Starting phenix.real_space_refine on Wed Feb 14 05:10:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/02_2024/8ihh_35444_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/02_2024/8ihh_35444.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/02_2024/8ihh_35444_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/02_2024/8ihh_35444_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/02_2024/8ihh_35444_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/02_2024/8ihh_35444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/02_2024/8ihh_35444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/02_2024/8ihh_35444_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/02_2024/8ihh_35444_updated.pdb" } resolution = 3.06 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= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5545 2.51 5 N 1473 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R ASP 97": "OD1" <-> "OD2" Residue "R ASP 221": "OD1" <-> "OD2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ASP 90": "OD1" <-> "OD2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 109": "OD1" <-> "OD2" Residue "S TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2381 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1698 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2480 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "S" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'P8A': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.62 Number of scatterers: 8670 At special positions: 0 Unit cell: (88.11, 117.81, 136.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1594 8.00 N 1473 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 16 sheets defined 32.7% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'R' and resid 24 through 26 No H-bonds generated for 'chain 'R' and resid 24 through 26' Processing helix chain 'R' and resid 30 through 54 removed outlier: 3.602A pdb=" N PHE R 54 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 88 removed outlier: 3.742A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 98 through 129 removed outlier: 4.939A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 162 removed outlier: 3.627A pdb=" N THR R 159 " --> pdb=" O THR R 155 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N HIS R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 195 Processing helix chain 'R' and resid 198 through 217 removed outlier: 3.519A pdb=" N GLY R 202 " --> pdb=" O PHE R 198 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE R 212 " --> pdb=" O SER R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 260 removed outlier: 3.657A pdb=" N THR R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.584A pdb=" N HIS R 259 " --> pdb=" O PHE R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 289 removed outlier: 4.118A pdb=" N SER R 271 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL R 272 " --> pdb=" O TYR R 269 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP R 273 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE R 276 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE R 277 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU R 280 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN R 286 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU R 289 " --> pdb=" O ASN R 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.547A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.583A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.778A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.168A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.694A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.609A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.647A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing sheet with id= A, first strand: chain 'R' and resid 10 through 12 Processing sheet with id= B, first strand: chain 'R' and resid 169 through 171 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.478A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.830A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.858A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.783A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.614A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.593A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.585A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.484A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 18 through 23 Processing sheet with id= L, first strand: chain 'S' and resid 33 through 35 Processing sheet with id= M, first strand: chain 'S' and resid 38 through 40 removed outlier: 3.503A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 