Starting phenix.real_space_refine on Sat Jul 20 21:13:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/07_2024/7o17_12692_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/07_2024/7o17_12692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/07_2024/7o17_12692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/07_2024/7o17_12692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/07_2024/7o17_12692_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/07_2024/7o17_12692_neut.cif" } resolution = 4.5 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= 0.003 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 341 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 7456 2.51 5 N 2054 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11679 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3057 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 386} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "D" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2030 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 264} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1938 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.47, per 1000 atoms: 0.55 Number of scatterers: 11679 At special positions: 0 Unit cell: (84.24, 81.648, 195.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 Mg 2 11.99 O 2127 8.00 N 2054 7.00 C 7456 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: 5.36 Conformation dependent library (CDL) restraints added in 2.2 seconds 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2746 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 43.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 375 through 383 removed outlier: 4.212A pdb=" N LEU A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 4.066A pdb=" N LEU A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.663A pdb=" N VAL A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.574A pdb=" N LEU A 427 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 429 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 90 through 103 removed outlier: 3.591A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.632A pdb=" N GLU B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.733A pdb=" N ALA B 122 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.616A pdb=" N GLN B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 173 removed outlier: 4.015A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.750A pdb=" N ALA B 193 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.556A pdb=" N LEU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.692A pdb=" N LEU B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.838A pdb=" N GLY B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.674A pdb=" N TYR B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 3.997A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 90 through 103 removed outlier: 3.626A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 4.472A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 143 removed outlier: 3.804A pdb=" N LEU C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.749A pdb=" N GLN C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.837A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.755A pdb=" N ALA C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 4.006A pdb=" N THR C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 242' Processing helix chain 'C' and resid 266 through 272 removed outlier: 3.739A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 298 Processing helix chain 'D' and resid 4 through 18 removed outlier: 3.742A pdb=" N ALA D 8 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 removed outlier: 4.312A pdb=" N LEU D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA D 32 " --> pdb=" O PHE D 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.611A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 75 removed outlier: 3.849A pdb=" N ALA D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 98 through 120 removed outlier: 3.755A pdb=" N LEU D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 103 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 112 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 removed outlier: 3.528A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 168 removed outlier: 3.528A pdb=" N LEU D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 159 " --> pdb=" O TRP D 155 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 164 " --> pdb=" O