Starting phenix.real_space_refine on Fri Nov 15 23:59:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7f_36039/11_2024/8j7f_36039_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7f_36039/11_2024/8j7f_36039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7f_36039/11_2024/8j7f_36039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7f_36039/11_2024/8j7f_36039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7f_36039/11_2024/8j7f_36039_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7f_36039/11_2024/8j7f_36039_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.101 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 54 5.16 5 C 6665 2.51 5 N 1513 2.21 5 O 1721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9961 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2331 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 281} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2334 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 281} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2340 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 281} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2337 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 281} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' CA': 1, 'CLR': 3, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' CA': 1, 'CLR': 3, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 115 Unusual residues: {' CA': 2, 'CLR': 3, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'CLR': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.62, per 1000 atoms: 0.66 Number of scatterers: 9961 At special positions: 0 Unit cell: (121.68, 121.68, 94.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 54 16.00 P 4 15.00 O 1721 8.00 N 1513 7.00 C 6665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 883.6 milliseconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 4 sheets defined 76.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.933A pdb=" N VAL A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 139 removed outlier: 3.692A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 4.358A pdb=" N GLY A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.519A pdb=" N ILE A 182 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.502A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 237 Proline residue: A 212 - end of helix removed outlier: 4.618A pdb=" N ASN A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 290 through 304 Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.848A pdb=" N ALA A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.932A pdb=" N VAL B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 141 removed outlier: 3.702A pdb=" N TRP B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 removed outlier: 4.358A pdb=" N GLY B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.519A pdb=" N ILE B 182 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 186 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 187 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.502A pdb=" N ARG B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 237 Proline residue: B 212 - end of helix removed outlier: 4.617A pdb=" N ASN B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 264 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 290 through 304 Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.848A pdb=" N ALA B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.932A pdb=" N VAL C 76 " --> pdb=" O HIS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 107 Processing helix chain 'C' and resid 114 through 139 removed outlier: 3.701A pdb=" N TRP C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 172 removed outlier: 4.357A pdb=" N GLY C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.519A pdb=" N ILE C 182 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 184 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG C 186 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 187 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.503A pdb=" N ARG C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 237 Proline residue: C 212 - end of helix removed outlier: 4.618A pdb=" N ASN