Starting phenix.real_space_refine on Thu Mar 14 22:54:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cad_30327/03_2024/7cad_30327.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cad_30327/03_2024/7cad_30327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cad_30327/03_2024/7cad_30327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cad_30327/03_2024/7cad_30327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cad_30327/03_2024/7cad_30327.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cad_30327/03_2024/7cad_30327.pdb" } resolution = 3.41 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 6464 2.51 5 N 1684 2.21 5 O 1845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 21": "NH1" <-> "NH2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ASP 344": "OD1" <-> "OD2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B ARG 266": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2913 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2917 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2131 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2065 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 256} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 5.73, per 1000 atoms: 0.57 Number of scatterers: 10026 At special positions: 0 Unit cell: (80.36, 93.48, 139.4, 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 33 16.00 O 1845 8.00 N 1684 7.00 C 6464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.85 Conformation dependent library (CDL) restraints added in 1.9 seconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2442 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 50.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 126 removed outlier: 4.125A pdb=" N ALA C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.914A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 172 through 189 removed outlier: 4.120A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.739A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 266 through 276 removed outlier: 3.641A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.716A pdb=" N ARG C 304 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 305' Processing helix chain 'C' and resid 335 through 343 removed outlier: 3.523A pdb=" N ALA C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 96 through 108 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 140 through 154 Processing helix chain 'D' and resid 173 through 189 removed outlier: 3.883A pdb=" N ASP D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.806A pdb=" N ALA D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 266 through 275 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.691A pdb=" N ALA D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'A' and resid 18 through 51 Proline residue: A 30 - end of helix removed outlier: 3.895A pdb=" N ALA A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 78 through 110 removed outlier: 3.784A pdb=" N ALA A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.960A pdb=" N VAL A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.693A pdb=" N TYR A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 190 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 193 through 204 removed outlier: 3.730A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.707A pdb=" N LEU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 235 removed outlier: 3.816A pdb=" N ILE A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 267 through 292 Processing helix chain 'B' and resid 7 through 37 removed outlier: 3.918A pdb=" N VAL B 16 " --> pdb=" O TRP B 12 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN B 17 " --> pdb=" O TRP B 13 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Proline residue: B 27 - end of helix removed outlier: 4.023A pdb=" N ILE B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 66 through 95 removed outlier: 3.567A pdb=" N SER B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.957A pdb=" N LEU B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 132 removed outlier: 4.033A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 3.876A pdb=" N ASN B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.526A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 