PHE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 removed outlier: 3.611A pdb=" N ALA D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 removed outlier: 3.895A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.678A pdb=" N LEU D 214 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.594A pdb=" N TYR D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.862A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 15 removed outlier: 3.966A pdb=" N ILE E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA E 8 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.883A pdb=" N LEU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 23 through 36 removed outlier: 3.561A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 72 removed outlier: 4.003A pdb=" N THR E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.665A pdb=" N ALA E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.781A pdb=" N LEU E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.803A pdb=" N GLY E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.531A pdb=" N LEU E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 removed outlier: 3.610A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 166 removed outlier: 4.591A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU E 164 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 177 through 187 removed outlier: 4.240A pdb=" N VAL E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 200 removed outlier: 3.502A pdb=" N LEU E 193 " --> pdb=" O PHE E 189 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 194 " --> pdb=" O ASP E 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 257 removed outlier: 3.547A pdb=" N LEU E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E 257 " --> pdb=" O TRP E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 removed outlier: 3.833A pdb=" N GLY E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 6.520A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 64 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA A 170 " --> pdb=" O HIS A 193 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU A 195 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 172 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASN A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A 217 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU A 194 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL A 238 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER A 259 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A 299 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE A 261 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 322 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 5.691A pdb=" N GLY A 50 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN A 73 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR A 52 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ALA A 70 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N TYR A 96 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 72 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN A 123 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP A 148 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N MET A 125 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 removed outlier: 7.005A pdb=" N PHE A 56 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A 81 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N HIS A 163 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 132 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR A 226 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 249 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE A 289 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 310 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE A 289 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 308 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LYS A 334 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 310 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 244 removed outlier: 6.372A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 24 removed outlier: 5.709A pdb=" N VAL B 18 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG B 12 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS B 20 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 10 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 22 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.794A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 