C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 264 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 290 through 304 Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.848A pdb=" N ALA C 315 " --> pdb=" O VAL C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 337 Processing helix chain 'C' and resid 338 through 357 Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.932A pdb=" N VAL D 76 " --> pdb=" O HIS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 107 Processing helix chain 'D' and resid 114 through 139 removed outlier: 3.701A pdb=" N TRP D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 172 removed outlier: 4.358A pdb=" N GLY D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 191 removed outlier: 3.519A pdb=" N ILE D 182 " --> pdb=" O MET D 179 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN D 184 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG D 186 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 187 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.503A pdb=" N ARG D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 237 Proline residue: D 212 - end of helix removed outlier: 4.618A pdb=" N ASN D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 264 Processing helix chain 'D' and resid 282 through 289 Processing helix chain 'D' and resid 290 through 304 Processing helix chain 'D' and resid 311 through 319 removed outlier: 3.848A pdb=" N ALA D 315 " --> pdb=" O VAL D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 337 Processing helix chain 'D' and resid 339 through 357 Processing helix chain 'E' and resid 3 through 21 Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 248 Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 248 Processing sheet with id=AA3, first strand: chain 'C' and resid 244 through 248 Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 248 648 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1487 1.30 - 1.43: 2955 1.43 - 1.56: 5706 1.56 - 1.68: 10 1.68 - 1.81: 84 Bond restraints: 10242 Sorted by residual: bond pdb=" C21 POV C 403 " pdb=" O21 POV C 403 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C21 POV A 402 " pdb=" O21 POV A 402 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C21 POV B 402 " pdb=" O21 POV B 402 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C21 POV D1101 " pdb=" O21 POV D1101 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C31 POV C 403 " pdb=" O31 POV C 403 " ideal model delta sigma weight residual 1.327 1.450 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 10237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 13581 3.10 - 6.21: 329 6.21 - 9.31: 48 9.31 - 12.41: 10 12.41 - 15.52: 3 Bond angle restraints: 13971 Sorted by residual: angle pdb=" N ILE B 339 " pdb=" CA ILE B 339 " pdb=" C ILE B 339 " ideal model delta sigma weight residual 111.05 124.82 -13.77 1.25e+00 6.40e-01 1.21e+02 angle pdb=" N GLN B 338 " pdb=" CA GLN B 338 " pdb=" C GLN B 338 " ideal model delta sigma weight residual 112.04 127.56 -15.52 1.44e+00 4.82e-01 1.16e+02 angle pdb=" N VAL B 340 " pdb=" CA VAL B 340 " pdb=" C VAL B 340 " ideal model delta sigma weight residual 111.56 119.81 -8.25 8.60e-01 1.35e+00 9.21e+01 angle pdb=" N TYR B 138 " pdb=" CA TYR B 138 " pdb=" C TYR B 138 " ideal model delta sigma weight residual 111.14 100.78 10.36 1.08e+00 8.57e-01 9.20e+01 angle pdb=" C GLN B 338 " pdb=" CA GLN B 338 " pdb=" CB GLN B 338 " ideal model delta sigma weight residual 110.56 97.70 12.86 1.83e+00 2.99e-01 4.94e+01 ... (remaining 13966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 5949 26.04 - 52.08: 416 52.08 - 78.12: 48 78.12 - 104.15: 14 104.15 - 130.19: 2 Dihedral angle restraints: 6429 sinusoidal: 2998 harmonic: 3431 Sorted by residual: dihedral pdb=" CA GLU B 355 " pdb=" C GLU B 355 " pdb=" N GLU B 356 " pdb=" CA GLU B 356 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU A 355 " pdb=" C GLU A 355 " pdb=" N GLU A 356 " pdb=" CA GLU A 356 " ideal model delta harmonic sigma weight residual 180.00 151.97 28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU C 355 " pdb=" C GLU C 355 " pdb=" N GLU C 356 " pdb=" CA GLU C 356 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 6426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1403 