Starting phenix.real_space_refine on Fri Mar 15 00:41:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/03_2024/8hsc_34993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/03_2024/8hsc_34993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/03_2024/8hsc_34993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/03_2024/8hsc_34993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/03_2024/8hsc_34993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/03_2024/8hsc_34993.pdb" } resolution = 3.22 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= 0.001 sd= 0.022 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 70 5.16 5 C 6469 2.51 5 N 1751 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 147": "OD1" <-> "OD2" Residue "R PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 74": "OD1" <-> "OD2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10180 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 747 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 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: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2008 Classifications: {'peptide': 273} Incomplete info: {'n_c_alpha_c_only': 11, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.74, per 1000 atoms: 0.56 Number of scatterers: 10180 At special positions: 0 Unit cell: (92.352, 121.472, 158.912, 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 70 16.00 O 1890 8.00 N 1751 7.00 C 6469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 309 " - pdb=" SG CYS E 374 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 122 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.75 Conformation dependent library (CDL) restraints added in 1.8 seconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 19 sheets defined 31.7% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.659A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.162A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.579A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.820A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.897A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.514A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'F' and resid 47 through 51 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'R' and resid 33 through 43 removed outlier: 3.947A pdb=" N GLU R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 49 removed outlier: 4.294A pdb=" N THR R 48 " --> pdb=" O GLU R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 79 removed outlier: 4.346A pdb=" N VAL R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 116 Proline residue: R 107 - end of helix removed outlier: 4.291A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA R 111 " --> pdb=" O PRO R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 130 through 133 removed outlier: 3.686A pdb=" N ASN R 133 " --> pdb=" O TYR R 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 130 through 133' Processing helix chain 'R' and resid 138 through 153 Processing helix chain 'R' and resid 162 through 183 removed outlier: 4.370A pdb=" N CYS R 166 " --> pdb=" O ARG R 162 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA R 167 " --> pdb=" O GLN R 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY R 179 " --> pdb=" O TRP R 175 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA R 180 " --> pdb=" O LEU R 176 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 205 removed outlier: 3.815A pdb=" N THR R 201 " --> pdb=" O VAL R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 223 removed outlier: 3.561A pdb=" N ARG R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 254 removed outlier: 3.870A pdb=" N MET R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL R 246 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 264 removed outlier: 3.812A pdb=" N HIS R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 282 removed outlier: 3.716A pdb=" N TYR R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 removed outlier: 3.733A pdb=" N ASN R 289 " --> pdb=" O LEU R 285 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER R 290 " --> pdb=" O SER R 286 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS R 291 " --> pdb=" O SER R 287 " (cutoff:3.500A) Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 311 removed outlier: 3.906A pdb=" N ALA R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR R 307 " --> pdb=" O GLY R 303 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL