REVERT: A 234 PHE cc_start: 0.8924 (t80) cc_final: 0.8582 (t80) REVERT: B 21 ILE cc_start: 0.9123 (tp) cc_final: 0.8479 (tp) REVERT: B 23 HIS cc_start: 0.8677 (t-170) cc_final: 0.8441 (t-170) REVERT: B 127 MET cc_start: 0.8258 (mtp) cc_final: 0.7978 (ttm) REVERT: B 129 VAL cc_start: 0.9110 (t) cc_final: 0.8902 (m) REVERT: B 173 GLN cc_start: 0.8130 (pm20) cc_final: 0.7454 (pp30) REVERT: B 287 TYR cc_start: 0.8549 (t80) cc_final: 0.8171 (t80) REVERT: C 125 LYS cc_start: 0.8026 (tmtt) cc_final: 0.7707 (tmtt) REVERT: C 127 MET cc_start: 0.8188 (mtt) cc_final: 0.7869 (mtm) REVERT: C 197 TRP cc_start: 0.4760 (t-100) cc_final: 0.4460 (t-100) REVERT: C 222 GLN cc_start: 0.8174 (pm20) cc_final: 0.7793 (pm20) REVERT: D 77 TRP cc_start: 0.6656 (p-90) cc_final: 0.4834 (p-90) REVERT: D 186 GLN cc_start: 0.7263 (mm110) cc_final: 0.6968 (mm-40) REVERT: D 215 LYS cc_start: 0.8471 (tptp) cc_final: 0.7529 (pttt) REVERT: D 220 TYR cc_start: 0.8673 (t80) cc_final: 0.8014 (t80) REVERT: D 440 TYR cc_start: 0.7636 (t80) cc_final: 0.7318 (t80) REVERT: E 81 ASP cc_start: 0.6981 (p0) cc_final: 0.6476 (t70) REVERT: E 197 TRP cc_start: 0.4830 (t-100) cc_final: 0.4544 (t-100) REVERT: E 222 GLN cc_start: 0.8161 (pm20) cc_final: 0.7800 (pm20) REVERT: E 440 TYR cc_start: 0.7504 (t80) cc_final: 0.7115 (t80) outliers start: 16 outliers final: 11 residues processed: 342 average time/residue: 0.1941 time to fit residues: 101.8486 Evaluate side-chains 295 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 284 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 132 optimal weight: 0.3980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104747 restraints weight = 22904.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108270 restraints weight = 13467.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110750 restraints weight = 9534.980| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12881 Z= 0.171 Angle : 0.689 14.624 17688 Z= 0.335 Chirality : 0.045 0.147 2174 Planarity : 0.004 0.033 2123 Dihedral : 4.639 27.601 1876 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.90 % Allowed : 17.02 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.95 (0.20), residues: 1610 helix: 1.22 (0.21), residues: 530 sheet: -0.18 (0.33), residues: 305 loop : -2.24 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 77 HIS 0.002 0.000 HIS D 161 PHE 0.028 0.002 PHE B 425 TYR 0.025 0.002 TYR C 220 ARG 0.004 0.000 ARG D 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 5) link_NAG-ASN : angle 0.67626 ( 15) hydrogen bonds : bond 0.04264 ( 586) hydrogen bonds : angle 4.83835 ( 1677) SS BOND : bond 0.00197 ( 5) SS BOND : angle 0.67266 ( 10) covalent geometry : bond 0.00399 (12871) covalent geometry : angle 0.68859 (17663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 301 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8135 (tt0) cc_final: 0.7842 (tt0) REVERT: A 227 MET cc_start: 0.8442 (tmm) cc_final: 0.8040 (tpp) REVERT: A 234 PHE cc_start: 0.8925 (t80) cc_final: 0.8579 (t80) REVERT: B 23 HIS cc_start: 0.8703 (t-170) cc_final: 0.8452 (t-170) REVERT: B 129 VAL cc_start: 0.9146 (t) cc_final: 0.8912 (m) REVERT: B 287 TYR cc_start: 0.8597 (t80) cc_final: 0.8060 (t80) REVERT: C 125 LYS cc_start: 0.8062 (tmtt) cc_final: 0.7595 (tptp) REVERT: C 127 MET cc_start: 0.8272 (mtt) cc_final: 0.7923 (mtm) REVERT: C 161 HIS cc_start: 0.8315 (p90) cc_final: 0.8036 (p90) REVERT: C 197 TRP cc_start: 0.4823 (t-100) cc_final: 0.4527 (t-100) REVERT: