Starting phenix.real_space_refine on Fri Mar 15 00:57:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnr_27577/03_2024/8dnr_27577_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnr_27577/03_2024/8dnr_27577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnr_27577/03_2024/8dnr_27577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnr_27577/03_2024/8dnr_27577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnr_27577/03_2024/8dnr_27577_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnr_27577/03_2024/8dnr_27577_neut.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.074 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 60 5.16 5 C 6459 2.51 5 N 1641 2.21 5 O 2031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 95": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 95": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10191 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3341 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3341 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3341 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.12, per 1000 atoms: 0.50 Number of scatterers: 10191 At special positions: 0 Unit cell: (101.52, 102.46, 104.34, 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 60 16.00 O 2031 8.00 N 1641 7.00 C 6459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 104 " - pdb=" SG CYS E 114 " distance=2.02 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 355 " - pdb=" SG CYS E 363 " distance=2.03 Simple disulfide: pdb=" SG CYS E 387 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 417 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 99 " " NAG A 602 " - " ASN A 67 " " NAG A 603 " - " ASN A 414 " " NAG A 604 " - " ASN A 464 " " NAG B 601 " - " ASN B 99 " " NAG B 602 " - " ASN B 67 " " NAG B 603 " - " ASN B 414 " " NAG B 604 " - " ASN B 464 " " NAG E 601 " - " ASN E 99 " " NAG E 602 " - " ASN E 67 " " NAG E 603 " - " ASN E 464 " " NAG E 604 " - " ASN E 414 " Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 15 sheets defined 38.7% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.504A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.550A pdb=" N CYS A 71 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 72' Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.549A pdb=" N GLY A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.655A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.949A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.692A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 471 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.803A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.567A pdb=" N CYS B 71 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 72' Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.583A pdb=" N GLY B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 3.712A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.976A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 191 through 215 removed outlier: 3.737A pdb=" N THR B 195 " --> pdb=" O PRO B 191 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.917A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 36 removed outlier: 3.593A pdb=" N ILE E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 removed outlier: 3.535A pdb=" N CYS E 71 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 72 " --> pdb=" O SER E 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 68 through 72' Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.553A pdb=" N GLY E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 89 - end of helix removed outlier: 3.686A pdb=" N TYR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.959A pdb=" N LYS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 191 through 215 removed outlier: 3.703A pdb=" N THR E 195 " --> pdb=" O PRO E 191 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 452 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 11.275A pdb=" N TYR A 170 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP A 56 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N PHE A 172 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 58 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 270 removed outlier: 3.659A pdb=" N ALA A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 277 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 4.554A pdb=" N CYS B 392 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 removed outlier: 5.965A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.546A pdb=" N CYS A 392 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 426 " --> pdb=" O MET E 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 162 removed outlier: 17.146A pdb=" N THR B 168 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N THR B 54 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N TYR B 170 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASP B 56 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N PHE B 172 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 58 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 46 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N SER B 50 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N GLU B 287 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N LEU B 285 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N THR B 54 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N ASP B 56 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N TYR B 281 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N VAL B 58 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N ARG