R 308 " --> pdb=" O PHE R 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.559A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.145A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.156A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 292 through 293 Processing sheet with id=AA2, first strand: chain 'E' and resid 297 through 298 removed outlier: 6.990A pdb=" N LEU E 297 " --> pdb=" O GLU E 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 330 through 334 removed outlier: 5.095A pdb=" N LEU E 332 " --> pdb=" O GLN E 323 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN E 323 " --> pdb=" O LEU E 332 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.616A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.753A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.062A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.737A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 150 through 151 removed outlier: 6.520A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.136A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.939A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AB4, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.522A pdb=" N GLU F 29 " --> pdb=" O MET F 137 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR F 139 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE F 53 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE F 69 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.522A pdb=" N GLU F 29 " --> pdb=" O MET F 137 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR F 139 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR F 131 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.052A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.052A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AC1, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.734A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1281 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: 2.90 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2587 1.33 - 1.46: 3257 1.46 - 1.60: 4449 1.60 - 1.73: 0 1.73 - 1.86: 98 Bond restraints: 10391 Sorted by residual: bond pdb=" CG ASN R 94 " pdb=" OD1 ASN R 94 " ideal model delta sigma weight residual 1.231 1.199 0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " ideal model delta sigma weight residual 1.808 1.861 -0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" C THR R 86 " pdb=" N PRO R 87 " ideal model delta sigma weight residual 1.334 1.357 -0.023 1.51e-02 4.39e+03 2.31e+00 bond pdb=" CG ASN R 94 " pdb=" ND2 ASN R 94 " ideal model delta sigma weight residual 1.328 1.297 0.031 2.10e-02 2.27e+03 2.18e+00 bond pdb=" CG ARG C 62 " pdb=" CD ARG C 62 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.84e+00 ... (remaining 10386 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.48: 158 105.48 - 112.64: 5427 112.64 - 119.80: 3409 119.80 - 126.95: 4969 126.95 - 134.11: 125 Bond angle restraints: 14088 Sorted by residual: angle pdb=" C LYS S 76 " pdb=" N ASN S 77 " pdb=" CA ASN S 77 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CA CYS R 119 " pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " ideal model delta sigma weight residual 114.40 123.17 -8.77 2.30e+00 1.89e-01 1.45e+01 angle pdb=" CG ARG C 62 " pdb=" CD ARG C 62 " pdb=" NE ARG C 62 " ideal model delta sigma weight residual 112.00 119.76 -7.76 2.20e+00 2.07e-01 1.24e+01 angle pdb=" CB MET C 21 " pdb=" CG MET C 21 " pdb=" SD MET C 21 " ideal model delta sigma weight residual 112.70 122.98 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA GLN E 375 " pdb=" CB GLN E 375 " pdb=" CG GLN E 375 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 ... (remaining 14083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5142 17.94 - 35.88: 732 35.88 - 53.82: 197 53.82 - 71.75: 42 71.75 - 89.69: 13 Dihedral angle restraints: 6126 sinusoidal: 2271 harmonic: 3855 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ASN R 133 " pdb=" C ASN R 133 " pdb=" N MET R 134 " pdb=" CA MET R 134 " ideal model delta harmonic sigma weight residual -180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ARG R 117 " pdb=" C ARG R 117 " pdb=" N GLY R 118 " pdb=" CA GLY R 118 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 6123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1334 0.057 - 0.115: 245 0.115 - 0.172: 26 0.172 - 0.229: 8 0.229 - 0.287: 1 Chirality restraints: 1614 Sorted by