49 through 51 Processing sheet with id= O, first strand: chain 'S' and resid 156 through 160 Processing sheet with id= P, first strand: chain 'S' and resid 226 through 231 removed outlier: 6.227A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2795 1.35 - 1.48: 2326 1.48 - 1.60: 3663 1.60 - 1.73: 0 1.73 - 1.86: 81 Bond restraints: 8865 Sorted by residual: bond pdb=" C6 P8A R 602 " pdb=" C7 P8A R 602 " ideal model delta sigma weight residual 1.528 1.477 0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" O P8A R 602 " pdb=" C7 P8A R 602 " ideal model delta sigma weight residual 1.259 1.307 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C7 P8A R 602 " pdb=" O1 P8A R 602 " ideal model delta sigma weight residual 1.259 1.222 0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" CA PHE R 255 " pdb=" C PHE R 255 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.35e-02 5.49e+03 3.26e+00 bond pdb=" C5 P8A R 602 " pdb=" C6 P8A R 602 " ideal model delta sigma weight residual 1.366 1.400 -0.034 2.00e-02 2.50e+03 2.88e+00 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.69: 186 106.69 - 113.51: 4861 113.51 - 120.34: 3127 120.34 - 127.17: 3762 127.17 - 133.99: 103 Bond angle restraints: 12039 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.10 108.53 4.57 9.70e-01 1.06e+00 2.22e+01 angle pdb=" CA CYS R 183 " pdb=" CB CYS R 183 " pdb=" SG CYS R 183 " ideal model delta sigma weight residual 114.40 122.34 -7.94 2.30e+00 1.89e-01 1.19e+01 angle pdb=" CB MET R 285 " pdb=" CG MET R 285 " pdb=" SD MET R 285 " ideal model delta sigma weight residual 112.70 122.80 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N CYS R 183 " pdb=" CA CYS R 183 " pdb=" C CYS R 183 " ideal model delta sigma weight residual 108.79 113.54 -4.75 1.53e+00 4.27e-01 9.62e+00 angle pdb=" N MET R 167 " pdb=" CA MET R 167 " pdb=" C MET R 167 " ideal model delta sigma weight residual 109.81 116.23 -6.42 2.21e+00 2.05e-01 8.44e+00 ... (remaining 12034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4520 17.79 - 35.59: 528 35.59 - 53.38: 115 53.38 - 71.17: 25 71.17 - 88.97: 7 Dihedral angle restraints: 5195 sinusoidal: 1919 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual -86.00 -146.12 60.12 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 51.47 41.53 1 1.00e+01 1.00e-02 2.41e+01 ... (remaining 5192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 938 0.035 - 0.070: 315 0.070 - 0.105: 87 0.105 - 0.140: 35 0.140 - 0.175: 2 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA CYS R 183 " pdb=" N CYS R 183 " pdb=" C CYS R 183 " pdb=" CB CYS R 183 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1374 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO R 32 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C THR B 87 " -0.032 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO S 236 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 292 2.71 - 3.26: 8419 3.26 - 3.81: 13603 3.81 - 4.35: 17793 4.35 - 4.90: 30668 Nonbonded interactions: 70775 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.165 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.233 2.440 nonbonded pdb=" OG SER R 62 " pdb=" OD2 ASP R 124 " model vdw 2.233 2.440 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.248 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.253 2.440 ... (remaining 70770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.760 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.020 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8865 Z= 0.173 Angle : 0.545 10.103 12039 Z= 0.293 Chirality : 0.040 0.175 1377 Planarity : 0.004 0.063 1523 Dihedral : 16.304 88.967 3068 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.22 % Allowed : 24.44 % Favored : 75.33 % 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: -0.71 (0.25), residues: 1115 helix: 0.06 (0.27), residues: 355 sheet: -0.01 (0.32), residues: 271 loop : -1.06 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.001 0.000 HIS B 183 PHE 0.010 0.001 PHE B 151 TYR 0.019 0.001 TYR S 235 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.048 Fit side-chains REVERT: R 50 TRP cc_start: 0.5776 (t60) cc_final: 0.5245 (t-100) REVERT: R 106 MET cc_start: 0.7405 (tpt) cc_final: 0.7200 (tpp) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2217 time to fit residues: 38.9633 Evaluate side-chains 120 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.054 8865 Z= 0.593 Angle : 0.719 9.419 12039 Z= 0.380 Chirality : 0.050 0.294 1377 Planarity : 0.005 0.052 1523 Dihedral : 6.161 89.903 1237 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.89 % Allowed : 23.56 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), residues: 1115 