C 227 MET cc_start: 0.8505 (tmm) cc_final: 0.8161 (tpp) REVERT: D 77 TRP cc_start: 0.6666 (p-90) cc_final: 0.4730 (p-90) REVERT: D 123 THR cc_start: 0.8508 (p) cc_final: 0.8254 (p) REVERT: D 220 TYR cc_start: 0.8662 (t80) cc_final: 0.8049 (t80) REVERT: D 227 MET cc_start: 0.8543 (tmm) cc_final: 0.8264 (tpp) REVERT: D 440 TYR cc_start: 0.7594 (t80) cc_final: 0.7328 (t80) REVERT: E 197 TRP cc_start: 0.4946 (t-100) cc_final: 0.4633 (t-100) REVERT: E 222 GLN cc_start: 0.8319 (pm20) cc_final: 0.7942 (mp10) REVERT: E 239 MET cc_start: 0.8200 (ttt) cc_final: 0.7930 (ttt) REVERT: E 291 MET cc_start: 0.8964 (mmm) cc_final: 0.8757 (mmm) REVERT: E 440 TYR cc_start: 0.7552 (t80) cc_final: 0.7186 (t80) outliers start: 24 outliers final: 20 residues processed: 314 average time/residue: 0.1938 time to fit residues: 93.1342 Evaluate side-chains 294 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 274 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 48 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102923 restraints weight = 22581.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106459 restraints weight = 13232.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108940 restraints weight = 9388.360| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12881 Z= 0.183 Angle : 0.690 13.310 17688 Z= 0.335 Chirality : 0.046 0.207 2174 Planarity : 0.003 0.030 2123 Dihedral : 4.319 15.087 1876 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.17 % Allowed : 20.19 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.85 (0.20), residues: 1610 helix: 1.22 (0.21), residues: 530 sheet: -0.18 (0.31), residues: 335 loop : -2.16 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 77 HIS 0.002 0.001 HIS B 161 PHE 0.028 0.002 PHE A 425 TYR 0.020 0.002 TYR D 223 ARG 0.005 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 5) link_NAG-ASN : angle 0.60544 ( 15) hydrogen bonds : bond 0.04211 ( 586) hydrogen bonds : angle 4.82927 ( 1677) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.65232 ( 10) covalent geometry : bond 0.00431 (12871) covalent geometry : angle 0.69051 (17663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8184 (tt0) cc_final: 0.7852 (tt0) REVERT: A 117 LEU cc_start: 0.8660 (tp) cc_final: 0.8437 (tp) REVERT: A 173 GLN cc_start: 0.8158 (pm20) cc_final: 0.7792 (pm20) REVERT: A 227 MET cc_start: 0.8470 (tmm) cc_final: 0.8117 (tpp) REVERT: A 234 PHE cc_start: 0.8906 (t80) cc_final: 0.8615 (t80) REVERT: B 23 HIS cc_start: 0.8701 (t-170) cc_final: 0.8449 (t-170) REVERT: B 129 VAL cc_start: 0.9145 (t) cc_final: 0.8900 (m) REVERT: B 270 ARG cc_start: 0.7436 (mmt-90) cc_final: 0.7114 (mpt-90) REVERT: B 287 TYR cc_start: 0.8653 (t80) cc_final: 0.8200 (t80) REVERT: C 125 LYS cc_start: 0.8128 (tmtt) cc_final: 0.7592 (tptp) REVERT: C 127 MET cc_start: 0.8231 (mtt) cc_final: 0.7871 (mtm) REVERT: C 161 HIS cc_start: 0.8386 (p90) cc_final: 0.8089 (p90) REVERT: C 197 TRP cc_start: 0.4884 (t-100) cc_final: 0.4591 (t-100) REVERT: C 222 GLN cc_start: 0.8178 (pm20) cc_final: 0.7775 (pm20) REVERT: C 223 TYR cc_start: 0.8864 (t80) cc_final: 0.8613 (t80) REVERT: C 227 MET cc_start: 0.8554 (tmm) cc_final: 0.8246 (tpp) REVERT: D 77 TRP cc_start: 0.6728 (p-90) cc_final: 0.5251 (p-90) REVERT: D 125 LYS cc_start: 0.8189 (tttp) cc_final: 0.7453 (tptp) REVERT: D 215 LYS cc_start: 0.8641 (tptp) cc_final: 0.7880 (pttm) REVERT: D 220 TYR cc_start: 0.8663 (t80) cc_final: 0.7964 (t80) REVERT: D 227 MET cc_start: 0.8545 (tmm) cc_final: 0.8295 (tpp) REVERT: D 440 TYR cc_start: 0.7651 (t80) cc_final: 0.7384 (t80) REVERT: E 125 LYS cc_start: 0.8484 (tttp) cc_final: 0.8073 (tptp) REVERT: E 197 TRP cc_start: 0.4932 (t-100) cc_final: 0.4604 (t-100) REVERT: E 222 GLN cc_start: 0.8346 (pm20) cc_final: 0.8131 (mp10) REVERT: E 239 MET cc_start: 0.8217 (ttt) cc_final: 0.7960 (ttt) REVERT: E 291 MET cc_start: 0.8990 (mmm) cc_final: 0.8726 (mmm) REVERT: E 440 TYR cc_start: 0.7558 (t80) cc_final: 0.7186 (t80) outliers start: 40 outliers final: 32 residues processed: 323 average time/residue: 0.1989 time to fit residues: 98.0926 Evaluate side-chains 309 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 277 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104356 restraints weight = 22521.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107907 restraints weight = 13401.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110422 restraints weight = 9536.768| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12881 Z= 0.141 Angle : 0.676 16.405 17688 Z= 0.325 Chirality : 0.045 0.228 2174 Planarity : 0.003 0.026 2123 Dihedral : 4.152 15.784 1876 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.69 % Allowed : 21.93 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.74 (0.20), residues: 1610 helix: 1.29 (0.21), residues: 530 sheet: -0.08 (0.31), residues: 335 loop : -2.11 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 77 HIS 0.003 0.001 HIS A 68 PHE 0.019 0.002 PHE B 425 TYR 0.024 0.001 TYR D 223 ARG 0.003 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 5) link_NAG-ASN : angle 0.39642 ( 15) hydrogen bonds : bond 0.04033 ( 586) hydrogen bonds : angle 4.71219 ( 1677) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.57223 ( 10) covalent geometry : bond 0.00329 (12871) covalent geometry : angle 0.67641 (17663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 303 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8207 (tt0) cc_final: 0.7950 (tt0) REVERT: A 173 GLN cc_start: 0.8130 (pm20) cc_final: 0.7774 (pm20) REVERT: A 227 MET cc_start: 0.8515 (tmm) cc_final: 0.8168 (tpp) REVERT: A 234 PHE cc_start: 0.8908 (t80) cc_final: 0.8655 (t80) REVERT: B 23 HIS cc_start: 0.8683 (t-170) cc_final: 0.8447 (t-170) REVERT: B 129 VAL cc_start: 0.9133 (t) cc_final: 0.8903 (m) REVERT: B 287 TYR cc_start: 0.8643 (t80) cc_final: 0.8260 (t80) REVERT: C 125 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7831 (tmtt) REVERT: C 173 GLN cc_start: 0.8148 (pm20) cc_final: 0.7836 (pm20) REVERT: C 197 TRP cc_start: 0.4825 (t-100) cc_final: 0.4534 (t-100) REVERT: C 222 GLN cc_start: 0.8201 (pm20) cc_final: 0.7846 (mp10) REVERT: C 223 TYR cc_start: 0.8848 (t80) cc_final: 0.8585 (t80) REVERT: C 227 MET cc_start: 0.8568 (tmm) cc_final: 0.8138 (tpp) REVERT: D 77 TRP cc_start: 0.6652 (p-90) cc_final: 0.5245 (p-90) REVERT: D 220 TYR cc_start: 0.8609 (t80) cc_final: 0.7987 (t80) REVERT: D 227 MET cc_start: 0.8536 (tmm) cc_final: 0.8136 (tpp) REVERT: D 440 TYR cc_start: 0.7660 (t80) cc_final: 0.7400 (t80) REVERT: E 125 LYS cc_start: 0.8471 (tttp) cc_final: 0.7945 (tptp) REVERT: E 197 TRP cc_start: 0.4858 (t-100) cc_final: 0.4513 (t-100) REVERT: E 222 GLN cc_start: 0.8393 (pm20) cc_final: 0.8131 (mp10) REVERT: E 239 MET cc_start: 0.8183 (ttt) cc_final: 0.7895 (ttt) REVERT: E 291 MET cc_start: 0.8978 (mmm) cc_final: 0.8627 (mmm) REVERT: E 440 TYR cc_start: 0.7584 (t80) cc_final: 0.7187 (t80) outliers start: 34 outliers final: 27 residues processed: 321 average time/residue: 0.1964 time to fit residues: 96.4036 Evaluate side-chains 305 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 158 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 111 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS E 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104268 restraints weight = 22734.