0.096 - 0.193: 112 0.193 - 0.289: 26 0.289 - 0.385: 14 0.385 - 0.482: 3 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CA GLU C 305 " pdb=" N GLU C 305 " pdb=" C GLU C 305 " pdb=" CB GLU C 305 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA ARG B 279 " pdb=" N ARG B 279 " pdb=" C ARG B 279 " pdb=" CB ARG B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA CYS B 337 " pdb=" N CYS B 337 " pdb=" C CYS B 337 " pdb=" CB CYS B 337 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 1555 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 338 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLN B 338 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN B 338 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE B 339 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 338 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C GLN C 338 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN C 338 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE C 339 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 338 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C GLN A 338 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN A 338 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 339 " -0.018 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 41 2.43 - 3.05: 6730 3.05 - 3.66: 15075 3.66 - 4.28: 24491 4.28 - 4.90: 39081 Nonbonded interactions: 85418 Sorted by model distance: nonbonded pdb=" O GLN D 338 " pdb=" CG2 ILE D 342 " model vdw 1.812 3.460 nonbonded pdb=" O GLN A 338 " pdb=" CG2 ILE A 342 " model vdw 1.964 3.460 nonbonded pdb=" O GLN C 338 " pdb=" CG2 ILE C 342 " model vdw 1.964 3.460 nonbonded pdb=" NH2 ARG A 279 " pdb=" OE2 GLU A 286 " model vdw 1.992 3.120 nonbonded pdb=" NE2 GLN B 300 " pdb=" OE1 GLU B 305 " model vdw 2.027 3.120 ... (remaining 85413 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 69 through 357 or resid 404)) selection = (chain 'B' and (resid 69 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 357 or resid 404)) selection = (chain 'C' and (resid 69 through 173 or (resid 174 through 175 and (name N or na \ me CA or name C or name O or name CB )) or resid 176 through 357 or resid 404)) selection = (chain 'D' and (resid 69 through 173 or (resid 174 through 175 and (name N or na \ me CA or name C or name O or name CB )) or resid 176 through 357 or resid 1104)) \ } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.000 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 : 0.009 0.125 10242 Z= 0.551 Angle : 1.115 15.518 13971 Z= 0.601 Chirality : 0.070 0.482 1558 Planarity : 0.005 0.033 1668 Dihedral : 16.629 130.192 4237 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 0.40 % Allowed : 15.16 % Favored : 84.44 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 1166 helix: -1.38 (0.15), residues: 806 sheet: -1.33 (0.61), residues: 48 loop : -1.56 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 106 HIS 0.004 0.001 HIS C 237 PHE 0.029 0.002 PHE C 144 TYR 0.025 0.003 TYR A 288 ARG 0.005 0.001 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6971 (ttpt) cc_final: 0.6631 (ttpt) REVERT: B 247 THR cc_start: 0.8216 (m) cc_final: 0.7981 (p) REVERT: B 349 LEU cc_start: 0.7889 (tp) cc_final: 0.7652 (tp) REVERT: C 179 MET cc_start: 0.6358 (mmm) cc_final: 0.5684 (mpm) REVERT: C 225 MET cc_start: 0.8036 (mtp) cc_final: 0.7829 (ttm) REVERT: D 111 ASP cc_start: 0.7359 (m-30) cc_final: 0.6996 (m-30) REVERT: D 189 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7524 (mtp85) REVERT: D 225 MET cc_start: 0.7746 (mtp) cc_final: 0.7537 (ttm) REVERT: D 238 MET cc_start: 0.8607 (mmm) cc_final: 0.8298 (tpt) REVERT: E 10 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5511 (ttm170) outliers start: 4 outliers final: 3 residues processed: 183 average time/residue: 1.1461 time to fit residues: 227.1691 Evaluate side-chains 127 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain E residue 10 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.1980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 343 ASN B 96 ASN D 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10242 Z= 0.213 Angle : 0.635 8.718 13971 Z= 0.323 Chirality : 0.043 0.332 1558 