residual: chirality pdb=" CG LEU B 210 " pdb=" CB LEU B 210 " pdb=" CD1 LEU B 210 " pdb=" CD2 LEU B 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB THR R 98 " pdb=" CA THR R 98 " pdb=" OG1 THR R 98 " pdb=" CG2 THR R 98 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU R 132 " pdb=" CB LEU R 132 " pdb=" CD1 LEU R 132 " pdb=" CD2 LEU R 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1611 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 86 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO R 87 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 87 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 87 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 140 " -0.023 2.00e-02 2.50e+03 1.77e-02 5.50e+00 pdb=" CG PHE R 140 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE R 140 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE R 140 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE R 140 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE R 140 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE R 140 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 173 " 0.010 2.00e-02 2.50e+03 1.51e-02 3.97e+00 pdb=" CG PHE R 173 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE R 173 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE R 173 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 173 " -0.000 2.00e-02 2.50e+03 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 400 2.71 - 3.26: 9543 3.26 - 3.80: 16632 3.80 - 4.35: 20168 4.35 - 4.90: 35260 Nonbonded interactions: 82003 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.161 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.228 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.234 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.247 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.264 2.440 ... (remaining 81998 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: 1.240 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: 0.000 Extract box with map and model: 5.480 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.860 Find NCS groups from input model: 0.270 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 0.053 10391 Z= 0.232 Angle : 0.696 10.276 14088 Z= 0.365 Chirality : 0.047 0.287 1614 Planarity : 0.005 0.067 1783 Dihedral : 18.311 89.693 3639 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.47 % Allowed : 36.23 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.23), residues: 1323 helix: -0.69 (0.26), residues: 361 sheet: -0.45 (0.26), residues: 390 loop : -1.08 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 267 HIS 0.005 0.001 HIS S 35 PHE 0.034 0.002 PHE R 173 TYR 0.024 0.002 TYR A 302 ARG 0.012 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8579 (tpp) cc_final: 0.8376 (tpp) REVERT: A 261 ASP cc_start: 0.8820 (p0) cc_final: 0.8584 (p0) REVERT: B 59 TYR cc_start: 0.8919 (m-80) cc_final: 0.8716 (m-80) REVERT: S 208 GLU cc_start: 0.8087 (mp0) cc_final: 0.7696 (mp0) outliers start: 5 outliers final: 3 residues processed: 173 average time/residue: 0.2172 time to fit residues: 53.1026 Evaluate side-chains 173 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain S residue 74 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN A 269 ASN A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN C 11 GLN R 273 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10391 Z= 0.341 Angle : 0.585 6.965 14088 Z= 0.313 Chirality : 0.043 0.178 1614 Planarity : 0.004 0.058 1783 Dihedral : 5.006 59.758 1451 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.98 % Allowed : 32.21 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.95 (0.23), residues: 1323 helix: 0.12 (0.28), residues: 371 sheet: -0.50 (0.26), residues: 386 loop : -1.11 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.006 0.001 HIS B 91 PHE 0.013 0.002 PHE B 241 TYR 0.022 0.002 TYR S 223 ARG 0.005 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 177 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: A 184 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8917 (tt) REVERT: A 302 TYR cc_start: 0.8597 (t80) cc_final: 0.8305 (t80) REVERT: A 306 GLN cc_start: 0.7913 (tt0) cc_final: 0.7566 (tt0) REVERT: B 59 TYR cc_start: 0.9113 (m-80) cc_final: 0.8813 (m-80) REVERT: C 58 GLU cc_start: 0.8494 (pm20) cc_final: 0.8225 (pm20) REVERT: F 58 GLN cc_start: 0.6855 (tm-30) cc_final: 0.6614 (tm-30) REVERT: F 117 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.7273 (ttp80) REVERT: R 175 TRP cc_start: 0.7047 (m100) cc_final: 0.6799 (m100) REVERT: S 221 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8234 (tt) outliers start: 64 outliers final: 35 residues processed: 218 average time/residue: 0.2190 time to fit residues: 66.8697 Evaluate side-chains 209 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN C 11 GLN R 273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10391 Z= 0.368 Angle : 0.593 7.002 14088 Z= 0.317 Chirality : 0.043 0.173 1614 Planarity : 0.004 0.052 1783 Dihedral : 4.893 44.981 1449 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 7.38 % Allowed : 32.31 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.96 (0.23), residues: 1323 helix: 0.39 (0.28), residues: 374 sheet: -0.72 (0.26), residues: 381 loop : -1.17 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 267 HIS 0.005 0.001 HIS B 91 PHE 0.014 0.002 PHE B 241 TYR 0.024 0.002 TYR S 223 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 178 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8664 (t80) cc_final: 0.8404 (t80) REVERT: A 306 GLN cc_start: 0.8009 (tt0) cc_final: 0.7620 (tt0) REVERT: B 59 TYR cc_start: 0.9112 (m-80) cc_final: 0.8832 (m-80) REVERT: B 234 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: F 56 ILE cc_start: 0.8964 (mp) cc_final: 0.8758 (tp) REVERT: F 58 GLN cc_start: 0.7027 (tm-30) cc_final: 0.6818 (tm-30) REVERT: F 105 LEU cc_start: 0.8081 (mt) cc_final: 0.7796 (mp) REVERT: F 117 ARG cc_start: 0.7663 (ttp-170) cc_final: 0.7281 (ttp-170) REVERT: R 78 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6982 (t80) REVERT: R 175 TRP cc_start: 0.7213 (m100) cc_final: 0.6938 (m100) REVERT: S 148 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7672 (ttp-110) outliers start: 79 outliers final: 51 residues processed: 230 average time/residue: 0.2034 time to fit residues: 66.7819 Evaluate side-chains 227 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN C 11 GLN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10391 Z= 0.223 Angle : 0.529 7.069 14088 Z= 0.280 Chirality : 0.041 0.154 1614 Planarity : 0.003 0.050 1783 Dihedral : 4.625 42.554 1449 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 6.72 % Allowed : 32.68 % Favored : 60.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.68 (0.24), residues: 1323 helix: 0.67 (0.29), residues: 372 sheet: -0.45 (0.26), residues: 378 loop : -1.13 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 267 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 173 TYR 0.017 0.001 TYR S 223 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 179 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: A 287 TYR cc_start: 0.8086 (m-80) cc_final: 0.7849 (m-80) REVERT: A 298 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: A 302 TYR cc_start: 0.8648 (t80) cc_final: 0.8363 (t80) REVERT: A 306 GLN cc_start: 0.7978 (tt0) cc_final: 0.7695 (tt0) REVERT: A 314 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7739 (mtpt) REVERT: B 234 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: C 47 GLU cc_start: 0.8479 (pm20) cc_final: 0.8204 (pm20) REVERT: C 58 GLU cc_start: 0.8406 (pm20) cc_final: 0.8175 (pm20) REVERT: F 56 ILE cc_start: 0.8983 (mp) cc_final: 0.8755 (tp) REVERT: F 58 GLN cc_start: 0.7067 (tm-30) cc_final: 0.6860 (tm-30) REVERT: F 105 LEU cc_start: 0.8164 (mt) cc_final: 0.7836 (mp) REVERT: F 117 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.6775 (ttp80) REVERT: R 78 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.7008 (t80) REVERT: R 142 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7480 (t) REVERT: R 175 TRP cc_start: 0.7187 (m100) cc_final: 0.6966 (m100) REVERT: R 261 GLN cc_start: 0.8231 (tp40) cc_final: 0.7839 (tp40) REVERT: S 72 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6498 (ptm-80) outliers start: 72 outliers final: 43 residues processed: 230 average time/residue: 0.2116 time to fit residues: 68.3547 Evaluate side-chains 225 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 64 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN B 183 HIS C 11 GLN R 46 HIS ** R 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.078 10391 Z= 0.675 Angle : 0.753 8.525 14088 Z= 0.402 Chirality : 0.049 0.199 1614 Planarity : 0.005 0.046 1783 Dihedral : 5.289 40.970 1448 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.47 % Favored : 91.46 % Rotamer: Outliers : 10.08 % Allowed : 29.88 % Favored : 60.