B 279 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LYS B 60 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE B 277 " --> pdb=" O LYS B 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 297 current: chain 'B' and resid 332 through 333 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 270 removed outlier: 3.625A pdb=" N ALA B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 277 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE B 277 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LYS B 60 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N ARG B 279 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N VAL B 58 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N TYR B 281 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N ASP B 56 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N THR B 54 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N LEU B 285 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N GLU B 287 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N SER B 50 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 46 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 39 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 102 removed outlier: 4.517A pdb=" N CYS E 392 " --> pdb=" O ILE E 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB3, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB4, first strand: chain 'E' and resid 158 through 162 removed outlier: 17.107A pdb=" N THR E 168 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 11.769A pdb=" N THR E 54 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N TYR E 170 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP E 56 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N PHE E 172 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL E 58 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS E 40 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU E 297 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE E 42 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR E 46 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA E 291 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N ILE E 48 " --> pdb=" O GLN E 289 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N GLN E 289 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N SER E 50 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N GLU E 287 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N LEU E 285 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N THR E 54 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N ASP E 56 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR E 281 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N VAL E 58 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ARG E 279 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N LYS E 60 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N ILE E 277 " --> pdb=" O LYS E 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 298 current: chain 'E' and resid 332 through 333 Processing sheet with id=AB5, first strand: chain 'E' and resid 263 through 270 removed outlier: 6.539A pdb=" N ILE E 277 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL E 269 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR E 275 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N ILE E 277 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N LYS E 60 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ARG E 279 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N VAL E 58 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR E 281 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N ASP E 56 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N THR E 54 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N LEU E 285 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N GLU E 287 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N SER E 50 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N GLN E 289 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N ILE E 48 " --> pdb=" O GLN E 289 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA E 291 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR E 46 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE E 42 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU E 297 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS E 40 " --> pdb=" O LEU E 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 60 current: chain 'E' and resid 322 through 326 Processing sheet with id=AB6, first strand: chain 'E' and resid 301 through 303 418 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3251 1.34 - 1.47: 2255 1.47 - 1.59: 4745 1.59 - 1.72: 0 1.72 - 1.84: 84 Bond restraints: 10335 Sorted by residual: bond pdb=" N GLY E 430 " pdb=" CA GLY E 430 " ideal model delta sigma weight residual 1.445 1.476 -0.032 9.90e-03 1.02e+04 1.04e+01 bond pdb=" N LEU E 429 " pdb=" CA LEU E 429 " ideal model delta sigma weight residual 1.452 1.490 -0.037 1.22e-02 6.72e+03 9.42e+00 bond pdb=" N ILE B 118 " pdb=" CA ILE B 118 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.30e-02 5.92e+03 7.35e+00 bond pdb=" N LYS E 431 " pdb=" CA LYS E 431 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N TYR E 432 " pdb=" CA TYR E 432 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.38e+00 ... (remaining 10330 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.01: 235 107.01 - 113.74: 6155 113.74 - 120.47: 3681 120.47 - 127.19: 3934 127.19 - 133.92: 50 Bond angle restraints: 14055 Sorted by residual: angle pdb=" N THR E 415 " pdb=" CA THR E 415 " pdb=" C THR E 415 " ideal