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107870 restraints weight = 13278.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110405 restraints weight = 9413.514| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12881 Z= 0.134 Angle : 0.675 15.536 17688 Z= 0.323 Chirality : 0.045 0.226 2174 Planarity : 0.003 0.027 2123 Dihedral : 4.099 17.576 1876 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.01 % Allowed : 23.36 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.70 (0.20), residues: 1610 helix: 1.30 (0.22), residues: 530 sheet: 0.08 (0.31), residues: 330 loop : -2.11 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 77 HIS 0.002 0.000 HIS D 68 PHE 0.019 0.002 PHE E 425 TYR 0.023 0.001 TYR E 287 ARG 0.005 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 5) link_NAG-ASN : angle 0.39386 ( 15) hydrogen bonds : bond 0.03959 ( 586) hydrogen bonds : angle 4.67178 ( 1677) SS BOND : bond 0.00180 ( 5) SS BOND : angle 0.51830 ( 10) covalent geometry : bond 0.00313 (12871) covalent geometry : angle 0.67533 (17663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8166 (tt0) cc_final: 0.7934 (tt0) REVERT: A 173 GLN cc_start: 0.8111 (pm20) cc_final: 0.7751 (pm20) REVERT: A 227 MET cc_start: 0.8527 (tmm) cc_final: 0.7930 (tpp) REVERT: A 431 LEU cc_start: 0.8778 (pp) cc_final: 0.8577 (tp) REVERT: B 23 HIS cc_start: 0.8670 (t-170) cc_final: 0.8450 (t-170) REVERT: B 129 VAL cc_start: 0.9115 (t) cc_final: 0.8900 (m) REVERT: B 270 ARG cc_start: 0.7351 (mmt-90) cc_final: 0.7077 (mpt-90) REVERT: B 287 TYR cc_start: 0.8574 (t80) cc_final: 0.8304 (t80) REVERT: C 125 LYS cc_start: 0.8147 (tmtt) cc_final: 0.7600 (tptp) REVERT: C 173 GLN cc_start: 0.8174 (pm20) cc_final: 0.7851 (pm20) REVERT: C 197 TRP cc_start: 0.4856 (t-100) cc_final: 0.4567 (t-100) REVERT: C 222 GLN cc_start: 0.8185 (pm20) cc_final: 0.7919 (mp10) REVERT: C 223 TYR cc_start: 0.8869 (t80) cc_final: 0.8652 (t80) REVERT: C 227 MET cc_start: 0.8578 (tmm) cc_final: 0.8163 (tpp) REVERT: D 77 TRP cc_start: 0.6583 (p-90) cc_final: 0.5178 (p-90) REVERT: D 186 GLN cc_start: 0.8212 (pt0) cc_final: 0.8007 (tp40) REVERT: D 215 LYS cc_start: 0.8556 (tptp) cc_final: 0.7866 (pttm) REVERT: D 220 TYR cc_start: 0.8601 (t80) cc_final: 0.7960 (t80) REVERT: D 227 MET cc_start: 0.8542 (tmm) cc_final: 0.8178 (tpp) REVERT: D 291 MET cc_start: 0.8608 (tpp) cc_final: 0.8398 (tpp) REVERT: D 440 TYR cc_start: 0.7621 (t80) cc_final: 0.7336 (t80) REVERT: E 81 ASP cc_start: 0.7162 (p0) cc_final: 0.6660 (t70) REVERT: E 125 LYS cc_start: 0.8425 (tttp) cc_final: 0.7830 (tptp) REVERT: E 197 TRP cc_start: 0.4837 (t-100) cc_final: 0.4498 (t-100) REVERT: E 220 TYR cc_start: 0.8773 (t80) cc_final: 0.8533 (t80) REVERT: E 222 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: E 239 MET cc_start: 0.8169 (ttt) cc_final: 0.7905 (ttt) REVERT: E 289 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8445 (t80) REVERT: E 291 MET cc_start: 0.9019 (mmm) cc_final: 0.8661 (mmm) REVERT: E 440 TYR cc_start: 0.7573 (t80) cc_final: 0.7223 (t80) outliers start: 38 outliers final: 30 residues processed: 324 average time/residue: 0.1943 time to fit residues: 96.3694 Evaluate side-chains 318 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 79 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101546 restraints weight = 22769.