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.23), residues: 1323 helix: 0.30 (0.28), residues: 371 sheet: -1.04 (0.25), residues: 397 loop : -1.36 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 297 HIS 0.009 0.002 HIS B 91 PHE 0.027 0.003 PHE R 110 TYR 0.036 0.002 TYR S 223 ARG 0.009 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 182 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: E 375 GLN cc_start: 0.6161 (mm110) cc_final: 0.5257 (mm110) REVERT: A 14 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: A 298 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: A 302 TYR cc_start: 0.8750 (t80) cc_final: 0.8514 (t80) REVERT: A 305 CYS cc_start: 0.8325 (m) cc_final: 0.8122 (t) REVERT: A 306 GLN cc_start: 0.8197 (tt0) cc_final: 0.7751 (tt0) REVERT: A 314 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7807 (mtpt) REVERT: B 45 MET cc_start: 0.8800 (mmm) cc_final: 0.8401 (mtt) REVERT: B 59 TYR cc_start: 0.9211 (m-80) cc_final: 0.8911 (m-80) REVERT: B 234 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: B 338 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8741 (mp) REVERT: C 47 GLU cc_start: 0.8682 (pm20) cc_final: 0.8445 (pm20) REVERT: F 42 LYS cc_start: 0.7954 (ptmt) cc_final: 0.7554 (ptpp) REVERT: F 56 ILE cc_start: 0.8974 (mp) cc_final: 0.8702 (tp) REVERT: F 58 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6926 (tm-30) REVERT: F 117 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.6566 (ttp-170) REVERT: R 220 MET cc_start: 0.8470 (mmp) cc_final: 0.8266 (mmp) REVERT: S 43 LYS cc_start: 0.8537 (mppt) cc_final: 0.8260 (mmmm) REVERT: S 72 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7001 (ptm-80) REVERT: S 148 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.7617 (ttp-110) REVERT: S 222 GLU cc_start: 0.5815 (mp0) cc_final: 0.5306 (mp0) outliers start: 108 outliers final: 83 residues processed: 260 average time/residue: 0.1985 time to fit residues: 73.3721 Evaluate side-chains 269 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 180 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 278 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN A 331 ASN C 11 GLN R 46 HIS S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10391 Z= 0.182 Angle : 0.544 7.507 14088 Z= 0.286 Chirality : 0.041 0.151 1614 Planarity : 0.003 0.045 1783 Dihedral : 4.685 39.994 1448 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.60 % Allowed : 34.55 % Favored : 59.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.78 (0.23), residues: 1323 helix: 0.76 (0.29), residues: 372 sheet: -0.60 (0.26), residues: 371 loop : -1.24 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 267 HIS 0.007 0.001 HIS R 46 PHE 0.019 0.001 PHE R 78 TYR 0.016 0.001 TYR S 178 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 188 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 375 GLN cc_start: 0.5918 (mm110) cc_final: 0.5201 (mm110) REVERT: A 298 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: A 306 GLN cc_start: 0.7983 (tt0) cc_final: 0.7707 (tt0) REVERT: A 314 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7758 (mtpt) REVERT: B 234 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: B 338 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8582 (mp) REVERT: C 47 GLU cc_start: 0.8565 (pm20) cc_final: 0.8332 (pm20) REVERT: F 56 ILE cc_start: 0.8994 (mp) cc_final: 0.8706 (tp) REVERT: F 105 LEU cc_start: 0.8055 (mt) cc_final: 0.7804 (mp) REVERT: F 117 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.6773 (ttp80) REVERT: R 142 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7508 (t) REVERT: R 147 ASP cc_start: 0.8763 (t0) cc_final: 0.8541 (t0) REVERT: S 43 LYS cc_start: 0.8386 (mppt) cc_final: 0.8117 (mmmm) REVERT: S 72 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6638 (ptm-80) outliers start: 60 outliers final: 41 residues processed: 235 average time/residue: 0.2128 time to fit residues: 70.3818 Evaluate side-chains 229 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 182 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN A 331 ASN C 11 GLN R 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10391 Z= 0.235 Angle : 0.559 8.174 14088 Z= 0.294 Chirality : 0.042 0.215 1614 Planarity : 0.004 0.043 1783 Dihedral : 4.621 40.434 1448 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.26 % Allowed : 33.71 % Favored : 60.