191 through 207 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 240 through 272 removed outlier: 3.910A pdb=" N SER B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Proline residue: B 255 - end of helix removed outlier: 6.832A pdb=" N ARG B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 5.492A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 82 through 85 removed outlier: 5.909A pdb=" N ALA C 83 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP C 163 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 85 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N VAL C 195 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N MET C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 209 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE C 220 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 211 " --> pdb=" O GLN C 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AA4, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AA5, first strand: chain 'C' and resid 291 through 293 removed outlier: 3.712A pdb=" N PHE C 308 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 315 through 317 removed outlier: 3.877A pdb=" N GLU C 316 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 31 removed outlier: 5.038A pdb=" N LYS D 25 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS D 11 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET D 29 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP D 7 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE D 31 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL D 5 " --> pdb=" O ILE D 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 162 through 163 removed outlier: 7.456A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 245 through 246 Processing sheet with id=AB1, first strand: chain 'D' and resid 250 through 251 removed outlier: 3.519A pdb=" N THR D 250 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 256 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 263 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.693A pdb=" N ILE D 368 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 315 through 317 removed outlier: 3.759A pdb=" N GLU D 316 " --> pdb=" O TYR D 323 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1338 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: 2.62 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1646 1.31 - 1.44: 2555 1.44 - 1.56: 5952 1.56 - 1.68: 0 1.68 - 1.81: 64 Bond restraints: 10217 Sorted by residual: bond pdb=" C LEU C 386 " pdb=" O LEU C 386 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.21e-02 6.83e+03 1.25e+01 bond pdb=" N ASP C 344 " pdb=" CA ASP C 344 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.37e+00 bond pdb=" N ASP D 344 " pdb=" CA ASP D 344 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.91e+00 bond pdb=" N THR A 177 " pdb=" CA THR A 177 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.33e-02 5.65e+03 8.02e+00 bond pdb=" N SER B 235 " pdb=" CA SER B 235 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.25e-02 6.40e+03 7.73e+00 ... (remaining 10212 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.39: 231 105.39 - 112.54: 5376 112.54 - 119.70: 3331 119.70 - 126.85: 4850 126.85 - 134.01: 121 Bond angle restraints: 13909 Sorted by residual: angle pdb=" N GLU B 239 " pdb=" CA GLU B 239 " pdb=" C GLU B 239 " ideal model delta sigma weight residual 113.16 104.58 8.58 1.24e+00 6.50e-01 4.79e+01 angle pdb=" N VAL C 254 " pdb=" CA VAL C 254 " pdb=" C VAL C 254 " ideal model delta sigma weight residual 113.20 107.80 5.40 9.60e-01 1.09e+00 3.16e+01 angle pdb=" N VAL B 42 " pdb=" CA VAL B 42 " pdb=" C VAL B 42 " ideal model delta sigma weight residual 112.98 108.06 4.92 1.25e+00 6.40e-01 1.55e+01 angle pdb=" N VAL C 235 " pdb=" CA VAL C 235 " pdb=" C VAL C 235 " ideal model delta sigma weight residual 112.98 108.21 4.77 1.25e+00 6.40e-01 1.46e+01 angle pdb=" CA GLU B 239 " pdb=" C GLU B 239 " pdb=" N GLU B 240 " ideal model delta sigma weight residual 118.32 113.21 5.11 1.35e+00 5.49e-01 1.43e+01 ... (remaining 13904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5553 17.30 - 34.60: 476 34.60 - 51.89: 