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105013 restraints weight = 13396.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107441 restraints weight = 9545.689| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12881 Z= 0.180 Angle : 0.713 15.315 17688 Z= 0.343 Chirality : 0.046 0.227 2174 Planarity : 0.003 0.026 2123 Dihedral : 4.135 16.463 1876 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.80 % Allowed : 23.99 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1610 helix: 1.35 (0.21), residues: 530 sheet: 0.08 (0.31), residues: 330 loop : -2.12 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 77 HIS 0.005 0.001 HIS E 68 PHE 0.018 0.002 PHE A 425 TYR 0.022 0.002 TYR E 287 ARG 0.005 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 5) link_NAG-ASN : angle 0.64336 ( 15) hydrogen bonds : bond 0.04066 ( 586) hydrogen bonds : angle 4.73000 ( 1677) SS BOND : bond 0.00213 ( 5) SS BOND : angle 0.58555 ( 10) covalent geometry : bond 0.00429 (12871) covalent geometry : angle 0.71319 (17663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 296 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8202 (tt0) cc_final: 0.7979 (tt0) REVERT: A 129 VAL cc_start: 0.9198 (t) cc_final: 0.8983 (m) REVERT: A 227 MET cc_start: 0.8511 (tmm) cc_final: 0.7961 (tpp) REVERT: B 23 HIS cc_start: 0.8711 (t-170) cc_final: 0.8498 (t-170) REVERT: B 69 GLU cc_start: 0.7942 (tt0) cc_final: 0.7737 (tt0) REVERT: B 87 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8328 (mmmm) REVERT: B 129 VAL cc_start: 0.9135 (t) cc_final: 0.8909 (m) REVERT: B 227 MET cc_start: 0.8531 (tmm) cc_final: 0.8023 (tmm) REVERT: B 287 TYR cc_start: 0.8650 (t80) cc_final: 0.8242 (t80) REVERT: C 125 LYS cc_start: 0.8282 (tmtt) cc_final: 0.7739 (tptp) REVERT: C 173 GLN cc_start: 0.8183 (pm20) cc_final: 0.7856 (pm20) REVERT: C 197 TRP cc_start: 0.4999 (t-100) cc_final: 0.4713 (t-100) REVERT: C 222 GLN cc_start: 0.8206 (pm20) cc_final: 0.7977 (mp10) REVERT: C 227 MET cc_start: 0.8617 (tmm) cc_final: 0.8255 (tpp) REVERT: D 77 TRP cc_start: 0.6631 (p-90) cc_final: 0.5194 (p-90) REVERT: D 125 LYS cc_start: 0.8337 (tttp) cc_final: 0.7824 (tptp) REVERT: D 215 LYS cc_start: 0.8562 (tptp) cc_final: 0.7896 (pttm) REVERT: D 220 TYR cc_start: 0.8638 (t80) cc_final: 0.7971 (t80) REVERT: D 227 MET cc_start: 0.8556 (tmm) cc_final: 0.8203 (tpp) REVERT: D 440 TYR cc_start: 0.7692 (t80) cc_final: 0.7380 (t80) REVERT: E 74 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7925 (tm-30) REVERT: E 197 TRP cc_start: 0.5007 (t-100) cc_final: 0.4672 (t-100) REVERT: E 222 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: E 227 MET cc_start: 0.8572 (tmm) cc_final: 0.7988 (tpp) REVERT: E 239 MET cc_start: 0.8184 (ttt) cc_final: 0.7886 (ttt) REVERT: E 289 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8541 (t80) REVERT: E 291 MET cc_start: 0.8991 (mmm) cc_final: 0.8591 (mmm) REVERT: E 440 TYR cc_start: 0.7552 (t80) cc_final: 0.7208 (t80) outliers start: 48 outliers final: 39 residues processed: 328 average time/residue: 0.1920 time to fit residues: 96.8216 Evaluate side-chains 322 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 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 = 0.3566 r_free = 0.3566 target = 0.126838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100082 restraints weight = 22946.