Starting phenix.real_space_refine on Fri Mar 15 12:34:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y64_33633/03_2024/7y64_33633_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y64_33633/03_2024/7y64_33633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y64_33633/03_2024/7y64_33633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y64_33633/03_2024/7y64_33633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y64_33633/03_2024/7y64_33633_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y64_33633/03_2024/7y64_33633_neut.pdb" } resolution = 2.9 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= 0.002 sd= 0.031 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 2120 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6058 2.51 5 N 1631 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 153": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D ARG 310": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9520 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1795 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 578 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Time building chain proxies: 5.75, per 1000 atoms: 0.60 Number of scatterers: 9520 At special positions: 0 Unit cell: (91.8, 119, 140.25, 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 66 16.00 O 1765 8.00 N 1631 7.00 C 6058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 54 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 55 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 39.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.732A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.593A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.662A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.635A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.754A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.501A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.693A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.759A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.645A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.509A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'D' and resid 34 through 66 removed outlier: 4.132A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE D 64 " --> pdb=" O TRP D 60 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 removed outlier: 3.702A pdb=" N PHE D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 4.105A pdb=" N LEU D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 110 Processing helix chain 'D' and resid 111 through 139 removed outlier: 3.856A pdb=" N LEU D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 removed outlier: 3.769A pdb=" N CYS D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 174 removed outlier: 3.616A pdb=" N TRP D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 195 through 209 removed outlier: 3.600A pdb=" N GLU D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 232 removed outlier: 4.110A pdb=" N ARG D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 268 removed outlier: 3.545A pdb=" N LYS D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Proline residue: D 257 - end of helix Processing helix chain 'D' and resid 272 through 280 removed outlier: 3.507A pdb=" N LYS D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 303 removed outlier: 4.394A pdb=" N ASN D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Proline residue: D 297 - end of helix removed outlier: 3.946A pdb=" N TYR D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 301 " --> pdb=" O PRO D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 removed outlier: 3.735A pdb=" N SER D 314 " --> pdb=" O ARG D 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 33 through 39 removed outlier: 3.584A pdb=" N ALA E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 63 removed outlier: 3.933A pdb=" N ALA E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.722A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.948A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.832A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.730A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.635A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.693A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.520A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.798A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.711A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL S 37 " --> pdb=" O TYR S 95 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.009A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'D' and resid 175 through 180 450 hydrogen bonds defined for protein. 