helix: 0.35 (0.27), residues: 360 sheet: -0.27 (0.30), residues: 268 loop : -1.42 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 47 HIS 0.005 0.001 HIS B 91 PHE 0.021 0.003 PHE A 189 TYR 0.043 0.003 TYR S 235 ARG 0.004 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 0.986 Fit side-chains REVERT: R 219 GLN cc_start: 0.7816 (mp10) cc_final: 0.7491 (mp10) REVERT: B 35 ASN cc_start: 0.7633 (t0) cc_final: 0.7396 (p0) REVERT: S 38 ARG cc_start: 0.8726 (ptt180) cc_final: 0.8467 (ptt180) REVERT: S 144 THR cc_start: 0.7255 (OUTLIER) cc_final: 0.7039 (m) REVERT: S 244 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7996 (ttmm) outliers start: 44 outliers final: 27 residues processed: 164 average time/residue: 0.2158 time to fit residues: 48.4568 Evaluate side-chains 151 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 189 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8865 Z= 0.158 Angle : 0.509 7.801 12039 Z= 0.268 Chirality : 0.041 0.203 1377 Planarity : 0.004 0.049 1523 Dihedral : 5.511 89.892 1235 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.22 % Allowed : 25.33 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1115 helix: 1.11 (0.27), residues: 360 sheet: -0.11 (0.30), residues: 271 loop : -1.13 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.000 HIS B 91 PHE 0.010 0.001 PHE A 354 TYR 0.028 0.001 TYR S 235 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 0.973 Fit side-chains REVERT: R 219 GLN cc_start: 0.7545 (mp10) cc_final: 0.7230 (mp10) REVERT: A 20 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: B 35 ASN cc_start: 0.7681 (t0) cc_final: 0.7357 (p0) REVERT: S 12 VAL cc_start: 0.6386 (p) cc_final: 0.6118 (p) REVERT: S 38 ARG cc_start: 0.8647 (ptt180) cc_final: 0.8375 (ptt180) REVERT: S 118 THR cc_start: 0.7248 (OUTLIER) cc_final: 0.7036 (p) REVERT: S 202 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7778 (mtm180) outliers start: 29 outliers final: 15 residues processed: 159 average time/residue: 0.2114 time to fit residues: 46.5194 Evaluate side-chains 144 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 237 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8865 Z= 0.342 Angle : 0.594 9.444 12039 Z= 0.307 Chirality : 0.044 0.245 1377 Planarity : 0.004 0.066 1523 Dihedral : 5.600 89.024 1235 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.11 % Allowed : 25.22 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1115 helix: 0.96 (0.27), residues: 370 sheet: -0.27 (0.30), residues: 272 loop : -1.19 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.002 PHE B 199 TYR 0.034 0.002 TYR S 235 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 129 time to evaluate : 1.089 Fit side-chains REVERT: R 219 GLN cc_start: 0.7766 (mp10) cc_final: 0.7429 (mp10) REVERT: A 20 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: B 35 ASN cc_start: 0.7695 (t0) cc_final: 0.7386 (p0) REVERT: S 38 ARG cc_start: 0.8733 (ptt180) cc_final: 0.8472 (ptt180) REVERT: S 160 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7349 (mtp-110) REVERT: S 202 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7708 (mtm180) REVERT: S 235 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.7191 (t80) REVERT: S 244 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8083 (ttmm) outliers start: 46 outliers final: 30 residues processed: 166 average time/residue: 0.2152 time to fit residues: 49.0425 Evaluate side-chains 155 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8865 Z= 0.189 Angle : 0.516 8.912 12039 Z= 0.268 Chirality : 0.041 0.198 1377 Planarity : 0.004 0.050 1523 Dihedral : 5.317 88.593 1235 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.11 % Allowed : 25.56 % Favored : 69.33 % 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: -0.14 (0.25), residues: 1115 helix: 1.35 (0.28), residues: 362 sheet: -0.20 (0.30), residues: 272 loop : -1.12 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE B 151 TYR 0.028 0.001 TYR S 235 ARG 0.003 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 1.085 Fit side-chains REVERT: R 219 GLN cc_start: 0.7633 (mp10) cc_final: 0.7294 (mp10) REVERT: A 20 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: B 35 ASN cc_start: 0.7671 (t0) cc_final: 0.7361 (p0) REVERT: S 6 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: S 38 ARG cc_start: 0.8693 (ptt180) cc_final: 0.8452 (ptt180) REVERT: S 160 ARG cc_start: 0.7562 (mtp-110) cc_final: 0.7290 (mtp-110) REVERT: S 202 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7485 (mtm110) REVERT: S 235 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6871 (t80) REVERT: S 244 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8010 (ttmm) outliers start: 46 