Starting phenix.real_space_refine on Sat Aug 3 14:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/08_2024/8wc4_37430_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/08_2024/8wc4_37430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/08_2024/8wc4_37430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/08_2024/8wc4_37430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/08_2024/8wc4_37430_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/08_2024/8wc4_37430_neut.cif" } resolution = 3.1 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= 0.079 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 56 5.16 5 C 5369 2.51 5 N 1426 2.21 5 O 1542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 359": "OE1" <-> "OE2" Residue "R ARG 221": "NH1" <-> "NH2" Residue "R ARG 309": "NH1" <-> "NH2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1844 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2484 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2054 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "S" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1622 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "Y" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 380 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.47 Number of scatterers: 8394 At special positions: 0 Unit cell: (89.25, 118.15, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 56 16.00 O 1542 8.00 N 1426 7.00 C 5369 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.20 Conformation dependent library (CDL) restraints added in 1.7 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.680A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.539A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.844A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.676A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.729A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.596A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 317 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.639A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 49 removed outlier: 3.721A pdb=" N ILE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE R 44 " --> pdb=" O ASN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 85 removed outlier: 4.223A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 94 through 126 removed outlier: 3.731A pdb=" N ALA R 123 " --> pdb=" O ASP R 119 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 135 through 160 removed outlier: 3.573A pdb=" N ILE R 139 " --> pdb=" O ASN R 135 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL R 141 " --> pdb=" O SER R 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET R 142 " --> pdb=" O THR R 138 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 175 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 198 through 226 removed outlier: 3.538A pdb=" N ILE R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 275 removed outlier: 3.587A pdb=" N THR R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 302 removed outlier: 4.043A pdb=" N ASN R 283 " --> pdb=" O PRO R 279 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR R 291 " --> pdb=" O TYR R 287 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 313 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.666A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.903A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.654A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 45 removed outlier: 3.604A pdb=" N ASP Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 190 removed outlier: 3.541A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.728A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.042A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.902A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.574A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.564A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.571A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.608A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 4 removed outlier: 3.693A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.658A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.566A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.445A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.577A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1077 