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103540 restraints weight = 13591.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105892 restraints weight = 9709.250| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12881 Z= 0.180 Angle : 0.711 16.012 17688 Z= 0.344 Chirality : 0.046 0.223 2174 Planarity : 0.003 0.026 2123 Dihedral : 4.182 16.944 1876 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.04 % Allowed : 24.07 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.77 (0.20), residues: 1610 helix: 1.33 (0.21), residues: 530 sheet: -0.02 (0.31), residues: 345 loop : -2.25 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 77 HIS 0.005 0.001 HIS E 68 PHE 0.017 0.002 PHE A 425 TYR 0.027 0.002 TYR E 287 ARG 0.006 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 5) link_NAG-ASN : angle 0.65143 ( 15) hydrogen bonds : bond 0.04050 ( 586) hydrogen bonds : angle 4.80056 ( 1677) SS BOND : bond 0.00215 ( 5) SS BOND : angle 0.57984 ( 10) covalent geometry : bond 0.00431 (12871) covalent geometry : angle 0.71085 (17663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 295 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8190 (tt0) cc_final: 0.7952 (tt0) REVERT: A 129 VAL cc_start: 0.9199 (t) cc_final: 0.8973 (m) REVERT: A 173 GLN cc_start: 0.7983 (pm20) cc_final: 0.7647 (pm20) REVERT: A 227 MET cc_start: 0.8526 (tmm) cc_final: 0.8009 (tpp) REVERT: B 23 HIS cc_start: 0.8730 (t-170) cc_final: 0.8516 (t-170) REVERT: B 129 VAL cc_start: 0.9134 (t) cc_final: 0.8913 (m) REVERT: C 125 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7757 (tptp) REVERT: C 173 GLN cc_start: 0.8234 (pm20) cc_final: 0.7928 (pm20) REVERT: C 197 TRP cc_start: 0.5021 (t-100) cc_final: 0.4724 (t-100) REVERT: C 227 MET cc_start: 0.8657 (tmm) cc_final: 0.8339 (tpp) REVERT: D 77 TRP cc_start: 0.6669 (p-90) cc_final: 0.5172 (p-90) REVERT: D 127 MET cc_start: 0.8483 (mtm) cc_final: 0.8216 (ttm) REVERT: D 215 LYS cc_start: 0.8568 (tptp) cc_final: 0.7911 (pttm) REVERT: D 220 TYR cc_start: 0.8646 (t80) cc_final: 0.8011 (t80) REVERT: D 227 MET cc_start: 0.8567 (tmm) cc_final: 0.8328 (tpp) REVERT: D 429 LEU cc_start: 0.8243 (mt) cc_final: 0.8031 (mt) REVERT: D 440 TYR cc_start: 0.7712 (t80) cc_final: 0.7411 (t80) REVERT: E 197 TRP cc_start: 0.5040 (t-100) cc_final: 0.4667 (t-100) REVERT: E 222 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: E 227 MET cc_start: 0.8655 (tmm) cc_final: 0.8179 (tpp) REVERT: E 239 MET cc_start: 0.8118 (ttt) cc_final: 0.7804 (ttt) REVERT: E 241 PHE cc_start: 0.7712 (m-10) cc_final: 0.7470 (m-80) REVERT: E 289 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8520 (t80) REVERT: E 291 MET cc_start: 0.9024 (mmm) cc_final: 0.8653 (mmm) REVERT: E 440 TYR cc_start: 0.7549 (t80) cc_final: 0.7196 (t80) outliers start: 51 outliers final: 40 residues processed: 328 average time/residue: 0.2003 time to fit residues: 100.5012 Evaluate side-chains 325 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 283 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 36 optimal weight: 0.0050 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 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 = 0.3606 r_free = 0.3606 target = 0.130108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104077 restraints weight = 22453.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107445 restraints weight = 13686.