71 51.89 - 69.19: 13 69.19 - 86.49: 5 Dihedral angle restraints: 6118 sinusoidal: 2332 harmonic: 3786 Sorted by residual: dihedral pdb=" CA GLY D 63 " pdb=" C GLY D 63 " pdb=" N GLU D 64 " pdb=" CA GLU D 64 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA TRP B 138 " pdb=" C TRP B 138 " pdb=" N PRO B 139 " pdb=" CA PRO B 139 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA SER D 62 " pdb=" C SER D 62 " pdb=" N GLY D 63 " pdb=" CA GLY D 63 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 6115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1182 0.046 - 0.091: 373 0.091 - 0.137: 111 0.137 - 0.182: 6 0.182 - 0.228: 3 Chirality restraints: 1675 Sorted by residual: chirality pdb=" CB ILE C 379 " pdb=" CA ILE C 379 " pdb=" CG1 ILE C 379 " pdb=" CG2 ILE C 379 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA GLU B 239 " pdb=" N GLU B 239 " pdb=" C GLU B 239 " pdb=" CB GLU B 239 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASP D 344 " pdb=" N ASP D 344 " pdb=" C ASP D 344 " pdb=" CB ASP D 344 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1672 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 386 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C LEU D 386 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU D 386 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN D 387 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 211 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C LEU A 211 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU A 211 " -0.013 2.00e-02 2.50e+03 pdb=" N THR A 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 222 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO D 223 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " 0.026 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 819 2.74 - 3.28: 10403 3.28 - 3.82: 15566 3.82 - 4.36: 18566 4.36 - 4.90: 33159 Nonbonded interactions: 78513 Sorted by model distance: nonbonded pdb=" O ALA D 90 " pdb=" NH2 ARG D 151 " model vdw 2.196 2.520 nonbonded pdb=" O ALA A 46 " pdb=" OG SER A 272 " model vdw 2.200 2.440 nonbonded pdb=" OG SER D 88 " pdb=" OD2 ASP A 195 " model vdw 2.203 2.440 nonbonded pdb=" OG SER D 140 " pdb=" OE1 GLN D 143 " model vdw 2.217 2.440 nonbonded pdb=" O ALA A 68 " pdb=" OG1 THR A 72 " model vdw 2.275 2.440 ... (remaining 78508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 2 through 111 or (resid 112 through 113 and (name N or nam \ e CA or name C or name O or name CB )) or resid 114 through 391)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.300 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.080 Find NCS groups from input model: 0.420 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 0.043 10217 Z= 0.256 Angle : 0.721 9.590 13909 Z= 0.405 Chirality : 0.047 0.228 1675 Planarity : 0.005 0.047 1764 Dihedral : 13.110 86.489 3676 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.58 % Favored : 92.27 % Rotamer: Outliers : 0.57 % Allowed : 6.17 % Favored : 93.26 % 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: -4.35 (0.19), residues: 1306 helix: -1.71 (0.18), residues: 620 sheet: -4.06 (0.44), residues: 86 loop : -4.09 (0.18), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 175 HIS 0.003 0.001 HIS C 268 PHE 0.013 0.001 PHE B 263 TYR 0.015 0.001 TYR D 194 ARG 0.003 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 178 time to evaluate : 1.165 Fit side-chains REVERT: D 127 ASP cc_start: 0.6754 (p0) cc_final: 0.6099 (p0) REVERT: D 146 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.7834 (mtm-85) REVERT: D 177 MET cc_start: 0.8287 (mmm) cc_final: 0.7934 (mmm) REVERT: A 48 TRP cc_start: 0.8223 (t60) cc_final: 0.7621 (t60) REVERT: A 250 ASP cc_start: 0.7611 (t70) cc_final: 0.7147 (t0) REVERT: A 287 PHE cc_start: 0.7000 (t80) cc_final: 0.6647 (t80) REVERT: A 291 LYS cc_start: 0.7674 (tttp) cc_final: 0.7205 (tttt) REVERT: B 146 ILE cc_start: 0.8354 (pt) cc_final: 0.8050 (mt) outliers start: 6 outliers final: 1 residues processed: 182 average time/residue: 0.2612 time to fit residues: 64.0347 Evaluate side-chains 140 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 386 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 168 ASN D 197 