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.72 (0.24), residues: 1323 helix: 0.71 (0.28), residues: 372 sheet: -0.54 (0.26), residues: 382 loop : -1.15 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 297 HIS 0.004 0.001 HIS S 35 PHE 0.023 0.001 PHE R 140 TYR 0.018 0.001 TYR S 223 ARG 0.003 0.000 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 184 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: E 375 GLN cc_start: 0.6168 (mm110) cc_final: 0.5503 (mm110) REVERT: A 298 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: A 314 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7731 (mtpt) REVERT: B 45 MET cc_start: 0.8686 (mtp) cc_final: 0.8310 (mtt) REVERT: B 234 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: B 318 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8565 (mp) REVERT: B 338 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 47 GLU cc_start: 0.8569 (pm20) cc_final: 0.8349 (pm20) REVERT: F 56 ILE cc_start: 0.9003 (mp) cc_final: 0.8668 (tp) REVERT: F 105 LEU cc_start: 0.8079 (mt) cc_final: 0.7803 (mp) REVERT: F 117 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.6740 (ttp80) REVERT: R 57 MET cc_start: 0.8356 (mmm) cc_final: 0.8137 (mmm) REVERT: R 142 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7470 (t) REVERT: R 147 ASP cc_start: 0.8729 (t0) cc_final: 0.8485 (t0) REVERT: S 43 LYS cc_start: 0.8366 (mppt) cc_final: 0.8099 (mmmm) REVERT: S 72 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6490 (ptm-80) outliers start: 67 outliers final: 52 residues processed: 236 average time/residue: 0.2102 time to fit residues: 70.3172 Evaluate side-chains 240 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 181 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 114 optimal weight: 0.4980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10391 Z= 0.338 Angle : 0.599 8.659 14088 Z= 0.316 Chirality : 0.044 0.224 1614 Planarity : 0.004 0.043 1783 Dihedral : 4.773 40.415 1448 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 7.66 % Allowed : 32.21 % Favored : 60.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.23), residues: 1323 helix: 0.63 (0.28), residues: 372 sheet: -0.67 (0.25), residues: 386 loop : -1.21 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 297 HIS 0.005 0.001 HIS B 183 PHE 0.046 0.002 PHE R 140 TYR 0.023 0.002 TYR S 223 ARG 0.004 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 189 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 375 GLN cc_start: 0.6140 (mm110) cc_final: 0.5635 (mm110) REVERT: A 287 TYR cc_start: 0.8061 (m-80) cc_final: 0.7816 (m-80) REVERT: A 298 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: A 306 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: A 314 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7765 (mtpt) REVERT: B 45 MET cc_start: 0.8741 (mtp) cc_final: 0.8466 (mtt) REVERT: B 59 TYR cc_start: 0.9148 (m-80) cc_final: 0.8830 (m-80) REVERT: B 234 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: B 260 GLU cc_start: 0.8421 (tt0) cc_final: 0.8212 (tt0) REVERT: B 318 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 338 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8636 (mp) REVERT: F 42 LYS cc_start: 0.7966 (ptmt) cc_final: 0.7544 (ptpp) REVERT: F 56 ILE cc_start: 0.9024 (mp) cc_final: 0.8671 (tp) REVERT: F 65 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7419 (mmtm) REVERT: F 105 LEU cc_start: 0.8085 (mt) cc_final: 0.7801 (mp) REVERT: F 117 ARG cc_start: 0.7698 (ttp-170) cc_final: 0.6677 (ttp80) REVERT: R 147 ASP cc_start: 0.8736 (t0) cc_final: 0.8500 (t0) REVERT: S 43 LYS cc_start: 0.8407 (mppt) cc_final: 0.8101 (mmmm) REVERT: S 72 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6555 (ptm-80) outliers start: 82 outliers final: 56 residues processed: 253 average time/residue: 0.2171 time to fit residues: 77.9410 Evaluate side-chains 251 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 188 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 0.049 10391 Z= 0.280 Angle : 0.586 9.304 14088 Z= 0.309 Chirality : 0.043 0.206 1614 Planarity : 0.004 0.043 1783 Dihedral : 4.686 40.204 1448 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 6.35 % Allowed : 33.43 % Favored : 60.