outliers final: 34 residues processed: 165 average time/residue: 0.2281 time to fit residues: 51.0564 Evaluate side-chains 164 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 167 MET Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 136 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8865 Z= 0.303 Angle : 0.563 7.480 12039 Z= 0.292 Chirality : 0.043 0.228 1377 Planarity : 0.004 0.043 1523 Dihedral : 5.511 89.064 1235 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.89 % Allowed : 25.11 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1115 helix: 1.34 (0.28), residues: 359 sheet: -0.27 (0.30), residues: 268 loop : -1.19 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.002 PHE B 199 TYR 0.033 0.002 TYR S 235 ARG 0.003 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 128 time to evaluate : 1.210 Fit side-chains REVERT: R 219 GLN cc_start: 0.7760 (mp10) cc_final: 0.7440 (mp10) REVERT: A 9 ASP cc_start: 0.7894 (t0) cc_final: 0.7529 (m-30) REVERT: A 20 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: B 35 ASN cc_start: 0.7675 (t0) cc_final: 0.7381 (p0) REVERT: S 6 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: S 13 GLN cc_start: 0.7671 (pm20) cc_final: 0.7232 (pp30) REVERT: S 38 ARG cc_start: 0.8708 (ptt180) cc_final: 0.8458 (ptt180) REVERT: S 202 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7680 (mtm110) REVERT: S 235 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.7004 (t80) REVERT: S 244 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8079 (ttmm) outliers start: 53 outliers final: 41 residues processed: 171 average time/residue: 0.2344 time to fit residues: 54.4944 Evaluate side-chains 170 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 125 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 167 MET Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 136 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 171 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8865 Z= 0.231 Angle : 0.531 6.625 12039 Z= 0.276 Chirality : 0.042 0.208 1377 Planarity : 0.004 0.055 1523 Dihedral : 5.432 87.652 1235 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.44 % Allowed : 25.00 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1115 helix: 1.44 (0.28), residues: 359 sheet: -0.15 (0.30), residues: 268 loop : -1.15 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 151 TYR 0.031 0.001 TYR S 235 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 128 time to evaluate : 1.002 Fit side-chains REVERT: R 219 GLN cc_start: 0.7676 (mp10) cc_final: 0.7347 (mp10) REVERT: A 9 ASP cc_start: 0.7810 (t0) cc_final: 0.7427 (m-30) REVERT: A 20 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: B 35 ASN cc_start: 0.7663 (t0) cc_final: 0.7374 (p0) REVERT: B 55 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8580 (mp) REVERT: S 6 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: S 13 GLN cc_start: 0.7607 (pm20) cc_final: 0.7228 (pp30) REVERT: S 38 ARG cc_start: 0.8722 (ptt180) cc_final: 0.8459 (ptt180) REVERT: S 202 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7674 (mtm110) REVERT: S 235 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6912 (t80) REVERT: S 244 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8035 (ttmm) outliers start: 58 outliers final: 46 residues processed: 171 average time/residue: 0.2040 time to fit residues: 48.4314 Evaluate side-chains 175 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 124 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 167 MET Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 136 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8865 Z= 0.307 Angle : 0.569 7.553 12039 Z= 0.294 Chirality : 0.043 0.229 1377 Planarity : 0.004 0.047 1523 Dihedral : 5.469 87.707 1235 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.44 % Allowed : 25.22 % Favored : 68.33 % 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: -0.23 (0.24), residues: 1115 helix: 1.36 (0.28), residues: 359 sheet: -0.29 (0.29), residues: 271 loop : -1.22 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.002 PHE B 199 TYR 0.034 0.002 TYR S 235 ARG 0.004 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 121 time to evaluate : 1.050 Fit side-chains REVERT: R 88 VAL cc_start: 0.7665 (OUTLIER) cc_final: 0.7452 (p) REVERT: A 20 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: B 35 ASN cc_start: 0.7624 (t0) cc_final: 0.7374 (p0) REVERT: B 55 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8584 (mp) REVERT: B 96 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7937 (mtt90) REVERT: S 6 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8372 (pt0) REVERT: S 13 GLN cc_start: 0.7675 (pm20) cc_final: 