Planarity : 0.004 0.034 1668 Dihedral : 10.927 88.857 2172 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.61 % Allowed : 17.77 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1166 helix: 0.11 (0.18), residues: 802 sheet: -0.48 (0.68), residues: 48 loop : -0.37 (0.42), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 307 HIS 0.003 0.001 HIS C 237 PHE 0.025 0.002 PHE D 144 TYR 0.013 0.002 TYR C 114 ARG 0.006 0.001 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.019 Fit side-chains REVERT: A 132 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5684 (pp20) REVERT: A 195 LYS cc_start: 0.6949 (ttpt) cc_final: 0.6656 (ttpt) REVERT: B 119 ARG cc_start: 0.6555 (mtm110) cc_final: 0.6274 (ttp80) REVERT: B 195 LYS cc_start: 0.6963 (ttpt) cc_final: 0.6718 (ttpt) REVERT: B 353 MET cc_start: 0.6985 (mtp) cc_final: 0.6504 (mtp) REVERT: C 123 PHE cc_start: 0.6962 (t80) cc_final: 0.6716 (t80) REVERT: C 179 MET cc_start: 0.6574 (mmm) cc_final: 0.5756 (mpm) REVERT: C 195 LYS cc_start: 0.7197 (ttpt) cc_final: 0.6796 (ttpt) REVERT: C 353 MET cc_start: 0.7014 (mtp) cc_final: 0.6494 (mtp) REVERT: D 111 ASP cc_start: 0.7415 (m-30) cc_final: 0.7061 (m-30) REVERT: D 119 ARG cc_start: 0.6531 (mtm110) cc_final: 0.6329 (ttp80) REVERT: D 189 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7310 (mtp180) REVERT: D 286 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.6589 (tp30) REVERT: D 353 MET cc_start: 0.6925 (mtp) cc_final: 0.6457 (mtp) REVERT: E 10 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.5787 (ttm170) REVERT: E 13 ARG cc_start: 0.5856 (OUTLIER) cc_final: 0.5366 (mpt-90) outliers start: 26 outliers final: 10 residues processed: 157 average time/residue: 1.2455 time to fit residues: 210.2767 Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 13 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 136 ASN B 136 ASN B 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10242 Z= 0.195 Angle : 0.580 7.885 13971 Z= 0.299 Chirality : 0.042 0.241 1558 Planarity : 0.004 0.026 1668 Dihedral : 9.732 83.150 2168 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.61 % Allowed : 18.47 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1166 helix: 0.74 (0.18), residues: 786 sheet: 0.08 (0.78), residues: 48 loop : -0.75 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 307 HIS 0.003 0.001 HIS C 237 PHE 0.021 0.001 PHE D 144 TYR 0.016 0.002 TYR D 109 ARG 0.006 0.001 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 MET cc_start: 0.6989 (mtp) cc_final: 0.6529 (mtp) REVERT: B 189 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7384 (mtp85) REVERT: B 195 LYS cc_start: 0.6947 (ttpt) cc_final: 0.6704 (ttpt) REVERT: B 353 MET cc_start: 0.6992 (mtp) cc_final: 0.6517 (mtp) REVERT: C 179 MET cc_start: 0.6492 (mmm) cc_final: 0.5844 (mpm) REVERT: C 189 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7437 (mtp85) REVERT: C 195 LYS cc_start: 0.7180 (ttpt) cc_final: 0.6763 (ttpt) REVERT: C 353 MET cc_start: 0.7259 (mtp) cc_final: 0.6858 (mtp) REVERT: D 111 ASP cc_start: 0.7469 (m-30) cc_final: 0.7140 (m-30) REVERT: D 189 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7410 (mtp180) REVERT: D 353 MET cc_start: 0.7205 (mtp) cc_final: 0.6689 (mtp) outliers start: 36 outliers final: 11 residues processed: 165 average time/residue: 1.2891 time to fit residues: 227.8711 Evaluate side-chains 144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 110 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN D 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10242 Z= 0.172 Angle : 0.557 8.803 13971 Z= 0.287 Chirality : 0.040 0.226 1558 Planarity : 0.004 0.028 1668 Dihedral : 9.315 78.571 2164 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.01 % Allowed : 19.18 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1166 helix: 1.13 (0.18), residues: 790 sheet: 0.11 (0.82), residues: 48 loop : 0.18 (0.42), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.002 0.001 HIS E 6 PHE 0.020 0.001 PHE D 144 TYR 0.022 0.002 TYR C 109 ARG 0.006 0.000 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6842 (ttpt) cc_final: 0.6580 (ttpt) REVERT: A 353 MET cc_start: 0.6917 (mtp) cc_final: 0.6397 (mtp) REVERT: B 189 