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: 2.23 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 1357 1.31 - 1.47: 3583 1.47 - 1.63: 3558 1.63 - 1.78: 7 1.78 - 1.94: 75 Bond restraints: 8580 Sorted by residual: bond pdb=" C PRO R 56 " pdb=" O PRO R 56 " ideal model delta sigma weight residual 1.238 1.158 0.080 1.24e-02 6.50e+03 4.16e+01 bond pdb=" C MET R 195 " pdb=" O MET R 195 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.16e-02 7.43e+03 2.59e+01 bond pdb=" CA ASN A 231 " pdb=" C ASN A 231 " ideal model delta sigma weight residual 1.525 1.474 0.051 1.02e-02 9.61e+03 2.49e+01 bond pdb=" C ASP B 312 " pdb=" O ASP B 312 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.38e-02 5.25e+03 2.46e+01 bond pdb=" CA PHE R 50 " pdb=" C PHE R 50 " ideal model delta sigma weight residual 1.524 1.490 0.034 7.00e-03 2.04e+04 2.41e+01 ... (remaining 8575 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.87: 126 104.87 - 112.73: 4529 112.73 - 120.59: 3744 120.59 - 128.45: 3195 128.45 - 136.31: 72 Bond angle restraints: 11666 Sorted by residual: angle pdb=" N GLN R 52 " pdb=" CA GLN R 52 " pdb=" C GLN R 52 " ideal model delta sigma weight residual 112.45 97.01 15.44 1.39e+00 5.18e-01 1.23e+02 angle pdb=" C ILE R 223 " pdb=" CA ILE R 223 " pdb=" CB ILE R 223 " ideal model delta sigma weight residual 111.70 102.14 9.56 1.28e+00 6.10e-01 5.58e+01 angle pdb=" N ALA R 311 " pdb=" CA ALA R 311 " pdb=" C ALA R 311 " ideal model delta sigma weight residual 112.90 103.86 9.04 1.31e+00 5.83e-01 4.76e+01 angle pdb=" C THR R 55 " pdb=" N PRO R 56 " pdb=" CA PRO R 56 " ideal model delta sigma weight residual 119.28 126.65 -7.37 1.10e+00 8.26e-01 4.49e+01 angle pdb=" N TYR R 305 " pdb=" CA TYR R 305 " pdb=" C TYR R 305 " ideal model delta sigma weight residual 109.72 117.84 -8.12 1.25e+00 6.40e-01 4.22e+01 ... (remaining 11661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4569 16.03 - 32.05: 349 32.05 - 48.08: 75 48.08 - 64.11: 12 64.11 - 80.13: 14 Dihedral angle restraints: 5019 sinusoidal: 1794 harmonic: 3225 Sorted by residual: dihedral pdb=" N LYS R 51 " pdb=" C LYS R 51 " pdb=" CA LYS R 51 " pdb=" CB LYS R 51 " ideal model delta harmonic sigma weight residual 122.80 139.77 -16.97 0 2.50e+00 1.60e-01 4.61e+01 dihedral pdb=" C LYS R 51 " pdb=" N LYS R 51 " pdb=" CA LYS R 51 " pdb=" CB LYS R 51 " ideal model delta harmonic sigma weight residual -122.60 -136.57 13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C ILE R 45 " pdb=" N ILE R 45 " pdb=" CA ILE R 45 " pdb=" CB ILE R 45 " ideal model delta harmonic sigma weight residual -122.00 -134.17 12.17 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 5016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1293 0.120 - 0.239: 39 0.239 - 0.359: 5 0.359 - 0.478: 3 0.478 - 0.598: 1 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA LYS R 51 " pdb=" N LYS R 51 " pdb=" C LYS R 51 " pdb=" CB LYS R 51 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" CA PHE R 50 " pdb=" N PHE R 50 " pdb=" C PHE R 50 " pdb=" CB PHE R 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE R 45 " pdb=" CA ILE R 45 " pdb=" CG1 ILE R 45 " pdb=" CG2 ILE R 45 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1338 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP R 88 " 0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C TRP R 88 " -0.079 2.00e-02 2.50e+03 pdb=" O TRP R 88 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR R 89 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 194 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C PHE R 194 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE R 194 " -0.027 2.00e-02 2.50e+03 pdb=" N MET R 195 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 55 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C THR R 55 " -0.058 2.00e-02 2.50e+03 pdb=" O THR R 55 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO R 56 " 0.019 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1141 2.75 - 3.29: 7801 3.29 - 3.83: 12896 3.83 - 4.36: 14793 4.36 - 4.90: 27137 Nonbonded interactions: 63768 Sorted by model distance: nonbonded pdb=" ND2 ASN R 40 " pdb=" OD1 ASP R 68 " model vdw 2.216 3.120 nonbonded pdb=" O GLN S 39 " pdb=" OG1 THR S 116 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.325 