model delta sigma weight residual 111.28 107.24 4.04 1.09e+00 8.42e-01 1.38e+01 angle pdb=" CA MET B 463 " pdb=" C MET B 463 " pdb=" N ASN B 464 " ideal model delta sigma weight residual 117.30 121.49 -4.19 1.16e+00 7.43e-01 1.30e+01 angle pdb=" CA CYS E 104 " pdb=" CB CYS E 104 " pdb=" SG CYS E 104 " ideal model delta sigma weight residual 114.40 122.62 -8.22 2.30e+00 1.89e-01 1.28e+01 angle pdb=" CA GLY E 430 " pdb=" C GLY E 430 " pdb=" O GLY E 430 " ideal model delta sigma weight residual 121.57 117.91 3.66 1.07e+00 8.73e-01 1.17e+01 angle pdb=" N ASN E 414 " pdb=" CA ASN E 414 " pdb=" C ASN E 414 " ideal model delta sigma weight residual 112.89 108.76 4.13 1.24e+00 6.50e-01 1.11e+01 ... (remaining 14050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 5742 16.24 - 32.48: 512 32.48 - 48.72: 178 48.72 - 64.96: 69 64.96 - 81.19: 12 Dihedral angle restraints: 6513 sinusoidal: 2655 harmonic: 3858 Sorted by residual: dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -156.11 70.11 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -146.68 60.68 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS E 71 " pdb=" SG CYS E 71 " pdb=" SG CYS E 192 " pdb=" CB CYS E 192 " ideal model delta sinusoidal sigma weight residual -86.00 -144.18 58.18 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1069 0.030 - 0.061: 406 0.061 - 0.091: 141 0.091 - 0.121: 144 0.121 - 0.151: 13 Chirality restraints: 1773 Sorted by residual: chirality pdb=" CB ILE B 118 " pdb=" CA ILE B 118 " pdb=" CG1 ILE B 118 " pdb=" CG2 ILE B 118 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA LEU E 429 " pdb=" N LEU E 429 " pdb=" C LEU E 429 " pdb=" CB LEU E 429 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE A 426 " pdb=" N ILE A 426 " pdb=" C ILE A 426 " pdb=" CB ILE A 426 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1770 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 604 " -0.044 2.00e-02 2.50e+03 3.70e-02 1.71e+01 pdb=" C7 NAG E 604 " 0.015 2.00e-02 2.50e+03 pdb=" C8 NAG E 604 " 0.011 2.00e-02 2.50e+03 pdb=" N2 NAG E 604 " 0.056 2.00e-02 2.50e+03 pdb=" O7 NAG E 604 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 74 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C THR E 74 " -0.030 2.00e-02 2.50e+03 pdb=" O THR E 74 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL E 75 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 413 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C ASP E 413 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP E 413 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN E 414 " 0.010 2.00e-02 2.50e+03 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 53 2.57 - 3.16: 8105 3.16 - 3.74: 15673 3.74 - 4.32: 23119 4.32 - 4.90: 37980 Nonbonded interactions: 84930 Sorted by model distance: nonbonded pdb=" CG LYS B 55 " pdb=" OH TYR B 248 " model vdw 1.992 3.440 nonbonded pdb=" CD LYS B 55 " pdb=" OH TYR B 248 " model vdw 2.152 3.440 nonbonded pdb=" OG SER A 458 " pdb=" OG SER E 351 " model vdw 2.187 2.440 nonbonded pdb=" OD1 ASN E 64 " pdb=" OG SER E 66 " model vdw 2.221 2.440 nonbonded pdb=" OG SER B 351 " pdb=" OG SER E 458 " model vdw 2.227 2.440 ... (remaining 84925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.370 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.360 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 0.037 10335 Z= 0.217 Angle : 0.521 8.218 14055 Z= 0.289 Chirality : 0.045 0.151 1773 Planarity : 0.003 0.039 1749 Dihedral : 15.267 81.194 3969 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 1.47 % Allowed : 15.15 % Favored : 83.38 % 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 (0.23), residues: 1302 helix: 1.39 (0.26), residues: 432 sheet: 0.43 (0.32), residues: 258 loop : -0.56 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 308 HIS 0.004 0.001 HIS E 102 PHE 0.007 0.001 PHE B 301 TYR 0.009 0.001 TYR E 432 ARG 0.002 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.130 Fit side-chains REVERT: A 95 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7579 (mm-30) REVERT: E 250 THR cc_start: 0.7513 (m) cc_final: 0.6775 (t) outliers start: 17 outliers final: 13 residues processed: 131 average time/residue: 0.9224 time to fit residues: 133.0349 Evaluate side-chains 118 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 371 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 314 ASN E 194 GLN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10335 Z= 0.175 Angle : 0.453 4.809 14055 Z= 0.239 Chirality : 0.045 0.150 1773 Planarity : 0.003 0.036 1749 Dihedral : 7.241 60.551 1667 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.94 % Allowed : 13.59 % Favored : 83.46 % 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: 0.61 (0.23), residues: 1302 helix: 1.69 (0.26), residues: 432 sheet: 0.38 (0.31), residues: 258 loop : -0.49 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 308 HIS 0.001 0.001 HIS B 29 PHE 0.008 0.001 PHE B 301 TYR 0.021 0.001 TYR B 248 ARG 0.001 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 1.078 Fit side-chains REVERT: A 95 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 335 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8510 (mptp) REVERT: B 220 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8079 (t0) outliers start: 34 outliers final: 11 residues processed: 132 average time/residue: 0.8441 time to fit residues: 123.7113 Evaluate side-chains 117 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 0.0060 chunk 94 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10335 Z= 0.172 Angle : 0.446 4.780 14055 Z= 0.234 Chirality : 0.045 0.151 