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7354 (mtp85) REVERT: B 195 LYS cc_start: 0.6957 (ttpt) cc_final: 0.6715 (ttpt) REVERT: B 353 MET cc_start: 0.7048 (mtp) cc_final: 0.6676 (mtp) REVERT: C 179 MET cc_start: 0.6349 (mmm) cc_final: 0.5713 (mpm) REVERT: C 195 LYS cc_start: 0.7138 (ttpt) cc_final: 0.6717 (ttpt) REVERT: C 353 MET cc_start: 0.7383 (mtp) cc_final: 0.6926 (mtp) REVERT: D 119 ARG cc_start: 0.6610 (mtm110) cc_final: 0.6357 (ttp80) REVERT: D 189 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7316 (mtp180) REVERT: D 353 MET cc_start: 0.7222 (mtp) cc_final: 0.6649 (mtp) REVERT: E 10 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5910 (ttm170) REVERT: E 13 ARG cc_start: 0.6018 (OUTLIER) cc_final: 0.5127 (mpt-90) outliers start: 30 outliers final: 12 residues processed: 159 average time/residue: 1.1679 time to fit residues: 200.6983 Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 13 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN D 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10242 Z= 0.159 Angle : 0.539 8.842 13971 Z= 0.276 Chirality : 0.040 0.203 1558 Planarity : 0.003 0.034 1668 Dihedral : 9.008 73.779 2162 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.51 % Allowed : 19.28 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1166 helix: 1.30 (0.18), residues: 790 sheet: 0.18 (0.82), residues: 48 loop : 0.29 (0.42), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 307 HIS 0.003 0.001 HIS E 6 PHE 0.018 0.001 PHE D 144 TYR 0.020 0.001 TYR A 109 ARG 0.005 0.000 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6802 (ttpt) cc_final: 0.6527 (ttpt) REVERT: A 353 MET cc_start: 0.7014 (mtp) cc_final: 0.6497 (mtp) REVERT: B 189 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7408 (mtp85) REVERT: B 195 LYS cc_start: 0.6905 (ttpt) cc_final: 0.6664 (ttpt) REVERT: B 353 MET cc_start: 0.7083 (mtp) cc_final: 0.6705 (mtp) REVERT: C 119 ARG cc_start: 0.6738 (ttm-80) cc_final: 0.6415 (ttp80) REVERT: C 195 LYS cc_start: 0.7021 (ttpt) cc_final: 0.6642 (ttpt) REVERT: C 221 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6168 (mtp) REVERT: C 353 MET cc_start: 0.7371 (mtp) cc_final: 0.6995 (mtp) REVERT: D 189 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7310 (mtp180) REVERT: D 353 MET cc_start: 0.7184 (mtp) cc_final: 0.6616 (mtp) outliers start: 25 outliers final: 12 residues processed: 155 average time/residue: 1.1295 time to fit residues: 189.7988 Evaluate side-chains 143 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 152 ASN C 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10242 Z= 0.218 Angle : 0.577 8.524 13971 Z= 0.298 Chirality : 0.042 0.207 1558 Planarity : 0.004 0.037 1668 Dihedral : 9.043 72.983 2162 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.91 % Allowed : 19.08 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1166 helix: 1.15 (0.18), residues: 810 sheet: 0.06 (0.82), residues: 48 loop : -0.32 (0.40), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 307 HIS 0.002 0.001 HIS E 6 PHE 0.017 0.002 PHE A 144 TYR 0.021 0.002 TYR C 109 ARG 0.006 0.001 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6813 (ttpt) cc_final: 0.6519 (ttpt) REVERT: A 353 MET cc_start: 0.7176 (mtp) cc_final: 0.6670 (mtp) REVERT: B 119 ARG cc_start: 0.6497 (mtm110) cc_final: 0.6195 (ttp80) REVERT: B 189 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7373 (mtp85) REVERT: B 195 LYS cc_start: 0.6883 (ttpt) cc_final: 0.6648 (ttpt) REVERT: B 353 MET cc_start: 0.7179 (mtp) cc_final: 0.6826 (mtp) REVERT: C 109 TYR cc_start: 0.6614 (m-80) cc_final: 0.6302 (m-80) REVERT: C 195 LYS cc_start: 0.7005 (ttpt) cc_final: 0.6588 (ttpt) REVERT: C 221 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6137 (mtp) REVERT: C 353 MET cc_start: 0.7345 (mtp) cc_final: 0.6977 (mtp) REVERT: D 119 ARG cc_start: 0.6652 (mtm110) cc_final: 0.6376 (ttp80) REVERT: D 189 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7392 (mtp85) REVERT: D 353 MET cc_start: 0.7142 (mtp) cc_final: 0.6582 (mtp) outliers start: 29 outliers final: 17 residues processed: 150 average time/residue: 1.0967 time to fit residues: 178.4182 Evaluate side-chains 144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 267 