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.333 3.120 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.334 3.120 ... (remaining 63763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 6.460 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.006 0.080 8580 Z= 0.387 Angle : 0.808 15.445 11666 Z= 0.487 Chirality : 0.059 0.598 1341 Planarity : 0.005 0.047 1474 Dihedral : 13.024 80.132 2927 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.93 % Allowed : 1.28 % Favored : 97.79 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1084 helix: 1.22 (0.27), residues: 377 sheet: 0.20 (0.33), residues: 256 loop : -1.62 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.012 0.002 HIS R 49 PHE 0.018 0.002 PHE R 214 TYR 0.030 0.002 TYR A 230 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 1.025 Fit side-chains REVERT: A 234 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7431 (tp-100) REVERT: A 238 ASN cc_start: 0.8730 (m110) cc_final: 0.8403 (m110) REVERT: A 323 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7818 (ttm110) REVERT: B 247 ASP cc_start: 0.7774 (t0) cc_final: 0.7573 (t0) REVERT: R 157 MET cc_start: 0.7804 (ttm) cc_final: 0.7443 (ttm) REVERT: R 224 ASN cc_start: 0.7546 (m-40) cc_final: 0.7288 (m110) REVERT: S 18 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7818 (ttm170) outliers start: 8 outliers final: 5 residues processed: 167 average time/residue: 0.2292 time to fit residues: 50.4455 Evaluate side-chains 135 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 54 HIS Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 310 ARG Chi-restraints excluded: chain Y residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 204 GLN B 32 GLN R 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8580 Z= 0.195 Angle : 0.589 10.165 11666 Z= 0.310 Chirality : 0.044 0.145 1341 Planarity : 0.004 0.042 1474 Dihedral : 5.874 59.781 1203 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.28 % Allowed : 6.99 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1084 helix: 1.85 (0.27), residues: 374 sheet: 0.31 (0.34), residues: 249 loop : -1.51 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.007 0.001 HIS R 62 PHE 0.019 0.001 PHE A 189 TYR 0.039 0.002 TYR R 287 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.965 Fit side-chains REVERT: A 24 GLN cc_start: 0.7424 (tt0) cc_final: 0.7124 (mt0) REVERT: A 238 ASN cc_start: 0.8732 (m110) cc_final: 0.8488 (m110) REVERT: B 247 ASP cc_start: 0.7651 (t0) cc_final: 0.7423 (t0) REVERT: R 157 MET cc_start: 0.7842 (ttm) cc_final: 0.7400 (ttm) REVERT: R 270 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7755 (mm) outliers start: 11 outliers final: 5 residues processed: 147 average time/residue: 0.2292 time to fit residues: 45.3564 Evaluate side-chains 132 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 54 HIS Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 chunk 98 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 261 GLN B 32 GLN B 268 ASN R 40 ASN ** R 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8580 Z= 0.145 Angle : 0.520 10.231 11666 Z= 0.271 Chirality : 0.042 0.155 1341 Planarity : 0.004 0.039 1474 Dihedral : 4.948 51.979 1197 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.17 % Allowed : 11.07 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1084 helix: 2.19 (0.27), residues: 373 sheet: 0.48 (0.33), residues: 262 loop : -1.58 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 PHE 0.015 0.001 PHE A 189 TYR 0.033 0.001 TYR R 287 ARG 0.005 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.818 Fit side-chains REVERT: A 24 GLN cc_start: 0.7387 (tt0) cc_final: 0.7085 (mt0) REVERT: A 238 ASN cc_start: 0.8705 (m110) cc_final: 0.8453 (m110) REVERT: R 157 MET cc_start: 0.7882 (ttm) cc_final: 0.7470 (ttm) REVERT: S 18 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.7815 (tpt90) outliers start: 10 outliers final: 7 residues processed: 152 average time/residue: 0.2081 time to fit residues: 42.9257 Evaluate side-chains 133 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8580 Z= 0.270 Angle : 0.602 12.745 11666 Z= 0.312 Chirality : 0.044 0.143 1341 Planarity : 0.004 0.041 1474 Dihedral : 4.737 51.070 1193 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.98 % Allowed : 12.47 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1084 helix: 2.30 (0.27), residues: 370 sheet: 0.54 (0.33), residues: 261 loop : -1.44 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.010 0.001 HIS R 62 PHE 0.017 0.002 PHE A 189 TYR 0.031 0.002 TYR R 287 ARG 0.007 0.001 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.959 Fit side-chains REVERT: A 24 GLN cc_start: 0.7525 (tt0) cc_final: 0.7222 (mt0) REVERT: A 234 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7589 (tp-100) REVERT: A 238 ASN cc_start: 0.8760 (m110) cc_final: 0.8492 (m110) REVERT: R 157 MET cc_start: 0.7911 (ttm) cc_final: 0.7485 (ttm) outliers start: 17 outliers final: 12 residues processed: 142 average time/residue: 0.2126 time to fit residues: 40.9678 Evaluate side-chains 141 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain S residue 62 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 261 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8580 Z= 0.146 Angle : 0.527 11.392 11666 Z= 0.272 Chirality : 0.041 0.138 1341 Planarity : 0.004 0.038 1474 Dihedral : 4.389 51.081 1193 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.86 % Allowed : 13.17 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1084 helix: 2.47 (0.27), residues: 368 sheet: 0.72 (0.33), residues: 255 loop : -1.45 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 PHE 0.014 0.001 PHE A 189 TYR 0.018 0.001 TYR A 230 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.942 Fit side-chains REVERT: A 24 GLN cc_start: 0.7456 (tt0) cc_final: 0.7143 (mt0) REVERT: A 238 ASN cc_start: 0.8711 (m110) cc_final: 0.8428 (m110) REVERT: R 157 MET cc_start: 0.7918 (ttm) cc_final: 0.7503 (ttm) REVERT: S 18 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.7767 (tpt90) REVERT: S 83 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6044 (mmt) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.1953 time to fit residues: 39.7281 Evaluate side-chains 144 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 190 GLN A 261 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8580 Z= 0.207 Angle : 0.556 11.831 11666 Z= 0.287 Chirality : 0.042 0.139 1341 Planarity : 0.004 0.038 1474 Dihedral : 4.466 51.161 1193 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.98 % Allowed : 13.52 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1084 helix: 2.46 (0.27), residues: 370 sheet: 0.71 (0.33), residues: 256 loop : -1.40 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 PHE 0.016 0.001 PHE A 189 TYR 0.028 0.002 TYR R 287 ARG 0.005 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.845 Fit side-chains REVERT: A 24 GLN cc_start: 0.7479 (tt0) cc_final: 0.7171 (mt0) REVERT: A 238 ASN cc_start: 0.8719 (m110) cc_final: 0.8445 (m110) REVERT: B 234 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8733 (t80) REVERT: R 157 MET cc_start: 0.7918 (ttm) cc_final: 0.7506 (ttm) REVERT: S 18 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.7753 (tpt90) REVERT: S 83 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6155 (mmt) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.2097 time to fit residues: 41.1709 Evaluate side-chains 146 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 190 GLN A 261 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8580 Z= 0.156 Angle : 0.524 10.634 11666 Z= 0.271 Chirality : 0.041 0.134 1341 Planarity : 0.003 0.037 1474 Dihedral : 4.052 20.199 1191 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.52 % Allowed : 13.87 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1084 helix: 2.55 (0.27), residues: 369 sheet: 0.69 (0.32), residues: 261 loop : -1.34 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 PHE 0.015 0.001 PHE A 189 TYR 0.027 0.001 TYR R 287 ARG 0.006 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.949 Fit side-chains REVERT: A 24 GLN cc_start: 0.7473 (tt0) cc_final: 0.7147 (mt0) REVERT: A 238 ASN cc_start: 0.8714 (m110) cc_final: 0.8446 (m110) REVERT: R 157 MET cc_start: 0.7921 (ttm) cc_final: 0.7515 (ttm) REVERT: S 18 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.7715 (tpt90) REVERT: S 83 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6055 (mmt) outliers start: 13 outliers final: 11 residues processed: 143 average time/residue: 0.2052 time to fit residues: 39.8795 Evaluate side-chains 142 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8580 Z= 0.175 Angle : 0.532 10.349 11666 Z= 0.277 