1773 Planarity : 0.003 0.036 1749 Dihedral : 6.260 55.377 1648 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.46 % Allowed : 13.42 % Favored : 83.12 % 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: 0.80 (0.23), residues: 1302 helix: 1.75 (0.25), residues: 447 sheet: 0.42 (0.31), residues: 258 loop : -0.30 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 308 HIS 0.001 0.000 HIS B 29 PHE 0.008 0.001 PHE B 301 TYR 0.009 0.001 TYR B 275 ARG 0.003 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 108 time to evaluate : 1.153 Fit side-chains REVERT: A 95 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 335 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8504 (mptp) REVERT: B 220 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8081 (t0) outliers start: 40 outliers final: 12 residues processed: 128 average time/residue: 0.8832 time to fit residues: 124.9064 Evaluate side-chains 118 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10335 Z= 0.215 Angle : 0.465 4.755 14055 Z= 0.242 Chirality : 0.045 0.144 1773 Planarity : 0.003 0.036 1749 Dihedral : 6.020 54.559 1648 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.20 % Allowed : 13.77 % Favored : 83.03 % 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: 0.77 (0.23), residues: 1302 helix: 1.70 (0.25), residues: 447 sheet: 0.40 (0.31), residues: 258 loop : -0.30 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 308 HIS 0.002 0.001 HIS B 29 PHE 0.009 0.001 PHE B 301 TYR 0.011 0.001 TYR B 275 ARG 0.003 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 0.926 Fit side-chains REVERT: A 95 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 335 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8458 (mptp) REVERT: B 220 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8107 (t0) REVERT: B 355 CYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8296 (t) REVERT: E 355 CYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8286 (t) outliers start: 37 outliers final: 15 residues processed: 123 average time/residue: 0.9079 time to fit residues: 122.8026 Evaluate side-chains 122 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 1 optimal weight: 0.0980 chunk 92 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10335 Z= 0.126 Angle : 0.419 4.738 14055 Z= 0.220 Chirality : 0.044 0.145 1773 Planarity : 0.003 0.035 1749 Dihedral : 5.398 54.017 1648 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.46 % Allowed : 13.51 % Favored : 83.03 % 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: 0.97 (0.23), residues: 1302 helix: 1.93 (0.26), residues: 447 sheet: 0.48 (0.31), residues: 258 loop : -0.21 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 308 HIS 0.001 0.000 HIS B 29 PHE 0.007 0.001 PHE E 376 TYR 0.008 0.001 TYR E 438 ARG 0.002 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 111 time to evaluate : 1.062 Fit side-chains REVERT: A 95 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7452 (mt-10) REVERT: A 335 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8489 (mptp) REVERT: A 422 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7864 (mt) REVERT: B 45 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8628 (ptmt) REVERT: B 220 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8055 (t0) REVERT: E 96 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8119 (tm) outliers start: 40 outliers final: 12 residues processed: 135 average time/residue: 0.9164 time to fit residues: 136.0553 Evaluate side-chains 122 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.1980 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 102 HIS E 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10335 Z= 0.234 Angle : 0.474 5.128 14055 Z= 0.245 Chirality : 0.045 0.139 1773 Planarity : 0.003 0.037 1749 Dihedral : 5.236 54.170 1645 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.94 % Allowed : 14.29 % Favored : 82.77 % 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: 0.82 (0.23), residues: 1302 helix: 1.73 (0.25), residues: 447 sheet: 0.44 (0.31), residues: 258 loop : -0.25 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 308 HIS 0.002 0.001 HIS B 29 PHE 0.010 0.001 PHE B 301 TYR 0.012 0.001 TYR B 275 ARG 0.004 0.000 ARG E 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 1.333 Fit side-chains REVERT: A 95 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7463 (mm-30) REVERT: A 335 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8433 (mptp) REVERT: A 422 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7823 (mt) REVERT: B 220 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8106 (t0) REVERT: E 96 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8095 (tm) outliers start: 34 outliers final: 13 residues processed: 121 average time/residue: 0.9363 time to fit residues: 125.0259 Evaluate side-chains 119 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN E 102 HIS E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10335 Z= 0.268 Angle : 0.500 5.910 14055 Z= 0.257 Chirality : 0.046 0.140 1773 Planarity : 0.003 0.037 1749 Dihedral : 5.362 54.143 1645 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.12 % Allowed : 14.29 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1302 helix: 1.59 (0.25), residues: 447 sheet: 0.38 (0.32), residues: 258 loop : -0.27 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 308 HIS 0.002 0.001 HIS B 29 PHE 0.010 0.001 PHE B 301 TYR 0.013 0.001 TYR B 275 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 1.213 Fit side-chains REVERT: A 95 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 335 