32 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.887A pdb=" N GLU B 281 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 248 removed outlier: 3.839A pdb=" N ARG B 248 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 24 removed outlier: 6.986A pdb=" N LEU C 24 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN C 7 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 79 removed outlier: 5.799A pdb=" N LEU C 150 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N CYS C 184 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 152 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 246 through 250 removed outlier: 3.595A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 227 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP C 279 " --> pdb=" O SER C 228 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 5.60 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: 3789 1.34 - 1.46: 2430 1.46 - 1.58: 5613 1.58 - 1.70: 11 1.70 - 1.82: 58 Bond restraints: 11901 Sorted by residual: bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.74e+01 bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C5 ATP C 401 " pdb=" C6 ATP C 401 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.94e+01 bond pdb=" C5 ATP B 401 " pdb=" C6 ATP B 401 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.90e+01 bond pdb=" C4 ATP B 401 " pdb=" N9 ATP B 401 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.00e-02 1.00e+04 2.92e+01 ... (remaining 11896 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.57: 183 104.57 - 112.54: 6058 112.54 - 120.52: 5617 120.52 - 128.49: 4219 128.49 - 136.46: 113 Bond angle restraints: 16190 Sorted by residual: angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 120.83 19.04 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP B 401 " pdb=" O3A ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 136.83 118.04 18.79 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 123.32 16.55 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 126.48 10.35 1.00e+00 1.00e+00 1.07e+02 angle pdb=" C5 ATP C 401 " pdb=" C4 ATP C 401 " pdb=" N3 ATP C 401 " ideal model delta sigma weight residual 126.80 119.16 7.64 1.00e+00 1.00e+00 5.84e+01 ... (remaining 16185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6099 17.91 - 35.82: 731 35.82 - 53.73: 174 53.73 - 71.65: 37 71.65 - 89.56: 10 Dihedral angle restraints: 7051 sinusoidal: 2740 harmonic: 4311 Sorted by residual: dihedral pdb=" CA GLY A 349 " pdb=" C GLY A 349 " pdb=" N ASN A 350 " pdb=" CA ASN A 350 " ideal model delta harmonic sigma weight residual 180.00 -139.80 -40.20 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CA ARG A 225 " pdb=" C ARG A 225 " pdb=" N THR A 226 " pdb=" CA THR A 226 " ideal model delta harmonic sigma weight residual 180.00 144.04 35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA VAL A 413 " pdb=" C VAL A 413 " pdb=" N GLN A 414 " pdb=" CA GLN A 414 " ideal model delta harmonic sigma weight residual 180.00 145.26 34.74 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 7048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1470 0.072 - 0.145: 343 0.145 - 0.217: 43 0.217 - 0.289: 14 0.289 - 0.361: 6 Chirality restraints: 1876 Sorted by residual: chirality pdb=" CB ILE A 298 " pdb=" CA ILE A 298 " pdb=" CG1 ILE A 298 " pdb=" CG2 ILE A 298 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA ASN A 248 " pdb=" N ASN A 248 " pdb=" C ASN A 248 " pdb=" CB ASN A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB VAL D 168 " pdb=" CA VAL D 168 " pdb=" CG1 VAL D 168 " pdb=" CG2 VAL D 168 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1873 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 112 " 0.052 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO A 113 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 66 " 0.051 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO E 67 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 28 " -0.050 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO A 29 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.042 5.00e-02 4.00e+02 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 311 2.65 - 3.21: 10782 3.21 - 3.78: 21353 3.78 - 4.34: 27551 4.34 - 4.90: 41656 Nonbonded interactions: 101653 Sorted by model distance: nonbonded pdb=" OG1 THR C 43 " pdb="MG MG C 402 " model vdw 2.089 2.170 nonbonded pdb=" O2B ATP B 401 " pdb="MG MG B 402 " model vdw 2.100 2.170 nonbonded pdb=" O3G ATP C 401 " pdb="MG MG C 