1275 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: 2.58 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3080 1.35 - 1.46: 2350 1.46 - 1.58: 4195 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 9716 Sorted by residual: bond pdb=" N TYR D 258 " pdb=" CA TYR D 258 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.45e+00 bond pdb=" C LEU D 256 " pdb=" N PRO D 257 " ideal model delta sigma weight residual 1.335 1.365 -0.029 1.30e-02 5.92e+03 5.11e+00 bond pdb=" N TYR D 290 " pdb=" CA TYR D 290 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.35e-02 5.49e+03 4.96e+00 bond pdb=" N GLN E 71 " pdb=" CA GLN E 71 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.21e-02 6.83e+03 4.60e+00 bond pdb=" N ILE D 291 " pdb=" CA ILE D 291 " ideal model delta sigma weight residual 1.458 1.485 -0.028 1.41e-02 5.03e+03 3.88e+00 ... (remaining 9711 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.55: 208 106.55 - 113.42: 5326 113.42 - 120.30: 3485 120.30 - 127.17: 4039 127.17 - 134.05: 102 Bond angle restraints: 13160 Sorted by residual: angle pdb=" N ILE D 291 " pdb=" CA ILE D 291 " pdb=" C ILE D 291 " ideal model delta sigma weight residual 112.04 105.77 6.27 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PHE D 182 " pdb=" C PHE D 182 " pdb=" O PHE D 182 " ideal model delta sigma weight residual 119.99 116.42 3.57 8.70e-01 1.32e+00 1.68e+01 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" CA TYR D 258 " pdb=" CB TYR D 258 " pdb=" CG TYR D 258 " ideal model delta sigma weight residual 113.90 119.41 -5.51 1.80e+00 3.09e-01 9.36e+00 angle pdb=" CA TYR D 258 " pdb=" C TYR D 258 " pdb=" O TYR D 258 " ideal model delta sigma weight residual 120.90 117.72 3.18 1.07e+00 8.73e-01 8.85e+00 ... (remaining 13155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5326 17.63 - 35.26: 393 35.26 - 52.89: 61 52.89 - 70.52: 7 70.52 - 88.15: 7 Dihedral angle restraints: 5794 sinusoidal: 2265 harmonic: 3529 Sorted by residual: dihedral pdb=" CB CYS E 21 " pdb=" SG CYS E 21 " pdb=" SG CYS E 47 " pdb=" CB CYS E 47 " ideal model delta sinusoidal sigma weight residual -86.00 -117.28 31.28 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CA LEU D 173 " pdb=" C LEU D 173 " pdb=" N TYR D 174 " pdb=" CA TYR D 174 " ideal model delta harmonic sigma weight residual -180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CG ARG A 32 " pdb=" CD ARG A 32 " pdb=" NE ARG A 32 " pdb=" CZ ARG A 32 " ideal model delta sinusoidal sigma weight residual 90.00 41.03 48.97 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 5791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 989 0.035 - 0.070: 368 0.070 - 0.105: 105 0.105 - 0.140: 33 0.140 - 0.175: 4 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA MET S 83 " pdb=" N MET S 83 " pdb=" C MET S 83 " pdb=" CB MET S 83 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA PHE D 182 " pdb=" N PHE D 182 " pdb=" C PHE D 182 " pdb=" CB PHE D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1496 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 181 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C TYR D 181 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR D 181 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE D 182 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 296 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO D 297 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 297 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 297 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 257 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C PRO D 257 " 0.035 2.00e-02 2.50e+03 pdb=" O PRO D 257 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR D 258 " -0.012 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 145 2.69 - 3.24: 8707 3.24 - 3.80: 13735 3.80 - 4.35: 18098 4.35 - 4.90: 31333 Nonbonded interactions: 72018 Sorted by model distance: nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.139 2.440 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.239 2.520 nonbonded pdb=" O PHE S 32 " pdb=" NH2 ARG S 72 " model vdw 2.240 2.520 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.256 2.440 nonbonded pdb=" OE2 GLU D 199 " pdb=" NZ LYS E 68 " model vdw 2.267 2.520 ... (remaining 72013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 4.190 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.820 Find NCS groups from input model: 0.280 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.002 0.033 9716 Z= 0.157 Angle : 0.583 7.404 13160 Z= 0.336 Chirality : 0.041 0.175 1499 Planarity : 0.004 0.060 1664 Dihedral : 12.471 88.151 3499 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.19 % Allowed : 0.10 