0.7329 (pp30) REVERT: S 38 ARG cc_start: 0.8726 (ptt180) cc_final: 0.8477 (ptt180) REVERT: S 202 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7656 (mtm110) REVERT: S 235 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.7045 (t80) REVERT: S 244 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8071 (ttmm) outliers start: 58 outliers final: 49 residues processed: 163 average time/residue: 0.2171 time to fit residues: 48.7815 Evaluate side-chains 174 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 119 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 167 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 136 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 171 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8865 Z= 0.148 Angle : 0.500 7.786 12039 Z= 0.259 Chirality : 0.041 0.172 1377 Planarity : 0.004 0.044 1523 Dihedral : 5.041 80.750 1235 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.67 % Allowed : 27.00 % Favored : 68.33 % 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: 0.04 (0.25), residues: 1115 helix: 1.66 (0.28), residues: 359 sheet: -0.11 (0.30), residues: 269 loop : -1.13 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.012 0.001 PHE R 54 TYR 0.026 0.001 TYR S 235 ARG 0.003 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.095 Fit side-chains REVERT: R 11 LEU cc_start: 0.5903 (tp) cc_final: 0.5667 (tp) REVERT: R 88 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7297 (p) REVERT: A 9 ASP cc_start: 0.7630 (t0) cc_final: 0.7330 (m-30) REVERT: A 20 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8191 (m-30) REVERT: B 35 ASN cc_start: 0.7631 (t0) cc_final: 0.7333 (p0) REVERT: B 55 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8523 (mp) REVERT: S 6 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: S 13 GLN cc_start: 0.7662 (pm20) cc_final: 0.7388 (pp30) REVERT: S 38 ARG cc_start: 0.8711 (ptt180) cc_final: 0.8478 (ptt180) REVERT: S 202 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7473 (mtm110) REVERT: S 235 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.6643 (t80) REVERT: S 244 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7928 (ttmm) outliers start: 42 outliers final: 30 residues processed: 161 average time/residue: 0.2117 time to fit residues: 46.9736 Evaluate side-chains 157 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 136 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.0670 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8865 Z= 0.125 Angle : 0.497 8.274 12039 Z= 0.256 Chirality : 0.041 0.150 1377 Planarity : 0.004 0.050 1523 Dihedral : 4.822 75.809 1235 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.44 % Allowed : 27.89 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1115 helix: 1.76 (0.28), residues: 360 sheet: -0.08 (0.30), residues: 273 loop : -1.04 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.011 0.001 PHE A 354 TYR 0.038 0.001 TYR R 87 ARG 0.004 0.000 ARG S 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 0.982 Fit side-chains REVERT: R 11 LEU cc_start: 0.5853 (tp) cc_final: 0.5608 (tp) REVERT: B 35 ASN cc_start: 0.7611 (t0) cc_final: 0.7352 (p0) REVERT: B 55 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8486 (mp) REVERT: S 13 GLN cc_start: 0.7611 (pm20) cc_final: 0.7351 (pp30) REVERT: S 202 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7510 (mtm110) REVERT: S 235 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6420 (t80) REVERT: S 244 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7928 (ttmm) outliers start: 31 outliers final: 23 residues processed: 152 average time/residue: 0.2198 time to fit residues: 45.5977 Evaluate side-chains 149 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 0.0970 chunk 89 optimal weight: 0.0040 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN B 88 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121369 restraints weight = 10742.209| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.50 r_work: 0.3413 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8865 Z= 0.171 Angle : 0.510 7.924 12039 Z= 0.263 Chirality : 0.041 0.165 1377 Planarity : 0.004 0.049 1523 Dihedral : 4.862 76.576 1235 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.33 % Allowed : 28.33 % Favored : 68.33 % 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: 0.16 (0.25), residues: 1115 helix: 1.73 (0.27), residues: 360 sheet: 0.08 (0.31), residues: 264 loop : -1.12 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.012 0.001 PHE R 186 TYR 0.025 0.001 TYR S 235 ARG 0.004 0.000 ARG S 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.51 seconds wall clock time: 42 minutes 18.49 seconds (2538.49 seconds total)