402 " model vdw 2.107 2.170 nonbonded pdb=" O3G ATP B 401 " pdb="MG MG B 402 " model vdw 2.114 2.170 nonbonded pdb=" O2B ATP C 401 " pdb="MG MG C 402 " model vdw 2.115 2.170 ... (remaining 101648 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 200 or (resid 201 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 202 through 204 and \ (name N or name CA or name C or name O or name CB )) or resid 205 through 230 o \ r resid 245 through 274)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.220 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.007 0.076 11901 Z= 0.444 Angle : 1.218 19.043 16190 Z= 0.689 Chirality : 0.066 0.361 1876 Planarity : 0.009 0.079 2067 Dihedral : 16.813 89.557 4305 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 1.09 % Allowed : 18.69 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -5.33 (0.16), residues: 1519 helix: -4.23 (0.11), residues: 546 sheet: -2.79 (0.31), residues: 214 loop : -3.18 (0.18), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 98 HIS 0.009 0.003 HIS B 120 PHE 0.022 0.003 PHE D 185 TYR 0.019 0.003 TYR C 13 ARG 0.027 0.003 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8540 (tpp) cc_final: 0.8263 (tpt) REVERT: A 105 MET cc_start: 0.8162 (tpt) cc_final: 0.7433 (tpp) REVERT: A 209 MET cc_start: 0.9416 (mmm) cc_final: 0.9066 (mmm) REVERT: A 386 VAL cc_start: 0.9641 (p) cc_final: 0.9259 (p) REVERT: A 390 MET cc_start: 0.9771 (mmp) cc_final: 0.9506 (mmm) REVERT: B 34 LEU cc_start: 0.9720 (mp) cc_final: 0.9443 (tp) REVERT: B 102 LYS cc_start: 0.9268 (mmmm) cc_final: 0.9020 (mmmt) REVERT: B 133 MET cc_start: 0.9123 (mtp) cc_final: 0.8819 (mtp) REVERT: B 295 MET cc_start: 0.9136 (mmm) cc_final: 0.8874 (mmm) REVERT: C 46 MET cc_start: 0.9090 (mmt) cc_final: 0.8820 (mmm) REVERT: C 127 LYS cc_start: 0.9382 (pttm) cc_final: 0.9093 (pttm) REVERT: C 133 MET cc_start: 0.9447 (mtp) cc_final: 0.9043 (mtm) REVERT: D 81 GLU cc_start: 0.9326 (mp0) cc_final: 0.9075 (mp0) REVERT: D 185 PHE cc_start: 0.9211 (t80) cc_final: 0.8635 (t80) REVERT: D 189 PHE cc_start: 0.9247 (t80) cc_final: 0.8599 (t80) REVERT: E 20 TRP cc_start: 0.7417 (m-10) cc_final: 0.6842 (m-90) REVERT: E 66 MET cc_start: 0.9428 (tpp) cc_final: 0.8656 (tpp) REVERT: E 72 LEU cc_start: 0.9653 (mm) cc_final: 0.9268 (pp) REVERT: E 76 ASP cc_start: 0.8902 (p0) cc_final: 0.8588 (p0) REVERT: E 170 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8444 (tm-30) REVERT: E 221 TYR cc_start: 0.8948 (t80) cc_final: 0.8689 (t80) outliers start: 13 outliers final: 5 residues processed: 166 average time/residue: 0.2448 time to fit residues: 57.6004 Evaluate side-chains 105 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN A 212 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN B 20 HIS B 23 ASN B 82 ASN C 20 HIS C 23 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 205 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11901 Z= 0.237 Angle : 0.722 9.366 16190 Z= 0.375 Chirality : 0.045 0.187 1876 Planarity : 0.005 0.059 2067 Dihedral : 9.038 87.857 1727 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.25 % Allowed : 6.96 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.99 (0.19), residues: 1519 helix: -2.43 (0.16), residues: 618 sheet: -2.47 (0.32), residues: 219 loop : -2.82 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 343 HIS 0.014 0.002 HIS C 97 PHE 0.015 0.002 PHE D 157 TYR 0.020 0.002 TYR B 86 ARG 0.004 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8645 (tpp) cc_final: 0.8361 (tpt) REVERT: A 208 TYR cc_start: 0.9253 (m-10) cc_final: 0.8893 (m-10) REVERT: A 209 MET cc_start: 0.9386 (mmm) cc_final: 0.8965 (mmm) REVERT: A 386 VAL cc_start: 0.9594 (p) cc_final: 0.9107 (p) REVERT: A 390 MET cc_start: 0.9755 (mmp) cc_final: 0.9471 (mmm) REVERT: A 402 GLN cc_start: 0.9701 (OUTLIER) cc_final: 0.9266 (mm110) REVERT: B 47 LYS cc_start: 0.9660 (mttm) cc_final: 0.9441 (mmtp) REVERT: B 102 LYS cc_start: 0.9275 (mmmm) cc_final: 0.9028 (mmmt) REVERT: B 133 MET cc_start: 0.9042 (mtp) cc_final: 0.8820 (mtp) REVERT: B 295 MET cc_start: 0.9094 (mmm) cc_final: 0.8784 (mmp) REVERT: C 46 MET cc_start: 0.9217 (mmt) cc_final: 0.9001 (mmm) REVERT: C 47 LYS cc_start: 0.9425 (mtmm) cc_final: 0.9135 (mtmt) REVERT: C 133 MET cc_start: 0.9098 (mtp) cc_final: 0.8727 (mtp) REVERT: D 14 ASP cc_start: 0.8907 (p0) cc_final: 0.8606 (p0) REVERT: D 66 MET cc_start: 0.9560 (tpp) cc_final: 0.8915 (tpp) REVERT: D 72 LEU cc_start: 0.9280 (pp) cc_final: 0.9044 (pp) REVERT: D 101 LEU cc_start: 0.9439 (mt) cc_final: 0.9199 (mt) REVERT: D 189 PHE cc_start: 0.8960 (t80) cc_final: 0.8470 (t80) REVERT: D 221 TYR cc_start: 0.8948 (t80) cc_final: 0.8648 (t80) REVERT: E 20 TRP cc_start: 0.7283 (m-10) cc_final: 0.6802 (m-90) REVERT: E 66 MET cc_start: 0.9269 (tpp) cc_final: 0.8605 (tpp) REVERT: E 72 LEU cc_start: 0.9667 (mm) cc_final: 0.9265 (tt) REVERT: E 76 ASP cc_start: 0.8927 (p0) cc_final: 0.8474 (p0) REVERT: E 88 MET cc_start: 0.9495 (ptp) cc_final: 0.9000 (mpp) REVERT: E 104 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9424 (tptp) REVERT: E 223 LEU cc_start: 0.9717 (mt) cc_final: 0.9420 (mt) outliers start: 3 outliers final: 1 residues processed: 138 average time/residue: 0.2307 time to fit residues: 46.3977 Evaluate side-chains 103 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 121 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11901 Z= 0.207 Angle : 0.664 8.661 16190 Z= 0.341 Chirality : 0.044 0.190 1876 Planarity : 0.004 0.053 2067 Dihedral : 8.343 86.226 1727 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.08 % Allowed : 7.21 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.06 (0.20), residues: 1519 helix: -1.39 (0.19), residues: 621 sheet: -2.36 (0.30), residues: 249 loop : -2.43 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 343 HIS 0.008 0.001 HIS C 97 PHE 0.022 0.002 PHE E 143 TYR 0.018 0.002 TYR C 168 ARG 0.003 0.000 ARG D 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8647 (tpp) cc_final: 0.8382 (tpt) REVERT: A 208 TYR cc_start: 0.9000 (m-10) cc_final: 0.8716 (m-10) REVERT: A 209 MET cc_start: 0.9326 (mmm) cc_final: 0.8651 (mmm) REVERT: A 386 VAL cc_start: 0.9599 (p) cc_final: 0.9203 (p) REVERT: A 390 MET cc_start: 0.9777 (mmp) cc_final: 0.9567 (mmm) REVERT: B 47 LYS cc_start: 0.9661 (mttm) cc_final: 0.9441 (mmtp) REVERT: B 82 ASN cc_start: 0.8932 (p0) cc_final: 0.8724 (p0) REVERT: B 85 PHE cc_start: 0.9326 (m-80) cc_final: 0.8974 (m-80) REVERT: B 102 LYS cc_start: 0.9308 (mmmm) cc_final: 0.9080 (mmmt) REVERT: B 295 MET cc_start: 0.9147 (mmm) cc_final: 0.8779 (mmm) REVERT: C 47 LYS cc_start: 0.9395 (mtmm) cc_final: 0.9138 (mtmt) REVERT: C 127 LYS cc_start: 0.9234 (pttm) cc_final: 0.8812 (pttm) REVERT: C 133 MET cc_start: 0.9137 (mtp) cc_final: 0.8724 (mtp) REVERT: D 66 MET cc_start: 0.9545 (tpp) cc_final: 0.9021 (tpp) REVERT: D 72 LEU cc_start: 0.9168 (pp) cc_final: 0.8938 (pp) REVERT: D 101 LEU cc_start: 0.9352 (mt) cc_final: 0.9111 (mt) REVERT: D 189 PHE cc_start: 0.9005 (t80) cc_final: 0.8609 (t80) REVERT: D 221 TYR cc_start: 0.8925 (t80) cc_final: 0.8693 (t80) REVERT: E 20 TRP cc_start: 0.7290 (m-10) cc_final: 0.6802 (m-90) REVERT: E 66 MET cc_start: 0.9269 (tpp) cc_final: 0.8602 (tpp) REVERT: E 76 ASP cc_start: 0.8974 (p0) cc_final: 0.8661 (p0) REVERT: E 104 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9336 (tptp) REVERT: E 223 LEU cc_start: 0.9721 (mt) cc_final: 0.9445 (mt) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.2224 time to fit residues: 45.7041 Evaluate side-chains 99 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11901 Z= 0.227 Angle : 0.675 8.629 16190 Z= 0.344 Chirality : 0.044 0.196 1876 Planarity : 0.004 0.049 2067 Dihedral : 7.945 85.690 1727 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.64 (0.21), residues: 1519 helix: -0.85 (0.20), residues: 637 sheet: -2.24 (0.31), residues: 254 loop : -2.38 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 236 HIS 0.006 0.001 HIS C 97 PHE 0.016 0.002 PHE D 157 TYR 0.016 0.002 TYR D 221 ARG 0.005 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8631 (tpp) cc_final: 0.8385 (tpt) REVERT: A 209 MET cc_start: 0.8893 (mmm) cc_final: 0.8629 (mmm) REVERT: A 386 VAL cc_start: 0.9662 (p) cc_final: 0.9062 (p) REVERT: A 388 LEU cc_start: 0.9248 (tp) cc_final: 0.8972 (tp) REVERT: A 390 MET cc_start: 0.9770 (mmp) cc_final: 0.9480 (mmm) REVERT: A 391 ASN cc_start: 0.9643 (t0) cc_final: 0.9322 (p0) REVERT: A 396 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8529 (mm-30) REVERT: B 25 ASN cc_start: 0.9089 (p0) cc_final: 0.8888 (p0) REVERT: B 143 LEU cc_start: 0.9786 (mm) cc_final: 0.9499 (mt) REVERT: B 295 MET cc_start: 0.9191 (mmm) cc_final: 0.8821 (mmm) REVERT: C 46 MET cc_start: 0.9303 (mmp) cc_final: 0.8999 (mmm) REVERT: C 47 LYS cc_start: 0.9405 (mtmm) cc_final: 0.9113 (mmtp) REVERT: C 133 MET cc_start: 0.9158 (mtp) cc_final: 0.8714 (mtp) REVERT: D 66 MET cc_start: 0.9536 (tpp) cc_final: 0.9082 (tpp) REVERT: D 72 LEU cc_start: 0.9164 (pp) cc_final: 0.8944 (pp) REVERT: D 101 