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.58 (0.25), residues: 1202 helix: 2.07 (0.26), residues: 427 sheet: 0.72 (0.32), residues: 284 loop : -1.41 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS S 35 PHE 0.017 0.002 PHE S 68 TYR 0.024 0.001 TYR D 258 ARG 0.010 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6862 (ttp80) cc_final: 0.6516 (ttp80) REVERT: A 197 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7434 (ttmm) REVERT: A 309 ASP cc_start: 0.6446 (m-30) cc_final: 0.6067 (m-30) REVERT: B 42 ARG cc_start: 0.7370 (tmm160) cc_final: 0.7117 (tmm-80) REVERT: B 155 ASN cc_start: 0.7615 (t0) cc_final: 0.6985 (t0) REVERT: D 137 LEU cc_start: 0.7689 (tp) cc_final: 0.7437 (tp) REVERT: D 193 SER cc_start: 0.8699 (m) cc_final: 0.8414 (m) outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 0.9638 time to fit residues: 253.9377 Evaluate side-chains 225 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 258 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.0770 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN A 347 ASN B 62 HIS B 110 ASN B 125 ASN B 230 ASN B 237 ASN B 239 ASN B 293 ASN S 194 ASN D 77 ASN D 194 HIS E 71 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9716 Z= 0.192 Angle : 0.535 7.208 13160 Z= 0.278 Chirality : 0.041 0.142 1499 Planarity : 0.004 0.041 1664 Dihedral : 3.989 22.441 1320 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.12 % Allowed : 10.13 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.73 (0.25), residues: 1202 helix: 2.26 (0.26), residues: 432 sheet: 0.62 (0.31), residues: 294 loop : -1.33 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.002 PHE B 199 TYR 0.019 0.001 TYR D 258 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7620 (ttmm) REVERT: A 240 MET cc_start: 0.7033 (pp-130) cc_final: 0.6796 (pp-130) REVERT: A 309 ASP cc_start: 0.6426 (m-30) cc_final: 0.5984 (m-30) REVERT: D 193 SER cc_start: 0.8606 (m) cc_final: 0.8314 (m) outliers start: 22 outliers final: 7 residues processed: 212 average time/residue: 1.0743 time to fit residues: 244.7684 Evaluate side-chains 201 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 347 ASN B 155 ASN B 237 ASN D 77 ASN D 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9716 Z= 0.257 Angle : 0.562 7.844 13160 Z= 0.292 Chirality : 0.042 0.170 1499 Planarity : 0.004 0.042 1664 Dihedral : 4.145 20.315 1318 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.80 % Allowed : 12.63 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.69 (0.24), residues: 1202 helix: 2.20 (0.26), residues: 433 sheet: 0.61 (0.31), residues: 294 loop : -1.35 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS S 35 PHE 0.018 0.002 PHE B 199 TYR 0.024 0.002 TYR D 258 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.6383 (t0) cc_final: 0.6050 (t0) REVERT: A 276 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.6139 (mt-10) REVERT: A 294 ASN cc_start: 0.8076 (t0) cc_final: 0.7820 (t0) REVERT: A 316 THR cc_start: 0.7856 (m) cc_final: 0.7623 (p) REVERT: A 345 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8131 (tttt) REVERT: B 42 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7183 (tmm-80) REVERT: B 90 VAL cc_start: 0.8192 (t) cc_final: 0.7923 (m) REVERT: B 155 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7774 (t0) REVERT: D 68 ARG cc_start: 0.6942 (mmt90) cc_final: 0.6691 (mmt90) REVERT: D 137 LEU cc_start: 0.7917 (tp) cc_final: 0.7710 (tp) REVERT: D 271 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7742 (p) outliers start: 29 outliers final: 17 residues processed: 204 average time/residue: 1.1661 time to fit residues: 256.2468 Evaluate side-chains 208 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 0.0020 chunk 52 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 255 ASN B 155 ASN B 237 ASN D 77 ASN D 101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9716 Z= 0.200 Angle : 0.528 8.495 13160 Z= 0.274 Chirality : 0.041 0.149 1499 Planarity : 0.004 0.049 1664 Dihedral : 4.029 22.751 1318 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.09 % Allowed : 13.89 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.77 (0.24), residues: 1202 helix: 2.29 (0.25), residues: 433 sheet: 0.68 (0.31), residues: 289 loop : -1.34 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.002 PHE B 199 TYR 0.018 0.001 TYR D 258 ARG 0.009 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7838 (ttmm) cc_final: 0.7458 (ttmm) REVERT: A 276 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6196 (mt-10) REVERT: A 294 ASN cc_start: 0.8071 (t0) cc_final: 0.7827 (t0) REVERT: B 90 VAL cc_start: 0.8192 (t) cc_final: 0.7928 (m) REVERT: B 129 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.5662 (tpm170) REVERT: S 83 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6091 (mpp) REVERT: D 68 ARG cc_start: 0.6928 (mmt90) cc_final: 0.6699 (mmt90) REVERT: D 120 MET cc_start: 0.7207 (mmm) cc_final: 0.6758 (mtt) REVERT: D 137 LEU cc_start: 0.7832 (tp) cc_final: 0.7602 (tp) REVERT: D 271 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7748 (p) REVERT: D 274 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7894 (p) outliers start: 32 outliers final: 19 residues processed: 198 average time/residue: 0.9416 time to fit residues: 202.7175 Evaluate side-chains 201 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 255 ASN A 331 ASN A 347 ASN B 155 ASN B 237 ASN D 77 ASN D 194 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9716 Z= 0.199 Angle : 0.528 9.639 13160 Z= 0.273 Chirality : 0.041 0.184 1499 Planarity : 0.004 0.052 1664 Dihedral : 4.011 23.184 1318 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.28 % Allowed : 14.95 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.82 (0.24), residues: 1202 helix: 2.34 (0.25), residues: 433 sheet: 0.62 (0.31), residues: 296 loop : -1.28 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.002 PHE B 199 TYR 0.018 0.001 TYR D 258 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7836 (ttmm) cc_final: 0.7510 (ttmm) REVERT: A 240 MET cc_start: 0.7450 (ppp) cc_final: 0.6791 (ppp) REVERT: A 276 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6226 (mt-10) REVERT: A 294 ASN cc_start: 0.8133 (t0) cc_final: 0.7906 (t0) REVERT: B 90 VAL cc_start: 0.8154 (t) cc_final: 0.7914 (m) REVERT: D 68 ARG cc_start: 0.6927 (mmt90) cc_final: 0.6701 (mmt90) REVERT: D 120 MET cc_start: 0.7176 (mmm) cc_final: 0.6806 (mtt) REVERT: D 271 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7735 (p) outliers start: 34 outliers final: 24 residues processed: 196 average time/residue: 0.8943 time to fit residues: 191.4391 Evaluate side-chains 206 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.0980 chunk 104 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.0060 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.0570 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 255 ASN A 331 ASN A 347 ASN B 155 ASN B 237 ASN D 71 ASN D 77 ASN D 194 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9716 Z= 0.133 Angle : 0.488 8.553 13160 Z= 0.251 Chirality : 0.040 0.151 1499 Planarity : 0.003 0.039 1664 Dihedral : 3.782 23.799 1318 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.99 % Allowed : 15.43 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.97 (0.25), residues: 1202 helix: 2.52 (0.25), residues: 433 sheet: 0.75 (0.31), residues: 299 loop : -1.30 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR S 228 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6915 (ttp80) cc_final: 0.6586 (ttp80) REVERT: A 197 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7491 (ttmm) REVERT: A 277 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7205 (mtpt) REVERT: D 68 ARG cc_start: 0.6902 (mmt90) cc_final: 0.6698 (mmt90) REVERT: D 120 MET cc_start: 0.7050 (mmm) cc_final: 0.6766 (mtt) REVERT: D 310 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6804 (mtp85) outliers start: 31 outliers final: 16 residues processed: 199 average time/residue: 0.9395 time to fit residues: 203.2121 Evaluate side-chains 205 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 310 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN A 331 ASN A 347 ASN B 220 GLN B 237 ASN D 77 ASN D 194 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9716 Z= 0.300 Angle : 0.578 8.568 13160 Z= 0.301 Chirality : 0.043 0.191 1499 Planarity : 0.004 0.039 1664 Dihedral : 4.124 21.358 1318 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.80 % Allowed : 16.49 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.81 (0.24), residues: 1202 helix: 2.29 (0.25), residues: 434 sheet: 0.64 (0.31), residues: 300 loop : -1.28 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 161 HIS 0.006 0.001 HIS S 35 PHE 0.020 0.002 PHE B 199 TYR 0.026 0.002 TYR D 258 ARG 0.006 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.6399 (t0) cc_final: 0.6041 (t0) REVERT: D 120 MET cc_start: 0.7161 (mmm) cc_final: 0.6908 (mtt) REVERT: D 310 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6812 (mtp85) outliers start: 29 outliers final: 22 residues processed: 193 average time/residue: 0.9600 time to fit residues: 201.0899 Evaluate side-chains 202 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 310 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 155 ASN B 237 ASN D 194 HIS D 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9716 Z= 0.330 Angle : 0.595 8.902 13160 Z= 0.311 Chirality : 0.044 0.204 1499 Planarity : 0.004 0.040 1664 Dihedral : 4.254 22.410 1318 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.38 % Allowed : 16.39 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.70 (0.24), residues: 1202 helix: 2.22 (0.25), residues: 428 sheet: 0.59 (0.31), residues: 300 loop : -1.32 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 161 HIS 0.007 0.001 HIS S 35 PHE 0.020 0.003 PHE B 199 TYR 0.028 0.002 TYR D 258 ARG 0.008 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7514 (ttmm) REVERT: A 245 GLU cc_start: 0.6464 (mm-30) cc_final: 0.6262 (mm-30) REVERT: A 261 ASP cc_start: 0.6420 (t0) cc_final: 0.6051 (t0) REVERT: D 120 MET cc_start: 0.7164 (mmm) cc_final: 0.6897 (mtt) REVERT: D 271 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7902 (p) REVERT: D 310 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.6801 (mtp85) outliers start: 35 outliers final: 27 residues processed: 205 average time/residue: 1.1047 time to fit residues: 244.3510 Evaluate side-chains 214 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 310 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 331 ASN B 155 ASN B 237 ASN D 77 ASN D 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9716 Z= 0.181 Angle : 0.525 9.215 13160 Z= 0.272 Chirality : 0.041 0.166 1499 Planarity : 0.004 0.041 1664 Dihedral : 4.001 25.540 1318 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.99 % Allowed : 16.97 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.88 (0.25), residues: 1202 helix: 2.49 (0.25), residues: 426 sheet: 0.67 (0.31), residues: 301 loop : -1.32 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.002 PHE B 199 TYR 0.016 0.001 TYR D 258 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7492 (ttmm) REVERT: B 119 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7561 (m-40) REVERT: D 52 VAL cc_start: 0.7881 (t) cc_final: 0.7622 (t) REVERT: D 120 MET cc_start: 0.7085 (mmm) cc_final: 0.6832 (mtt) REVERT: D 271 SER cc_start: 0.8153 (t) cc_final: 0.7838 (p) REVERT: D 310 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6741 (mtp85) outliers start: 31 outliers final: 22 residues processed: 193 average time/residue: 0.9703 time to fit residues: 203.0946 Evaluate side-chains 203 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 310 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 0.1980 chunk 110 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 331 ASN A 347 ASN B 155 ASN D 77 ASN D 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9716 Z= 0.232 Angle : 0.558 9.807 13160 Z= 0.288 Chirality : 0.042 0.229 1499 Planarity : 0.004 0.039 1664 Dihedral : 4.054 24.287 1318 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.60 % Allowed : 18.13 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.24), residues: 1202 helix: 2.44 (0.25), residues: 428 sheet: 0.62 (0.31), residues: 301 loop : -1.30 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 161 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.002 PHE B 199 TYR 0.021 0.002 TYR D 258 ARG 0.008 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7488 (ttmm) REVERT: A 261 ASP cc_start: 0.6380 (t0) cc_final: 0.6024 (t0) REVERT: A 277 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7563 (mtpt) REVERT: B 119 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7573 (m-40) REVERT: D 52 VAL cc_start: 0.7871 (t) cc_final: 0.7631 (t) REVERT: D 120 MET cc_start: 0.7100 (mmm) cc_final: 0.6870 (mtt) REVERT: D 271 SER cc_start: 0.8184 (t) cc_final: 0.7860 (p) REVERT: D 310 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6767 (mtp85) outliers start: 27 outliers final: 24 residues processed: 201 average time/residue: 1.0627 time to fit residues: 230.2122 Evaluate side-chains 212 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 310 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 347 ASN B 155 ASN D 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111011 restraints weight = 13033.221| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.07 r_work: 0.3295 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9716 Z= 0.210 Angle : 0.547 9.935 13160 Z= 0.282 Chirality : 0.041 0.184 1499 Planarity : 0.004 0.039 1664 Dihedral : 4.018 24.406 1318 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.89 % Allowed : 18.03 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.25), residues: 1202 helix: 2.49 (0.25), residues: 427 sheet: 0.58 (0.31), residues: 307 loop : -1.34 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.002 PHE B 199 TYR 0.019 0.001 TYR D 258 ARG 0.008 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4049.61 seconds wall clock time: 72 minutes 22.51 seconds (4342.51 seconds total)