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN B 56 ASN B 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 10217 Z= 0.378 Angle : 0.731 12.527 13909 Z= 0.358 Chirality : 0.048 0.211 1675 Planarity : 0.005 0.041 1764 Dihedral : 4.949 43.178 1417 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 1.90 % Allowed : 13.01 % Favored : 85.09 % 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: -3.37 (0.21), residues: 1306 helix: -0.68 (0.20), residues: 641 sheet: -3.86 (0.37), residues: 118 loop : -3.84 (0.20), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.006 0.001 HIS D 197 PHE 0.015 0.001 PHE C 36 TYR 0.020 0.002 TYR D 194 ARG 0.004 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.127 Fit side-chains REVERT: D 127 ASP cc_start: 0.6920 (p0) cc_final: 0.6233 (p0) REVERT: D 146 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.7840 (mtm-85) REVERT: D 177 MET cc_start: 0.8381 (mmm) cc_final: 0.7973 (mmm) REVERT: A 48 TRP cc_start: 0.8246 (t60) cc_final: 0.7679 (t60) REVERT: A 78 TYR cc_start: 0.6515 (t80) cc_final: 0.6026 (t80) REVERT: A 250 ASP cc_start: 0.7639 (t70) cc_final: 0.7217 (t0) REVERT: A 287 PHE cc_start: 0.7003 (t80) cc_final: 0.6648 (t80) REVERT: A 291 LYS cc_start: 0.7726 (tttp) cc_final: 0.7191 (tttt) outliers start: 20 outliers final: 16 residues processed: 156 average time/residue: 0.2453 time to fit residues: 52.2855 Evaluate side-chains 155 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10217 Z= 0.288 Angle : 0.668 9.925 13909 Z= 0.327 Chirality : 0.045 0.191 1675 Planarity : 0.005 0.043 1764 Dihedral : 4.718 27.030 1417 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.61 % Allowed : 14.34 % Favored : 82.05 % 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: -2.80 (0.22), residues: 1306 helix: -0.21 (0.21), residues: 641 sheet: -3.74 (0.39), residues: 106 loop : -3.54 (0.21), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 80 HIS 0.012 0.001 HIS D 197 PHE 0.011 0.001 PHE D 326 TYR 0.015 0.001 TYR D 194 ARG 0.004 0.000 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 1.005 Fit side-chains REVERT: D 127 ASP cc_start: 0.6935 (p0) cc_final: 0.6238 (p0) REVERT: D 146 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.7787 (mtm-85) REVERT: D 177 MET cc_start: 0.8366 (mmm) cc_final: 0.7951 (mmm) REVERT: A 78 TYR cc_start: 0.6470 (t80) cc_final: 0.6008 (t80) REVERT: A 287 PHE cc_start: 0.6992 (t80) cc_final: 0.6643 (t80) REVERT: A 291 LYS cc_start: 0.7713 (tttp) cc_final: 0.7201 (tttt) outliers start: 38 outliers final: 31 residues processed: 165 average time/residue: 0.2292 time to fit residues: 52.6651 Evaluate side-chains 161 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10217 Z= 0.207 Angle : 0.625 9.557 13909 Z= 0.304 Chirality : 0.044 0.189 1675 Planarity : 0.004 0.043 1764 Dihedral : 4.429 25.335 1415 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.99 % Allowed : 16.33 % Favored : 79.68 % 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: -2.43 (0.22), residues: 1306 helix: 0.15 (0.21), residues: 634 sheet: -3.72 (0.39), residues: 106 loop : -3.36 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 141 HIS 0.002 0.001 HIS C 268 PHE 0.012 0.001 PHE B 263 TYR 0.013 0.001 TYR B 155 ARG 0.005 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 1.078 Fit side-chains REVERT: D 127 ASP cc_start: 0.6832 (p0) cc_final: 0.6108 (p0) REVERT: D 146 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.7772 (mtm-85) REVERT: D 177 MET cc_start: 0.8323 (mmm) cc_final: 0.7934 (mmm) REVERT: A 78 TYR cc_start: 0.6415 (t80) cc_final: 0.5929 (t80) REVERT: A 141 TRP cc_start: 0.7884 (m100) cc_final: 0.7661 (m100) REVERT: A 287 PHE cc_start: 0.6993 (t80) cc_final: 0.6654 (t80) REVERT: A 291 LYS cc_start: 0.7683 (tttp) cc_final: 0.7161 (tttt) outliers start: 42 outliers final: 29 residues processed: 161 average time/residue: 0.2247 time to fit residues: 50.5017 Evaluate side-chains 153 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 86 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10217 Z= 0.218 Angle : 0.622 9.317 13909 Z= 0.300 Chirality : 0.044 0.189 1675 Planarity : 0.004 0.045 1764 Dihedral : 4.320 24.464 1415 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.99 % Allowed : 16.52 % Favored : 79.49 % 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: -2.22 (0.23), residues: 1306 helix: 0.33 (0.21), residues: 634 sheet: -3.60 (0.40), residues: 106 loop : -3.26 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 175 HIS 0.002 0.001 HIS D 197 PHE 0.014 0.001 PHE B 263 TYR 0.015 0.001 TYR D 194 ARG 0.004 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.160 Fit side-chains REVERT: D 100 ASN cc_start: 0.8414 (m-40) cc_final: 0.8092 (t0) REVERT: D 127 ASP cc_start: 0.6782 (p0) cc_final: 0.6061 (p0) REVERT: D 146 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.7835 (mtm-85) REVERT: D 177 MET cc_start: 0.8307 (mmm) cc_final: 0.7905 (mmm) REVERT: A 287 PHE cc_start: 0.6985 (t80) cc_final: 0.6654 (t80) REVERT: A 291 LYS cc_start: 0.7707 (tttp) cc_final: 0.7211 (tttt) outliers start: 42 outliers final: 37 residues processed: 162 average time/residue: 0.2178 time to fit residues: 49.7700 Evaluate side-chains 165 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 0.0020 chunk 31 optimal weight: 0.2980 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10217 Z= 0.140 Angle : 0.578 9.528 13909 Z= 0.279 Chirality : 0.042 0.179 1675 Planarity : 0.004 0.047 1764 Dihedral : 4.050 21.948 1415 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.70 % Allowed : 17.00 % Favored : 79.30 % 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: -1.84 (0.23), residues: 1306 helix: 0.63 (0.22), residues: 639 sheet: -3.53 (0.39), residues: 106 loop : -3.07 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 175 HIS 0.002 0.001 HIS D 268 PHE 0.013 0.001 PHE B 263 TYR 0.014 0.001 TYR D 194 ARG 0.008 0.000 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.135 Fit side-chains REVERT: D 100 ASN cc_start: 0.8330 (m-40) cc_final: 0.8055 (t0) REVERT: D 177 MET cc_start: 0.8153 (mmm) cc_final: 0.7850 (mmm) REVERT: A 250 ASP cc_start: 0.7080 (t0) cc_final: 0.6770 (t0) REVERT: A 287 PHE cc_start: 0.6981 (t80) cc_final: 0.6649 (t80) REVERT: A 291 LYS cc_start: 0.7627 (tttp) cc_final: 0.7107 (pttt) REVERT: B 72 ASN cc_start: 0.8045 (m110) cc_final: 0.7811 (m-40) outliers start: 39 outliers final: 23 residues processed: 173 average time/residue: 0.2228 time to fit residues: 53.9760 Evaluate side-chains 159 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.0000 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10217 Z= 0.238 Angle : 0.619 8.833 13909 Z= 0.297 Chirality : 0.044 0.165 1675 Planarity : 0.004 0.045 1764 Dihedral : 4.101 22.705 1415 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.80 % Allowed : 17.38 % Favored : 78.82 % 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: -1.84 (0.23), residues: 1306 helix: 0.66 (0.22), residues: 639 sheet: -3.41 (0.38), residues: 140 loop : -3.06 (0.23), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 141 HIS 0.003 0.001 HIS D 268 PHE 0.011 0.001 PHE B 263 TYR 0.015 0.001 TYR D 194 ARG 0.009 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.156 Fit side-chains REVERT: D 100 ASN cc_start: 0.8389 (m-40) cc_final: 0.8111 (t0) REVERT: A 287 PHE cc_start: 0.6982 (t80) cc_final: 0.6644 (t80) REVERT: A 291 LYS cc_start: 0.7623 (tttp) cc_final: 0.7178 (pttt) outliers start: 40 outliers final: 35 residues processed: 164 average time/residue: 0.2187 time to fit residues: 50.7840 Evaluate side-chains 167 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10217 Z= 0.236 Angle : 0.625 10.870 13909 Z= 0.299 Chirality : 0.044 0.207 1675 Planarity : 0.004 0.057 1764 Dihedral : 4.131 23.571 1415 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.37 % Allowed : 17.28 % Favored : 78.35 % 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: -1.71 (0.23), residues: 1306 helix: 0.70 (0.22), residues: 639 sheet: -3.45 (0.41), residues: 106 loop : -2.94 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 141 HIS 0.003 0.001 HIS D 268 PHE 0.010 0.001 PHE B 263 TYR 0.015 0.001 TYR D 194 ARG 0.007 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 1.099 Fit side-chains REVERT: C 127 ASP cc_start: 0.6029 (t70) cc_final: 0.5625 (t0) REVERT: D 100 ASN cc_start: 0.8405 (m-40) cc_final: 0.8096 (t0) REVERT: D 168 ASN cc_start: 0.8716 (m-40) cc_final: 0.8493 (m110) REVERT: A 287 PHE