LEU cc_start: 0.9374 (mt) cc_final: 0.9140 (mt) REVERT: D 221 TYR cc_start: 0.9099 (t80) cc_final: 0.8739 (t80) REVERT: E 66 MET cc_start: 0.9231 (tpp) cc_final: 0.8704 (tpp) REVERT: E 72 LEU cc_start: 0.9652 (mm) cc_final: 0.9259 (tt) REVERT: E 104 LYS cc_start: 0.9659 (mmmt) cc_final: 0.9340 (tptp) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2162 time to fit residues: 41.0242 Evaluate side-chains 98 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 0.0770 chunk 130 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11901 Z= 0.182 Angle : 0.651 8.269 16190 Z= 0.324 Chirality : 0.044 0.243 1876 Planarity : 0.004 0.049 2067 Dihedral : 7.550 86.631 1727 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.37 (0.22), residues: 1519 helix: -0.61 (0.21), residues: 646 sheet: -2.13 (0.31), residues: 254 loop : -2.28 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 236 HIS 0.004 0.001 HIS C 97 PHE 0.015 0.001 PHE A 289 TYR 0.017 0.001 TYR C 168 ARG 0.003 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8565 (tpp) cc_final: 0.8317 (tpt) REVERT: A 209 MET cc_start: 0.9016 (mmm) cc_final: 0.8790 (mmm) REVERT: A 386 VAL cc_start: 0.9652 (p) cc_final: 0.9052 (p) REVERT: A 388 LEU cc_start: 0.9312 (tp) cc_final: 0.8982 (tp) REVERT: A 390 MET cc_start: 0.9793 (mmp) cc_final: 0.9459 (mmm) REVERT: A 391 ASN cc_start: 0.9697 (t0) cc_final: 0.9273 (p0) REVERT: A 396 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8599 (mm-30) REVERT: B 133 MET cc_start: 0.9589 (mtm) cc_final: 0.9335 (mtp) REVERT: B 143 LEU cc_start: 0.9788 (mm) cc_final: 0.9474 (mt) REVERT: B 295 MET cc_start: 0.9185 (mmm) cc_final: 0.8803 (mmm) REVERT: C 46 MET cc_start: 0.9311 (mmp) cc_final: 0.8924 (mmm) REVERT: C 47 LYS cc_start: 0.9390 (mtmm) cc_final: 0.9075 (mmtp) REVERT: C 133 MET cc_start: 0.9228 (mtp) cc_final: 0.8758 (mtp) REVERT: C 295 MET cc_start: 0.9468 (tmm) cc_final: 0.9242 (tmm) REVERT: D 66 MET cc_start: 0.9519 (tpp) cc_final: 0.9145 (tpp) REVERT: D 101 LEU cc_start: 0.9322 (mt) cc_final: 0.9047 (mt) REVERT: D 179 LEU cc_start: 0.9177 (pp) cc_final: 0.8943 (pp) REVERT: D 221 TYR cc_start: 0.9026 (t80) cc_final: 0.8759 (t80) REVERT: E 66 MET cc_start: 0.9276 (tpp) cc_final: 0.8782 (tpp) REVERT: E 72 LEU cc_start: 0.9643 (mm) cc_final: 0.9287 (tt) REVERT: E 120 PHE cc_start: 0.9032 (t80) cc_final: 0.8669 (t80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2195 time to fit residues: 42.9811 Evaluate side-chains 99 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11901 Z= 0.300 Angle : 0.719 9.487 16190 Z= 0.369 Chirality : 0.044 0.204 1876 Planarity : 0.005 0.073 2067 Dihedral : 7.677 89.215 1727 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.25 (0.22), residues: 1519 helix: -0.43 (0.21), residues: 635 sheet: -2.15 (0.31), residues: 254 loop : -2.23 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.008 0.002 HIS B 120 PHE 0.037 0.002 PHE E 183 TYR 0.013 0.002 TYR D 221 ARG 0.004 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8634 (tpp) cc_final: 0.8409 (tpt) REVERT: A 208 TYR cc_start: 0.8663 (m-10) cc_final: 0.8196 (m-10) REVERT: A 209 MET cc_start: 0.8997 (mmm) cc_final: 0.8737 (mmm) REVERT: A 386 VAL cc_start: 0.9682 (p) cc_final: 0.9138 (p) REVERT: A 388 LEU cc_start: 0.9268 (tp) cc_final: 0.8897 (tp) REVERT: A 390 MET cc_start: 0.9786 (mmp) cc_final: 0.9455 (mmm) REVERT: A 391 ASN cc_start: 0.9698 (t0) cc_final: 0.9295 (p0) REVERT: A 395 ILE cc_start: 0.9242 (mm) cc_final: 0.8944 (mm) REVERT: A 396 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8577 (mm-30) REVERT: B 133 MET cc_start: 0.9531 (mtm) cc_final: 0.9134 (mtp) REVERT: B 295 MET cc_start: 0.9215 (mmm) cc_final: 0.8792 (mmm) REVERT: C 46 MET cc_start: 0.9300 (mmp) cc_final: 0.8937 (mmm) REVERT: C 47 LYS cc_start: 0.9405 (mtmm) cc_final: 0.9131 (mtmt) REVERT: C 127 LYS cc_start: 0.9265 (pttm) cc_final: 0.8707 (pttm) REVERT: D 66 MET cc_start: 0.9562 (tpp) cc_final: 0.9223 (tpp) REVERT: D 101 LEU cc_start: 0.9382 (mt) cc_final: 0.9127 (mt) REVERT: D 158 LEU cc_start: 0.9653 (mt) cc_final: 0.9418 (mt) REVERT: D 189 PHE cc_start: 0.9221 (t80) cc_final: 0.8836 (t80) REVERT: D 221 TYR cc_start: 0.9159 (t80) cc_final: 0.8893 (t80) REVERT: E 66 MET cc_start: 0.9241 (tpp) cc_final: 0.8674 (tpp) REVERT: E 104 LYS cc_start: 0.9574 (mmmt) cc_final: 0.9311 (tptp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2172 time to fit residues: 39.0156 Evaluate side-chains 94 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11901 Z= 0.228 