Starting phenix.real_space_refine on Fri Jul 19 17:41:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/07_2024/8u4p_41890.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/07_2024/8u4p_41890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/07_2024/8u4p_41890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/07_2024/8u4p_41890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/07_2024/8u4p_41890.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/07_2024/8u4p_41890.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2008 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4508 2.51 5 N 1179 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 97": "OD1" <-> "OD2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 153": "OE1" <-> "OE2" Residue "R TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7006 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1777 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2516 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 345 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2304 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'CLR': 1, 'VH6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.58, per 1000 atoms: 0.65 Number of scatterers: 7006 At special positions: 0 Unit cell: (73.1, 102, 130.9, 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 48 16.00 O 1271 8.00 N 1179 7.00 C 4508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 45.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.662A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.652A pdb=" N LYS A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.501A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.526A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.641A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 34 through 65 Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 73 through 90 Processing helix chain 'R' and resid 90 through 100 removed outlier: 4.186A pdb=" N TRP R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 140 removed outlier: 3.789A pdb=" N VAL R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 167 removed outlier: 3.613A pdb=" N LYS R 149 " --> pdb=" O GLN R 145 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR R 157 " --> pdb=" O GLU R 153 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 192 through 208 removed outlier: 3.682A pdb=" N VAL R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 227 removed outlier: 3.669A pdb=" N LYS R 225 " --> pdb=" O ILE R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 267 removed outlier: 3.863A pdb=" N ALA R 237 " --> pdb=" O GLN R 233 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU R 244 " --> pdb=" O THR R 240 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU R 246 " --> pdb=" O VAL R 242 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS R 251 " --> pdb=" O ALA R 247 " (cutoff:3.500A) Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 273 through 292 removed outlier: 3.670A pdb=" N GLU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.584A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.843A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.822A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.076A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.595A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.676A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.620A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.835A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 175 through 180 removed outlier: 3.597A pdb=" N ASN R 176 " --> pdb=" O ASP R 187 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1062 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: 2.05 Time building geometry restraints manager: 2.95 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: 2220 1.34 - 1.46: 1251 1.46 - 1.57: 3618 1.57 - 1.69: 4 1.69 - 1.81: 65 Bond restraints: 7158 Sorted by residual: bond pdb=" C22 VH6 R 702 " pdb=" N23 VH6 R 702 " ideal model delta sigma weight residual 1.446 1.535 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C24 VH6 R 702 " pdb=" N23 VH6 R 702 " ideal model delta sigma weight residual 1.457 1.527 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C36 VH6 R 702 " pdb=" N23 VH6 R 702 " ideal model delta sigma weight residual 1.455 1.520 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C07 VH6 R 702 " pdb=" N08 VH6 R 702 " ideal model delta sigma weight residual 1.455 1.513 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C15 VH6 R 702 " pdb=" N08 VH6 R 702 " ideal model delta sigma weight residual 1.456 1.513 -0.057 2.00e-02 2.50e+03 8.10e+00 ... (remaining 7153 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.65: 89 105.65 - 112.74: 3868 112.74 - 119.84: 2335 119.84 - 126.93: 3330 126.93 - 134.03: 85 Bond angle restraints: 9707 Sorted by residual: angle pdb=" C22 CLR R 701 " pdb=" C23 CLR R 701 " pdb=" C24 CLR R 701 " ideal model delta sigma weight residual 111.95 104.11 7.84 3.00e+00 1.11e-01 6.84e+00 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.45e+00 angle pdb=" C24 VH6 R 702 " pdb=" N23 VH6 R 702 " pdb=" C36 VH6 R 702 " ideal model delta sigma weight residual 115.20 107.60 7.60 3.00e+00 1.11e-01 6.42e+00 angle pdb=" N LEU R 91 " pdb=" CA LEU R 91 " pdb=" C LEU R 91 " ideal model delta sigma weight residual 109.81 115.19 -5.38 2.21e+00 2.05e-01 5.94e+00 angle pdb=" C GLY R 159 " pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 122.35 119.56 2.79 1.18e+00 7.18e-01 5.57e+00 ... (remaining 9702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3860 17.81 - 35.61: 358 35.61 - 53.42: 64 53.42 - 71.23: 5 71.23 - 89.03: 9 Dihedral angle restraints: 4296 sinusoidal: 1690 harmonic: 2606 Sorted by residual: dihedral pdb=" CB GLU B 260 " pdb=" CG GLU B 260 " pdb=" CD GLU B 260 " pdb=" OE1 GLU B 260 " ideal model delta sinusoidal sigma weight residual 0.00 89.03 -89.03 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 276 " pdb=" CG GLU A 276 " pdb=" CD GLU A 276 " pdb=" OE1 GLU A 276 " ideal model delta sinusoidal sigma weight residual 0.00 87.27 -87.27 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CG ARG B 22 " pdb=" CD ARG B 22 " pdb=" NE ARG B 22 " pdb=" CZ ARG B 22 " ideal model delta sinusoidal sigma weight residual -180.00 -136.41 -43.59 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 4293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1016 0.071 - 0.142: 99 0.142 - 0.212: 0 0.212 - 0.283: 1 0.283 - 0.354: 3 Chirality restraints: 1119 Sorted by residual: chirality pdb=" C17 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C16 CLR R 701 " pdb=" C20 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C20 CLR R 701 " pdb=" C17 CLR R 701 " pdb=" C21 CLR R 701 " pdb=" C22 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.59 2.90 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -3.23 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1116 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 152 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C ALA R 152 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA R 152 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU R 153 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 298 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO R 299 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 299 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 299 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 158 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" C VAL R 158 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL R 158 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY R 159 " 0.008 2.00e-02 2.50e+03 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1206 2.77 - 3.30: 6419 3.30 - 3.84: 10965 3.84 - 4.37: 12820 4.37 - 4.90: 23460 Nonbonded interactions: 54870 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.240 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.245 2.440 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.281 2.440 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.313 2.520 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.315 2.520 ... (remaining 54865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 7158 Z= 0.238 Angle : 0.530 7.844 9707 Z= 0.265 Chirality : 0.044 0.354 1119 Planarity : 0.003 0.036 1208 Dihedral : 14.369 89.035 2603 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.52 (0.29), residues: 882 helix: 1.74 (0.28), residues: 381 sheet: -0.17 (0.38), residues: 180 loop : -1.02 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 PHE 0.012 0.001 PHE A 189 TYR 0.008 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.802 Fit side-chains REVERT: A 53 MET cc_start: 0.3392 (ttt) cc_final: 0.3191 (ttp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2198 time to fit residues: 27.0490 Evaluate side-chains 76 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7158 Z= 0.181 Angle : 0.477 5.971 9707 Z= 0.257 Chirality : 0.040 0.134 1119 Planarity : 0.003 0.035 1208 Dihedral : 4.707 30.144 1057 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.21 % Allowed : 6.07 % Favored : 92.71 % 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: 0.86 (0.29), residues: 882 helix: 2.04 (0.28), residues: 381 sheet: -0.17 (0.37), residues: 186 loop : -0.75 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 PHE 0.014 0.001 PHE B 199 TYR 0.008 0.001 TYR R 116 ARG 0.003 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.815 Fit side-chains REVERT: A 10 LYS cc_start: 0.7611 (tptt) cc_final: 0.7272 (tppt) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 0.2353 time to fit residues: 26.3260 Evaluate side-chains 80 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7158 Z= 0.141 Angle : 0.440 5.763 9707 Z= 0.238 Chirality : 0.039 0.130 1119 Planarity : 0.003 0.036 1208 Dihedral : 4.458 29.777 1057 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.75 % Allowed : 7.02 % Favored : 91.23 % 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: 1.05 (0.29), residues: 882 helix: 2.22 (0.28), residues: 383 sheet: -0.09 (0.38), residues: 180 loop : -0.69 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.702 Fit side-chains REVERT: A 10 LYS cc_start: 0.7595 (tptt) cc_final: 0.7253 (tppt) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.2417 time to fit residues: 27.5244 Evaluate side-chains 80 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7158 Z= 0.194 Angle : 0.465 5.855 9707 Z= 0.250 Chirality : 0.041 0.155 1119 Planarity : 0.003 0.035 1208 Dihedral : 4.565 27.968 1057 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.02 % Allowed : 8.37 % Favored : 89.61 % 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 (0.29), residues: 882 helix: 2.24 (0.28), residues: 383 sheet: -0.14 (0.38), residues: 180 loop : -0.73 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS R 79 PHE 0.015 0.001 PHE A 189 TYR 0.008 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.776 Fit side-chains REVERT: A 10 LYS cc_start: 0.7623 (tptt) cc_final: 0.7257 (tppt) REVERT: A 53 MET cc_start: 0.3482 (ttt) cc_final: 0.3175 (ttp) outliers start: 15 outliers final: 12 residues processed: 87 average time/residue: 0.2277 time to fit residues: 25.8528 Evaluate side-chains 84 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.0070 chunk 35 optimal weight: 0.0870 chunk 72 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7158 Z= 0.103 Angle : 0.417 5.672 9707 Z= 0.226 Chirality : 0.039 0.141 1119 Planarity : 0.003 0.035 1208 Dihedral : 4.198 28.007 1057 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.48 % Allowed : 10.39 % Favored : 88.12 % 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: 1.28 (0.29), residues: 882 helix: 2.45 (0.28), residues: 383 sheet: 0.08 (0.39), residues: 177 loop : -0.66 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS R 79 PHE 0.011 0.001 PHE A 189 TYR 0.006 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.823 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.2297 time to fit residues: 27.4210 Evaluate side-chains 83 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7158 Z= 0.152 Angle : 0.438 5.636 9707 Z= 0.236 Chirality : 0.040 0.131 1119 Planarity : 0.003 0.038 1208 Dihedral : 4.246 26.665 1057 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.02 % Allowed : 10.39 % Favored : 87.58 % 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: 1.28 (0.29), residues: 882 helix: 2.49 (0.28), residues: 383 sheet: 0.01 (0.39), residues: 178 loop : -0.67 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR B 59 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.780 Fit side-chains REVERT: A 10 LYS cc_start: 0.7594 (tptt) cc_final: 0.7247 (tppt) REVERT: B 154 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8471 (t0) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.2520 time to fit residues: 28.1340 Evaluate side-chains 87 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7158 Z= 0.144 Angle : 0.438 5.703 9707 Z= 0.235 Chirality : 0.039 0.130 1119 Planarity : 0.003 0.037 1208 Dihedral : 4.245 26.641 1057 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.43 % Allowed : 10.80 % Favored : 86.77 % 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: 1.28 (0.29), residues: 882 helix: 2.50 (0.28), residues: 383 sheet: -0.02 (0.38), residues: 178 loop : -0.67 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.772 Fit side-chains REVERT: A 10 LYS cc_start: 0.7597 (tptt) cc_final: 0.7243 (tppt) REVERT: B 154 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8457 (t0) outliers start: 18 outliers final: 16 residues processed: 89 average time/residue: 0.2434 time to fit residues: 27.8182 Evaluate side-chains 89 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 0.0170 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7158 Z= 0.134 Angle : 0.431 5.748 9707 Z= 0.232 Chirality : 0.039 0.130 1119 Planarity : 0.003 0.037 1208 Dihedral : 4.194 26.105 1057 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.43 % Allowed : 10.93 % Favored : 86.64 % 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: 1.32 (0.29), residues: 882 helix: 2.53 (0.28), residues: 383 sheet: -0.00 (0.38), residues: 178 loop : -0.66 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR B 59 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.743 Fit side-chains REVERT: A 10 LYS cc_start: 0.7587 (tptt) cc_final: 0.7233 (tppt) REVERT: B 154 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8465 (t0) outliers start: 18 outliers final: 16 residues processed: 88 average time/residue: 0.2267 time to fit residues: 25.8911 Evaluate side-chains 88 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.0020 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.0270 chunk 71 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 0.0370 overall best weight: 0.2524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7158 Z= 0.104 Angle : 0.415 5.530 9707 Z= 0.223 Chirality : 0.039 0.140 1119 Planarity : 0.003 0.036 1208 Dihedral : 3.999 25.123 1057 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.89 % Allowed : 11.88 % Favored : 86.23 % 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: 1.38 (0.29), residues: 882 helix: 2.58 (0.28), residues: 384 sheet: 0.08 (0.38), residues: 177 loop : -0.65 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS R 79 PHE 0.011 0.001 PHE A 189 TYR 0.006 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.779 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 85 average time/residue: 0.2379 time to fit residues: 26.2095 Evaluate side-chains 85 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7158 Z= 0.165 Angle : 0.449 5.623 9707 Z= 0.241 Chirality : 0.040 0.132 1119 Planarity : 0.003 0.037 1208 Dihedral : 4.206 24.797 1057 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.02 % Allowed : 11.61 % Favored : 86.37 % 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: 1.31 (0.29), residues: 882 helix: 2.54 (0.28), residues: 383 sheet: -0.08 (0.38), residues: 178 loop : -0.62 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 PHE 0.014 0.001 PHE A 189 TYR 0.008 0.001 TYR B 59 ARG 0.004 0.000 ARG R 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.720 Fit side-chains REVERT: A 10 LYS cc_start: 0.7607 (tptt) cc_final: 0.7243 (tppt) outliers start: 15 outliers final: 15 residues processed: 84 average time/residue: 0.2298 time to fit residues: 25.0569 Evaluate side-chains 86 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.0170 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** 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 = 0.3667 r_free = 0.3667 target = 0.149771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109583 restraints weight = 7732.491| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.38 r_work: 0.2894 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7158 Z= 0.141 Angle : 0.436 5.690 9707 Z= 0.234 Chirality : 0.039 0.135 1119 Planarity : 0.003 0.036 1208 Dihedral : 4.174 25.119 1057 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.89 % Allowed : 11.61 % Favored : 86.50 % 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: 1.32 (0.29), residues: 882 helix: 2.54 (0.28), residues: 383 sheet: -0.06 (0.38), residues: 179 loop : -0.62 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.00 seconds wall clock time: 33 minutes 50.79 seconds (2030.79 seconds total)