Chirality : 0.042 0.135 1341 Planarity : 0.004 0.038 1474 Dihedral : 4.051 19.716 1191 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.21 % Allowed : 14.10 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1084 helix: 2.54 (0.27), residues: 371 sheet: 0.68 (0.32), residues: 261 loop : -1.30 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 PHE 0.015 0.001 PHE A 189 TYR 0.024 0.001 TYR R 287 ARG 0.006 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.035 Fit side-chains REVERT: A 24 GLN cc_start: 0.7467 (tt0) cc_final: 0.7138 (mt0) REVERT: A 238 ASN cc_start: 0.8706 (m110) cc_final: 0.8430 (m110) REVERT: B 259 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7910 (mm-40) REVERT: R 157 MET cc_start: 0.7925 (ttm) cc_final: 0.7519 (ttm) REVERT: S 18 ARG cc_start: 0.8299 (tpp-160) cc_final: 0.7718 (tpt170) REVERT: S 83 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6115 (mmt) outliers start: 19 outliers final: 15 residues processed: 148 average time/residue: 0.1982 time to fit residues: 40.6490 Evaluate side-chains 146 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8580 Z= 0.164 Angle : 0.523 9.498 11666 Z= 0.272 Chirality : 0.041 0.133 1341 Planarity : 0.004 0.040 1474 Dihedral : 3.992 18.342 1191 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.98 % Allowed : 14.69 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1084 helix: 2.53 (0.27), residues: 371 sheet: 0.72 (0.32), residues: 261 loop : -1.26 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 59 HIS 0.008 0.001 HIS R 62 PHE 0.014 0.001 PHE A 189 TYR 0.023 0.001 TYR R 287 ARG 0.005 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 0.939 Fit side-chains REVERT: A 24 GLN cc_start: 0.7477 (tt0) cc_final: 0.7142 (mt0) REVERT: A 238 ASN cc_start: 0.8701 (m110) cc_final: 0.8430 (m110) REVERT: R 157 MET cc_start: 0.7938 (ttm) cc_final: 0.7532 (ttm) REVERT: S 18 ARG cc_start: 0.8270 (tpp-160) cc_final: 0.7702 (tpt170) REVERT: S 83 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6035 (mmt) outliers start: 17 outliers final: 12 residues processed: 145 average time/residue: 0.2112 time to fit residues: 41.8804 Evaluate side-chains 142 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.0370 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8580 Z= 0.135 Angle : 0.509 8.596 11666 Z= 0.265 Chirality : 0.041 0.128 1341 Planarity : 0.003 0.041 1474 Dihedral : 3.867 17.550 1191 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.52 % Allowed : 15.85 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1084 helix: 2.61 (0.27), residues: 369 sheet: 0.79 (0.32), residues: 259 loop : -1.24 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.008 0.001 HIS R 62 PHE 0.012 0.001 PHE A 189 TYR 0.036 0.001 TYR R 287 ARG 0.006 0.000 ARG Y 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 0.937 Fit side-chains REVERT: A 238 ASN cc_start: 0.8677 (m110) cc_final: 0.8421 (m110) REVERT: B 259 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7856 (mm-40) REVERT: R 157 MET cc_start: 0.7943 (ttm) cc_final: 0.7216 (ttp) REVERT: S 18 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7703 (tpt170) REVERT: S 83 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6045 (mmt) outliers start: 13 outliers final: 12 residues processed: 145 average time/residue: 0.2226 time to fit residues: 43.4099 Evaluate side-chains 143 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 86 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.147544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112715 restraints weight = 10733.760| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.53 r_work: 0.3135 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8580 Z= 0.184 Angle : 0.542 9.154 11666 Z= 0.281 Chirality : 0.042 0.137 1341 Planarity : 0.004 0.044 1474 Dihedral : 4.004 17.757 1191 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.10 % Allowed : 15.62 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1084 helix: 2.56 (0.27), residues: 371 sheet: 0.81 (0.33), residues: 255 loop : -1.26 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 59 HIS 0.008 0.001 HIS R 62 PHE 0.013 0.001 PHE A 189 TYR 0.036 0.001 TYR R 287 ARG 0.004 0.000 ARG Y 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2251.37 seconds wall clock time: 40 minutes 49.05 seconds (2449.05 seconds total)