cc_start: 0.6980 (t80) cc_final: 0.6635 (t80) REVERT: A 291 LYS cc_start: 0.7578 (tttp) cc_final: 0.7167 (pttt) outliers start: 46 outliers final: 41 residues processed: 172 average time/residue: 0.2110 time to fit residues: 51.0767 Evaluate side-chains 172 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 0.0670 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10217 Z= 0.159 Angle : 0.592 9.889 13909 Z= 0.284 Chirality : 0.043 0.186 1675 Planarity : 0.004 0.046 1764 Dihedral : 3.961 21.782 1415 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.51 % Allowed : 18.61 % Favored : 77.87 % 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: -1.55 (0.24), residues: 1306 helix: 0.88 (0.22), residues: 640 sheet: -3.38 (0.37), residues: 140 loop : -2.85 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 175 HIS 0.005 0.001 HIS C 268 PHE 0.025 0.001 PHE B 263 TYR 0.014 0.001 TYR D 194 ARG 0.007 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.019 Fit side-chains REVERT: C 127 ASP cc_start: 0.6041 (t70) cc_final: 0.5646 (t0) REVERT: D 100 ASN cc_start: 0.8333 (m-40) cc_final: 0.8055 (t0) REVERT: D 168 ASN cc_start: 0.8684 (m-40) cc_final: 0.8453 (m110) REVERT: D 257 ARG cc_start: 0.7647 (tpp-160) cc_final: 0.7376 (tpp-160) REVERT: A 287 PHE cc_start: 0.6975 (t80) cc_final: 0.6635 (t80) REVERT: A 291 LYS cc_start: 0.7562 (tttp) cc_final: 0.7162 (pttt) REVERT: B 175 ASP cc_start: 0.8576 (m-30) cc_final: 0.8364 (m-30) outliers start: 37 outliers final: 31 residues processed: 166 average time/residue: 0.2086 time to fit residues: 48.7963 Evaluate side-chains 166 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.0270 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 10 optimal weight: 0.0470 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 0.0030 chunk 109 optimal weight: 3.9990 overall best weight: 1.0150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10217 Z= 0.221 Angle : 0.625 9.730 13909 Z= 0.298 Chirality : 0.044 0.182 1675 Planarity : 0.004 0.051 1764 Dihedral : 4.014 22.808 1415 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.23 % Allowed : 19.28 % Favored : 77.49 % 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: -1.47 (0.24), residues: 1306 helix: 0.85 (0.22), residues: 639 sheet: -3.37 (0.40), residues: 106 loop : -2.76 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 79 HIS 0.004 0.001 HIS C 268 PHE 0.023 0.001 PHE B 263 TYR 0.015 0.001 TYR D 194 ARG 0.008 0.000 ARG D 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.025 Fit side-chains REVERT: C 127 ASP cc_start: 0.6059 (t70) cc_final: 0.5664 (t0) REVERT: D 100 ASN cc_start: 0.8365 (m-40) cc_final: 0.8069 (t0) REVERT: D 168 ASN cc_start: 0.8712 (m-40) cc_final: 0.8480 (m110) REVERT: A 213 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8242 (mttp) REVERT: A 287 PHE cc_start: 0.6992 (t80) cc_final: 0.6640 (t80) REVERT: A 291 LYS cc_start: 0.7546 (tttp) cc_final: 0.7125 (pttt) REVERT: B 175 ASP cc_start: 0.8610 (m-30) cc_final: 0.8387 (m-30) outliers start: 34 outliers final: 31 residues processed: 159 average time/residue: 0.2230 time to fit residues: 49.7386 Evaluate side-chains 161 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.0070 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 0.0170 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.181427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155114 restraints weight = 12673.532| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.04 r_work: 0.3704 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10217 Z= 0.163 Angle : 0.595 9.339 13909 Z= 0.285 Chirality : 0.043 0.179 1675 Planarity : 0.004 0.044 1764 Dihedral : 3.915 21.452 1415 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.13 % Allowed : 19.47 % Favored : 77.40 % 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: -1.39 (0.24), residues: 1306 helix: 0.97 (0.22), residues: 640 sheet: -3.26 (0.37), residues: 140 loop : -2.72 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.005 0.001 HIS C 268 PHE 0.022 0.001 PHE B 263 TYR 0.014 0.001 TYR D 194 ARG 0.008 0.000 ARG D 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.91 seconds wall clock time: 41 minutes 6.22 seconds (2466.22 seconds total)