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10242 Z= 0.207 Angle : 0.562 8.152 13971 Z= 0.291 Chirality : 0.041 0.202 1558 Planarity : 0.004 0.040 1668 Dihedral : 9.002 71.819 2162 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.61 % Allowed : 19.48 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1166 helix: 1.17 (0.18), residues: 810 sheet: -0.07 (0.81), residues: 48 loop : -0.31 (0.40), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 120 HIS 0.002 0.001 HIS A 237 PHE 0.017 0.001 PHE C 144 TYR 0.026 0.002 TYR B 109 ARG 0.006 0.001 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6785 (ttpt) cc_final: 0.6495 (ttpt) REVERT: A 209 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7603 (mttp) REVERT: A 353 MET cc_start: 0.7151 (mtp) cc_final: 0.6610 (mtp) REVERT: B 175 MET cc_start: 0.5207 (tpt) cc_final: 0.4709 (tpp) REVERT: B 189 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7396 (mtp85) REVERT: B 195 LYS cc_start: 0.6836 (ttpt) cc_final: 0.6606 (ttpt) REVERT: B 353 MET cc_start: 0.7152 (mtp) cc_final: 0.6766 (mtp) REVERT: C 109 TYR cc_start: 0.6765 (m-80) cc_final: 0.6525 (m-80) REVERT: C 195 LYS cc_start: 0.6970 (ttpt) cc_final: 0.6567 (ttpt) REVERT: C 221 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6186 (mtp) REVERT: C 353 MET cc_start: 0.7380 (mtp) cc_final: 0.6902 (mtp) REVERT: D 109 TYR cc_start: 0.6738 (m-80) cc_final: 0.6421 (m-80) REVERT: D 119 ARG cc_start: 0.6637 (mtm110) cc_final: 0.6339 (ttp80) REVERT: D 189 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7365 (mtp85) REVERT: D 353 MET cc_start: 0.7179 (mtp) cc_final: 0.6617 (mtp) outliers start: 26 outliers final: 18 residues processed: 150 average time/residue: 1.0740 time to fit residues: 175.0486 Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 267 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.0270 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 10 optimal weight: 0.0020 chunk 86 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.3046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10242 Z= 0.151 Angle : 0.521 7.844 13971 Z= 0.269 Chirality : 0.039 0.178 1558 Planarity : 0.004 0.042 1668 Dihedral : 8.649 72.092 2162 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.81 % Allowed : 19.88 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1166 helix: 1.25 (0.18), residues: 826 sheet: 0.03 (0.82), residues: 48 loop : 0.71 (0.45), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 120 HIS 0.002 0.001 HIS A 320 PHE 0.018 0.001 PHE C 123 TYR 0.027 0.001 TYR B 109 ARG 0.007 0.001 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6558 (ttpt) cc_final: 0.6292 (ttpt) REVERT: A 353 MET cc_start: 0.7149 (mtp) cc_final: 0.6589 (mtp) REVERT: B 179 MET cc_start: 0.5782 (mmt) cc_final: 0.5433 (tpp) REVERT: B 195 LYS cc_start: 0.6635 (ttpt) cc_final: 0.6415 (ttpt) REVERT: B 209 LYS cc_start: 0.7610 (mtmt) cc_final: 0.7390 (mttp) REVERT: B 353 MET cc_start: 0.7134 (mtp) cc_final: 0.6769 (mtp) REVERT: C 109 TYR cc_start: 0.6708 (m-80) cc_final: 0.6435 (m-80) REVERT: C 119 ARG cc_start: 0.6805 (ttm-80) cc_final: 0.6455 (ttp80) REVERT: C 175 MET cc_start: 0.5093 (tpt) cc_final: 0.4391 (tpp) REVERT: C 195 LYS cc_start: 0.6919 (ttpt) cc_final: 0.6520 (ttpt) REVERT: C 221 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6093 (mtp) REVERT: C 353 MET cc_start: 0.7363 (mtp) cc_final: 0.6829 (mtp) REVERT: D 119 ARG cc_start: 0.6491 (mtm110) cc_final: 0.6220 (ttp80) REVERT: D 189 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7282 (mtp85) REVERT: D 221 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6087 (mtp) REVERT: D 353 MET cc_start: 0.7189 (mtp) cc_final: 0.6583 (mtp) outliers start: 18 outliers final: 11 residues processed: 144 average time/residue: 1.0556 time to fit residues: 165.4238 Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN B 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10242 Z= 0.227 Angle : 0.578 8.041 13971 Z= 0.301 Chirality : 0.042 0.190 1558 Planarity : 0.004 0.042 1668 Dihedral : 8.796 71.607 2162 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.21 % Allowed : 19.78 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1166 helix: 1.34 (0.18), residues: 798 sheet: -0.03 (0.80), residues: 