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8418 (mptp) REVERT: A 422 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7817 (mt) REVERT: B 210 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8073 (tt) REVERT: B 220 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8119 (t0) REVERT: E 96 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8085 (tm) outliers start: 36 outliers final: 12 residues processed: 126 average time/residue: 0.9374 time to fit residues: 130.1220 Evaluate side-chains 120 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN E 102 HIS E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10335 Z= 0.177 Angle : 0.453 6.161 14055 Z= 0.235 Chirality : 0.045 0.144 1773 Planarity : 0.003 0.037 1749 Dihedral : 5.100 53.316 1645 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.16 % Allowed : 15.32 % Favored : 82.51 % 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: 0.86 (0.23), residues: 1302 helix: 1.77 (0.25), residues: 447 sheet: 0.40 (0.32), residues: 258 loop : -0.21 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 308 HIS 0.001 0.000 HIS A 102 PHE 0.008 0.001 PHE B 301 TYR 0.007 0.001 TYR B 275 ARG 0.003 0.000 ARG E 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.253 Fit side-chains REVERT: A 95 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 335 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8383 (mptp) REVERT: A 422 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7854 (mt) REVERT: B 220 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8082 (t0) REVERT: E 96 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8081 (tm) outliers start: 25 outliers final: 12 residues processed: 120 average time/residue: 0.9620 time to fit residues: 127.0209 Evaluate side-chains 118 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 104 optimal weight: 0.0970 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN E 102 HIS E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10335 Z= 0.155 Angle : 0.445 6.301 14055 Z= 0.230 Chirality : 0.044 0.141 1773 Planarity : 0.003 0.036 1749 Dihedral : 4.961 53.478 1645 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.25 % Allowed : 15.41 % Favored : 82.34 % 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: 0.94 (0.23), residues: 1302 helix: 1.87 (0.25), residues: 447 sheet: 0.43 (0.31), residues: 258 loop : -0.19 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 308 HIS 0.001 0.000 HIS A 102 PHE 0.007 0.001 PHE B 301 TYR 0.007 0.001 TYR E 438 ARG 0.003 0.000 ARG E 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.049 Fit side-chains REVERT: A 335 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8397 (mptp) REVERT: A 422 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7846 (mt) REVERT: B 45 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8629 (ptmt) REVERT: B 210 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8102 (tp) REVERT: B 220 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8079 (t0) REVERT: E 96 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8105 (tm) outliers start: 26 outliers final: 11 residues processed: 120 average time/residue: 0.9222 time to fit residues: 121.9232 Evaluate side-chains 119 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.0980 chunk 85 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN E 102 HIS E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10335 Z= 0.180 Angle : 0.458 6.453 14055 Z= 0.236 Chirality : 0.045 0.140 1773 Planarity : 0.003 0.036 1749 Dihedral : 4.995 53.707 1645 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.82 % Allowed : 15.76 % Favored : 82.42 % 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: 0.91 (0.23), residues: 1302 helix: 1.83 (0.25), residues: 447 sheet: 0.45 (0.32), residues: 258 loop : -0.21 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 308 HIS 0.002 0.001 HIS A 102 PHE 0.007 0.001 PHE B 301 TYR 0.009 0.001 TYR B 275 ARG 0.002 0.000 ARG E 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.161 Fit side-chains REVERT: A 95 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 335 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8411 (mptp) REVERT: A 422 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7858 (mt) REVERT: B 45 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8618 (ptmt) REVERT: B 210 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8100 (tt) REVERT: B 220 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8089 (t0) REVERT: E 96 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8100 (tm) outliers start: 21 outliers final: 11 residues processed: 116 average time/residue: 0.9807 time to fit residues: 124.8877 Evaluate side-chains 119 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN E 102 HIS E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.097541 restraints weight = 11163.917| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.79 r_work: 0.2853 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10335 Z= 0.145 Angle : 0.440 6.896 14055 Z= 0.227 Chirality : 0.044 0.142 1773 Planarity : 0.003 0.036 1749 Dihedral : 4.857 53.325 1645 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.08 % Allowed : 15.50 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1302 helix: 1.93 (0.25), residues: 447 sheet: 0.50 (0.32), residues: 258 loop : -0.17 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 308 HIS 0.001 0.000 HIS A 102 PHE 0.007 0.001 PHE A 376 TYR 0.008 0.001 TYR A 438 ARG 0.003 0.000 ARG E 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.24 seconds wall clock time: 54 minutes 13.91 seconds (3253.91 seconds total)