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109840 restraints weight = 9917.578| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12881 Z= 0.137 Angle : 0.731 16.615 17688 Z= 0.349 Chirality : 0.046 0.361 2174 Planarity : 0.003 0.030 2123 Dihedral : 4.138 17.612 1876 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.09 % Allowed : 25.97 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.76 (0.21), residues: 1610 helix: 1.30 (0.22), residues: 530 sheet: -0.05 (0.33), residues: 310 loop : -2.09 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 77 HIS 0.003 0.000 HIS D 68 PHE 0.018 0.002 PHE A 425 TYR 0.025 0.002 TYR E 287 ARG 0.007 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 5) link_NAG-ASN : angle 0.42345 ( 15) hydrogen bonds : bond 0.04000 ( 586) hydrogen bonds : angle 4.76367 ( 1677) SS BOND : bond 0.00166 ( 5) SS BOND : angle 0.49395 ( 10) covalent geometry : bond 0.00319 (12871) covalent geometry : angle 0.73176 (17663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8115 (tt0) cc_final: 0.7908 (tt0) REVERT: A 129 VAL cc_start: 0.9163 (t) cc_final: 0.8958 (m) REVERT: A 173 GLN cc_start: 0.7979 (pm20) cc_final: 0.7671 (pm20) REVERT: A 227 MET cc_start: 0.8516 (tmm) cc_final: 0.7960 (tpp) REVERT: B 23 HIS cc_start: 0.8698 (t-170) cc_final: 0.8487 (t-170) REVERT: B 440 TYR cc_start: 0.7440 (t80) cc_final: 0.7081 (t80) REVERT: C 125 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7765 (tptp) REVERT: C 173 GLN cc_start: 0.8283 (pm20) cc_final: 0.8002 (pm20) REVERT: C 197 TRP cc_start: 0.4884 (t-100) cc_final: 0.4578 (t-100) REVERT: C 227 MET cc_start: 0.8699 (tmm) cc_final: 0.8390 (tpp) REVERT: D 77 TRP cc_start: 0.6565 (p-90) cc_final: 0.5143 (p-90) REVERT: D 215 LYS cc_start: 0.8561 (tptp) cc_final: 0.7932 (pttt) REVERT: D 220 TYR cc_start: 0.8638 (t80) cc_final: 0.8063 (t80) REVERT: D 429 LEU cc_start: 0.8193 (mt) cc_final: 0.7979 (mt) REVERT: D 440 TYR cc_start: 0.7739 (t80) cc_final: 0.7413 (t80) REVERT: E 117 LEU cc_start: 0.8659 (tp) cc_final: 0.8370 (tp) REVERT: E 197 TRP cc_start: 0.4915 (t-100) cc_final: 0.4552 (t-100) REVERT: E 227 MET cc_start: 0.8666 (tmm) cc_final: 0.8204 (tpp) REVERT: E 239 MET cc_start: 0.8141 (ttt) cc_final: 0.7896 (ttt) REVERT: E 241 PHE cc_start: 0.7656 (m-10) cc_final: 0.7405 (m-80) REVERT: E 289 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8512 (t80) REVERT: E 291 MET cc_start: 0.9039 (mmm) cc_final: 0.8710 (mmm) REVERT: E 440 TYR cc_start: 0.7446 (t80) cc_final: 0.7120 (t80) outliers start: 39 outliers final: 30 residues processed: 328 average time/residue: 0.2016 time to fit residues: 101.7026 Evaluate side-chains 314 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 99 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102096 restraints weight = 22475.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105511 restraints weight = 13512.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107926 restraints weight = 9687.941| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12881 Z= 0.160 Angle : 0.751 16.164 17688 Z= 0.360 Chirality : 0.048 0.360 2174 Planarity : 0.004 0.034 2123 Dihedral : 4.156 17.347 1876 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.33 % Allowed : 27.00 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.69 (0.21), residues: 1610 helix: 1.32 (0.22), residues: 525 sheet: 0.19 (0.31), residues: 330 loop : -2.16 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 77 HIS 0.003 0.000 HIS A 68 PHE 0.043 