48 loop : 0.34 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 120 HIS 0.002 0.001 HIS B 237 PHE 0.016 0.002 PHE B 123 TYR 0.028 0.002 TYR A 109 ARG 0.006 0.001 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6689 (ttpt) cc_final: 0.6402 (ttpt) REVERT: A 353 MET cc_start: 0.7238 (mtp) cc_final: 0.6748 (mtp) REVERT: B 166 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6661 (mtp) REVERT: B 175 MET cc_start: 0.5215 (tpt) cc_final: 0.4537 (tpp) REVERT: B 179 MET cc_start: 0.5828 (mmt) cc_final: 0.5353 (tpp) REVERT: B 195 LYS cc_start: 0.6629 (ttpt) cc_final: 0.6406 (ttpt) REVERT: B 209 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7516 (mttp) REVERT: B 353 MET cc_start: 0.7178 (mtp) cc_final: 0.6812 (mtp) REVERT: C 195 LYS cc_start: 0.6946 (ttpt) cc_final: 0.6551 (ttpt) REVERT: C 221 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6189 (mtp) REVERT: C 353 MET cc_start: 0.7402 (mtp) cc_final: 0.6906 (mtp) REVERT: D 189 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7326 (mtp85) REVERT: D 221 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6058 (mtp) REVERT: D 353 MET cc_start: 0.7213 (mtp) cc_final: 0.6680 (mtp) outliers start: 22 outliers final: 13 residues processed: 145 average time/residue: 1.0455 time to fit residues: 165.1821 Evaluate side-chains 146 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10242 Z= 0.223 Angle : 0.573 8.026 13971 Z= 0.299 Chirality : 0.042 0.190 1558 Planarity : 0.004 0.042 1668 Dihedral : 8.825 72.123 2162 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.91 % Allowed : 19.88 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1166 helix: 1.24 (0.18), residues: 818 sheet: -0.06 (0.81), residues: 48 loop : -0.24 (0.41), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 120 HIS 0.003 0.001 HIS E 6 PHE 0.018 0.002 PHE B 123 TYR 0.030 0.002 TYR C 109 ARG 0.006 0.001 ARG C 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6709 (ttpt) cc_final: 0.6414 (ttpt) REVERT: A 353 MET cc_start: 0.7283 (mtp) cc_final: 0.6784 (mtp) REVERT: B 119 ARG cc_start: 0.6576 (mtm110) cc_final: 0.6287 (ttp80) REVERT: B 166 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6644 (mtp) REVERT: B 175 MET cc_start: 0.5327 (tpt) cc_final: 0.4720 (tpp) REVERT: B 179 MET cc_start: 0.5945 (mmt) cc_final: 0.5481 (tpp) REVERT: B 195 LYS cc_start: 0.6640 (ttpt) cc_final: 0.6418 (ttpt) REVERT: B 353 MET cc_start: 0.7172 (mtp) cc_final: 0.6786 (mtp) REVERT: C 175 MET cc_start: 0.5118 (tpt) cc_final: 0.4344 (tpp) REVERT: C 179 MET cc_start: 0.5437 (mmt) cc_final: 0.5125 (tpp) REVERT: C 195 LYS cc_start: 0.6925 (ttpt) cc_final: 0.6528 (ttpt) REVERT: C 221 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6155 (mtp) REVERT: C 353 MET cc_start: 0.7400 (mtp) cc_final: 0.6905 (mtp) REVERT: D 119 ARG cc_start: 0.6676 (mtm110) cc_final: 0.6441 (ttp80) REVERT: D 189 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7307 (mtp85) REVERT: D 221 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6037 (mtp) REVERT: D 353 MET cc_start: 0.7220 (mtp) cc_final: 0.6678 (mtp) outliers start: 19 outliers final: 14 residues processed: 141 average time/residue: 1.0756 time to fit residues: 164.9217 Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 267 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 90 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.192151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152018 restraints weight = 9664.941| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.71 r_work: 0.3525 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10242 Z= 0.175 Angle : 0.547 7.796 13971 Z= 0.285 Chirality : 0.040 0.173 1558 Planarity : 0.004 0.043 1668 Dihedral : 8.636 72.647 2162 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.91 % Allowed : 20.58 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1166 helix: 1.20 (0.18), residues: 826 sheet: -0.10 (0.82), residues: 48 loop : 0.65 (0.45), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 120 HIS 0.002 0.001 HIS E 6 PHE 0.017 0.001 PHE B 123 TYR 0.026 0.002 TYR C 109 ARG 0.007 0.001 ARG C 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3748.01 seconds wall clock time: 68 minutes 12.22 seconds (4092.22 seconds total)