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1323 helix: 0.62 (0.28), residues: 372 sheet: -0.64 (0.25), residues: 386 loop : -1.16 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 267 HIS 0.004 0.001 HIS B 183 PHE 0.038 0.002 PHE R 140 TYR 0.022 0.002 TYR A 302 ARG 0.003 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 187 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 375 GLN cc_start: 0.6100 (mm110) cc_final: 0.5649 (mm110) REVERT: A 14 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: A 287 TYR cc_start: 0.8098 (m-80) cc_final: 0.7857 (m-80) REVERT: A 298 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: A 306 GLN cc_start: 0.7974 (tt0) cc_final: 0.7672 (tt0) REVERT: A 314 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7696 (mtpt) REVERT: B 45 MET cc_start: 0.8761 (mtp) cc_final: 0.8504 (mtt) REVERT: B 59 TYR cc_start: 0.9129 (m-80) cc_final: 0.8724 (m-80) REVERT: B 234 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: B 318 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 338 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8587 (mp) REVERT: F 42 LYS cc_start: 0.8008 (ptmt) cc_final: 0.7569 (ptpp) REVERT: F 56 ILE cc_start: 0.9008 (mp) cc_final: 0.8612 (tp) REVERT: F 105 LEU cc_start: 0.8089 (mt) cc_final: 0.7814 (mp) REVERT: F 117 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.6699 (ttp80) REVERT: R 57 MET cc_start: 0.8331 (mmm) cc_final: 0.8099 (mmm) REVERT: S 43 LYS cc_start: 0.8383 (mppt) cc_final: 0.8100 (mmmm) REVERT: S 72 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6464 (ptm-80) outliers start: 68 outliers final: 58 residues processed: 238 average time/residue: 0.2100 time to fit residues: 70.8089 Evaluate side-chains 249 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 184 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 130 optimal weight: 0.0000 chunk 120 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10391 Z= 0.313 Angle : 0.607 9.482 14088 Z= 0.319 Chirality : 0.044 0.213 1614 Planarity : 0.004 0.043 1783 Dihedral : 4.746 40.392 1448 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 6.07 % Allowed : 33.71 % Favored : 60.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.84 (0.23), residues: 1323 helix: 0.61 (0.28), residues: 372 sheet: -0.64 (0.25), residues: 386 loop : -1.20 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 267 HIS 0.005 0.001 HIS B 183 PHE 0.033 0.002 PHE R 140 TYR 0.023 0.002 TYR A 302 ARG 0.004 0.000 ARG C 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 182 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 375 GLN cc_start: 0.6107 (mm110) cc_final: 0.5602 (mm110) REVERT: A 14 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 298 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: A 306 GLN cc_start: 0.8013 (tt0) cc_final: 0.7699 (tt0) REVERT: A 314 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7757 (mtpt) REVERT: B 234 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: B 318 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8565 (mp) REVERT: B 338 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 47 GLU cc_start: 0.8623 (pm20) cc_final: 0.8178 (pm20) REVERT: F 42 LYS cc_start: 0.7997 (ptmt) cc_final: 0.7569 (ptpp) REVERT: F 65 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7672 (mmtm) REVERT: F 117 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.6652 (ttp80) REVERT: S 43 LYS cc_start: 0.8385 (mppt) cc_final: 0.8068 (mmmm) REVERT: S 72 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6480 (ptm-80) outliers start: 65 outliers final: 56 residues processed: 232 average time/residue: 0.2094 time to fit residues: 68.5625 Evaluate side-chains 245 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 182 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 227 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.164469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.113197 restraints weight = 13981.907| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.94 r_work: 0.3388 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10391 Z= 0.191 Angle : 0.561 9.648 14088 Z= 0.293 Chirality : 0.042 0.180 1614 Planarity : 0.003 0.045 1783 Dihedral : 4.488 40.461 1448 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.23 % Allowed : 34.55 % Favored : 60.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.64 (0.24), residues: 1323 helix: 0.73 (0.28), residues: 372 sheet: -0.46 (0.26), residues: 381 loop : -1.09 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 267 HIS 0.005 0.001 HIS S 35 PHE 0.025 0.001 PHE R 140 TYR 0.023 0.001 TYR A 302 ARG 0.002 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.95 seconds wall clock time: 46 minutes 56.23 seconds (2816.23 seconds total)