Angle : 0.684 8.004 16190 Z= 0.345 Chirality : 0.045 0.255 1876 Planarity : 0.004 0.061 2067 Dihedral : 7.564 88.783 1727 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.12 (0.22), residues: 1519 helix: -0.36 (0.21), residues: 643 sheet: -2.13 (0.31), residues: 255 loop : -2.11 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 358 HIS 0.007 0.001 HIS B 194 PHE 0.033 0.002 PHE E 183 TYR 0.019 0.001 TYR B 86 ARG 0.003 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8603 (tpp) cc_final: 0.8378 (tpt) REVERT: A 386 VAL cc_start: 0.9703 (p) cc_final: 0.9164 (p) REVERT: A 390 MET cc_start: 0.9723 (mmp) cc_final: 0.9506 (mmm) REVERT: A 391 ASN cc_start: 0.9713 (t0) cc_final: 0.9378 (t0) REVERT: A 395 ILE cc_start: 0.9194 (mm) cc_final: 0.8904 (mm) REVERT: A 396 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8631 (mm-30) REVERT: B 133 MET cc_start: 0.9553 (mtm) cc_final: 0.9179 (mtp) REVERT: B 295 MET cc_start: 0.9233 (mmm) cc_final: 0.8820 (mmm) REVERT: C 46 MET cc_start: 0.9301 (mmp) cc_final: 0.8869 (mmm) REVERT: C 47 LYS cc_start: 0.9397 (mtmm) cc_final: 0.9136 (mtmt) REVERT: C 127 LYS cc_start: 0.9337 (pttm) cc_final: 0.8812 (pttm) REVERT: C 133 MET cc_start: 0.9153 (mtp) cc_final: 0.8724 (mtp) REVERT: D 66 MET cc_start: 0.9524 (tpp) cc_final: 0.9182 (tpp) REVERT: D 101 LEU cc_start: 0.9375 (mt) cc_final: 0.9121 (mt) REVERT: D 158 LEU cc_start: 0.9647 (mt) cc_final: 0.9396 (mt) REVERT: D 221 TYR cc_start: 0.9123 (t80) cc_final: 0.8888 (t80) REVERT: E 66 MET cc_start: 0.9198 (tpp) cc_final: 0.8717 (tpp) REVERT: E 76 ASP cc_start: 0.8974 (p0) cc_final: 0.8767 (p0) REVERT: E 143 PHE cc_start: 0.9264 (m-80) cc_final: 0.9057 (m-80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2317 time to fit residues: 44.3229 Evaluate side-chains 96 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 126 optimal weight: 0.1980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11901 Z= 0.239 Angle : 0.693 7.924 16190 Z= 0.350 Chirality : 0.045 0.215 1876 Planarity : 0.004 0.053 2067 Dihedral : 7.535 88.347 1727 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.05 (0.22), residues: 1519 helix: -0.29 (0.21), residues: 635 sheet: -2.16 (0.31), residues: 255 loop : -2.05 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 20 HIS 0.009 0.002 HIS B 194 PHE 0.031 0.002 PHE E 183 TYR 0.016 0.002 TYR B 86 ARG 0.003 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8605 (tpp) cc_final: 0.8382 (tpt) REVERT: A 386 VAL cc_start: 0.9660 (p) cc_final: 0.9163 (p) REVERT: A 390 MET cc_start: 0.9707 (mmp) cc_final: 0.9439 (mmm) REVERT: A 391 ASN cc_start: 0.9672 (t0) cc_final: 0.9388 (t0) REVERT: A 396 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8661 (mm-30) REVERT: B 133 MET cc_start: 0.9541 (mtm) cc_final: 0.9180 (mtp) REVERT: B 143 LEU cc_start: 0.9778 (mm) cc_final: 0.9493 (mt) REVERT: B 295 MET cc_start: 0.9187 (mmm) cc_final: 0.8813 (mmm) REVERT: C 46 MET cc_start: 0.9316 (mmp) cc_final: 0.8889 (mmm) REVERT: C 47 LYS cc_start: 0.9432 (mtmm) cc_final: 0.9186 (mtmt) REVERT: C 127 LYS cc_start: 0.9354 (pttm) cc_final: 0.8804 (pttm) REVERT: C 133 MET cc_start: 0.9121 (mtp) cc_final: 0.8717 (mtp) REVERT: D 66 MET cc_start: 0.9528 (tpp) cc_final: 0.9193 (tpp) REVERT: D 101 LEU cc_start: 0.9368 (mt) cc_final: 0.9114 (mt) REVERT: D 158 LEU cc_start: 0.9676 (mt) cc_final: 0.9434 (mt) REVERT: D 189 PHE cc_start: 0.9215 (t80) cc_final: 0.8834 (t80) REVERT: D 222 ARG cc_start: 0.9510 (mtm-85) cc_final: 0.8786 (mtm-85) REVERT: E 66 MET cc_start: 0.9190 (tpp) cc_final: 0.8721 (tpp) REVERT: E 72 LEU cc_start: 0.9629 (mm) cc_final: 0.9308 (tt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2184 time to fit residues: 40.3446 Evaluate side-chains 91 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 0.0270 chunk 121 optimal weight: 30.0000 chunk 127 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11901 Z= 0.164 Angle : 0.680 9.921 16190 Z= 0.331 Chirality : 0.045 0.227 1876 Planarity : 0.004 0.049 2067 Dihedral : 7.228 87.410 1727 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -1.95 (0.22), residues: 1519 helix: -0.17 (0.22), residues: 636 sheet: -2.07 (0.31), residues: 254 loop : -2.06 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 20 HIS 0.006 0.001 HIS B 97 PHE 0.027 0.002 PHE E 183 TYR 0.017 0.001 TYR B 86 ARG 0.003 0.000 ARG E 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8486 (tpp) cc_final: 0.8260 (tpt) REVERT: A 209 MET cc_start: 0.8259 (mmp) cc_final: 0.7741 (mmm) REVERT: A 386 VAL