0.002 PHE B 425 TYR 0.022 0.002 TYR A 220 ARG 0.006 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 5) link_NAG-ASN : angle 0.58792 ( 15) hydrogen bonds : bond 0.04067 ( 586) hydrogen bonds : angle 4.86294 ( 1677) SS BOND : bond 0.00180 ( 5) SS BOND : angle 0.51890 ( 10) covalent geometry : bond 0.00381 (12871) covalent geometry : angle 0.75109 (17663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8690 (tmtt) cc_final: 0.8377 (tttm) REVERT: A 173 GLN cc_start: 0.7976 (pm20) cc_final: 0.7665 (pm20) REVERT: A 227 MET cc_start: 0.8513 (tmm) cc_final: 0.7939 (tpp) REVERT: B 23 HIS cc_start: 0.8677 (t-170) cc_final: 0.8470 (t-170) REVERT: B 440 TYR cc_start: 0.7436 (t80) cc_final: 0.7078 (t80) REVERT: C 125 LYS cc_start: 0.8211 (tmtt) cc_final: 0.7727 (tptp) REVERT: C 173 GLN cc_start: 0.8263 (pm20) cc_final: 0.7989 (pm20) REVERT: C 197 TRP cc_start: 0.4957 (t-100) cc_final: 0.4636 (t-100) REVERT: C 227 MET cc_start: 0.8684 (tmm) cc_final: 0.8366 (tpp) REVERT: D 77 TRP cc_start: 0.6627 (p-90) cc_final: 0.5234 (p-90) REVERT: D 127 MET cc_start: 0.8426 (mtm) cc_final: 0.8148 (ttm) REVERT: D 215 LYS cc_start: 0.8594 (tptp) cc_final: 0.7963 (pttt) REVERT: D 220 TYR cc_start: 0.8661 (t80) cc_final: 0.8176 (t80) REVERT: D 429 LEU cc_start: 0.8245 (mt) cc_final: 0.8008 (mt) REVERT: D 440 TYR cc_start: 0.7725 (t80) cc_final: 0.7421 (t80) REVERT: E 117 LEU cc_start: 0.8657 (tp) cc_final: 0.8358 (tp) REVERT: E 197 TRP cc_start: 0.4977 (t-100) cc_final: 0.4607 (t-100) REVERT: E 227 MET cc_start: 0.8691 (tmm) cc_final: 0.8321 (tpp) REVERT: E 239 MET cc_start: 0.8100 (ttt) cc_final: 0.7808 (ttt) REVERT: E 289 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8547 (t80) REVERT: E 291 MET cc_start: 0.9049 (mmm) cc_final: 0.8695 (mmm) REVERT: E 440 TYR cc_start: 0.7426 (t80) cc_final: 0.7111 (t80) outliers start: 42 outliers final: 35 residues processed: 316 average time/residue: 0.1938 time to fit residues: 94.2865 Evaluate side-chains 314 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 0.5980 chunk 58 optimal weight: 0.0270 chunk 84 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 151 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.130390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104132 restraints weight = 22431.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107619 restraints weight = 13452.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110061 restraints weight = 9641.037| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12881 Z= 0.138 Angle : 0.760 16.307 17688 Z= 0.363 Chirality : 0.047 0.341 2174 Planarity : 0.003 0.038 2123 Dihedral : 4.118 17.950 1876 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.85 % Allowed : 27.87 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.79 (0.20), residues: 1610 helix: 1.28 (0.22), residues: 525 sheet: -0.04 (0.33), residues: 310 loop : -2.10 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 77 HIS 0.003 0.001 HIS D 68 PHE 0.036 0.002 PHE B 425 TYR 0.020 0.002 TYR E 112 ARG 0.006 0.000 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 5) link_NAG-ASN : angle 0.41497 ( 15) hydrogen bonds : bond 0.04060 ( 586) hydrogen bonds : angle 4.80614 ( 1677) SS BOND : bond 0.00156 ( 5) SS BOND : angle 0.47871 ( 10) covalent geometry : bond 0.00317 (12871) covalent geometry : angle 0.76005 (17663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4183.33 seconds wall clock time: 73 minutes 27.03 seconds (4407.03 seconds total)