cc_start: 0.9640 (p) cc_final: 0.9359 (m) REVERT: A 391 ASN cc_start: 0.9675 (t0) cc_final: 0.9362 (t0) REVERT: A 396 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8602 (mm-30) REVERT: B 133 MET cc_start: 0.9541 (mtm) cc_final: 0.9329 (mtp) REVERT: B 143 LEU cc_start: 0.9785 (mm) cc_final: 0.9472 (mt) REVERT: B 295 MET cc_start: 0.9187 (mmm) cc_final: 0.8910 (mmm) REVERT: C 46 MET cc_start: 0.9313 (mmp) cc_final: 0.8861 (mmm) REVERT: C 47 LYS cc_start: 0.9428 (mtmm) cc_final: 0.9169 (mtmt) REVERT: C 127 LYS cc_start: 0.9433 (pttm) cc_final: 0.9001 (pttm) REVERT: C 133 MET cc_start: 0.9272 (mtp) cc_final: 0.8886 (mtp) REVERT: D 66 MET cc_start: 0.9508 (tpp) cc_final: 0.9178 (tpp) REVERT: D 101 LEU cc_start: 0.9344 (mt) cc_final: 0.9045 (mt) REVERT: D 158 LEU cc_start: 0.9622 (mt) cc_final: 0.9347 (mt) REVERT: D 189 PHE cc_start: 0.9202 (t80) cc_final: 0.8829 (t80) REVERT: D 222 ARG cc_start: 0.9562 (mtm-85) cc_final: 0.8805 (mtm-85) REVERT: E 66 MET cc_start: 0.9147 (tpp) cc_final: 0.8660 (tpp) REVERT: E 72 LEU cc_start: 0.9589 (mm) cc_final: 0.9376 (tt) REVERT: E 76 ASP cc_start: 0.8957 (p0) cc_final: 0.8695 (p0) REVERT: E 118 ILE cc_start: 0.8727 (tp) cc_final: 0.8401 (tp) REVERT: E 143 PHE cc_start: 0.9142 (m-80) cc_final: 0.8940 (m-80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2172 time to fit residues: 42.3678 Evaluate side-chains 102 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11901 Z= 0.318 Angle : 0.762 11.562 16190 Z= 0.388 Chirality : 0.046 0.216 1876 Planarity : 0.005 0.050 2067 Dihedral : 7.563 89.968 1727 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 28.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.00 (0.22), residues: 1519 helix: -0.26 (0.21), residues: 633 sheet: -2.08 (0.31), residues: 249 loop : -2.03 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 37 HIS 0.010 0.002 HIS B 194 PHE 0.031 0.002 PHE E 183 TYR 0.026 0.002 TYR C 86 ARG 0.005 0.001 ARG C 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8635 (tpp) cc_final: 0.8420 (tpt) REVERT: A 209 MET cc_start: 0.8595 (mmp) cc_final: 0.8159 (mmm) REVERT: A 386 VAL cc_start: 0.9664 (p) cc_final: 0.9147 (p) REVERT: A 390 MET cc_start: 0.9675 (mmp) cc_final: 0.9438 (mmm) REVERT: A 391 ASN cc_start: 0.9685 (t0) cc_final: 0.9397 (t0) REVERT: A 396 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8668 (mm-30) REVERT: B 133 MET cc_start: 0.9549 (mtm) cc_final: 0.9139 (mtp) REVERT: B 143 LEU cc_start: 0.9778 (mm) cc_final: 0.9480 (mt) REVERT: B 295 MET cc_start: 0.9224 (mmm) cc_final: 0.8938 (mmm) REVERT: C 46 MET cc_start: 0.9325 (mmp) cc_final: 0.8905 (mmm) REVERT: C 47 LYS cc_start: 0.9436 (mtmm) cc_final: 0.9213 (mtmt) REVERT: C 127 LYS cc_start: 0.9370 (pttm) cc_final: 0.8869 (pttm) REVERT: C 133 MET cc_start: 0.9094 (mtp) cc_final: 0.8708 (mtp) REVERT: D 66 MET cc_start: 0.9552 (tpp) cc_final: 0.9219 (tpp) REVERT: D 101 LEU cc_start: 0.9382 (mt) cc_final: 0.9145 (mt) REVERT: D 158 LEU cc_start: 0.9642 (mt) cc_final: 0.9350 (mt) REVERT: D 189 PHE cc_start: 0.9278 (t80) cc_final: 0.8920 (t80) REVERT: D 222 ARG cc_start: 0.9588 (mtm-85) cc_final: 0.8851 (mtm-85) REVERT: E 66 MET cc_start: 0.9215 (tpp) cc_final: 0.8758 (tpp) REVERT: E 72 LEU cc_start: 0.9653 (mm) cc_final: 0.9301 (tt) REVERT: E 76 ASP cc_start: 0.8944 (p0) cc_final: 0.8737 (p0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2183 time to fit residues: 39.3031 Evaluate side-chains 93 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.0270 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 122 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.036541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.027212 restraints weight = 99053.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.028031 restraints weight = 64905.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.028605 restraints weight = 47886.909| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11901 Z= 0.181 Angle : 0.688 10.759 16190 Z= 0.339 Chirality : 0.044 0.221 1876 Planarity : 0.004 0.049 2067 Dihedral : 7.311 87.930 1727 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -1.85 (0.22), residues: 1519 helix: -0.12 (0.22), residues: 633 sheet: -2.06 (0.31), residues: 254 loop : -1.93 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 20 HIS 0.006 0.001 HIS B 194 PHE 0.027 0.002 PHE E 183 TYR 0.014 0.001 TYR B 86 ARG 0.003 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.27 seconds wall clock time: 37 minutes 16.61 seconds (2236.61 seconds total)