Starting phenix.real_space_refine on Fri May 16 11:49:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctj_45908/05_2025/9ctj_45908.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctj_45908/05_2025/9ctj_45908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctj_45908/05_2025/9ctj_45908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctj_45908/05_2025/9ctj_45908.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctj_45908/05_2025/9ctj_45908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctj_45908/05_2025/9ctj_45908.cif" } resolution = 3.74 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= 0.003 sd= 0.027 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 82 5.16 5 C 9352 2.51 5 N 2360 2.21 5 O 2671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14465 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2708 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "B" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2719 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2701 Classifications: {'peptide': 329} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2672 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1725 Classifications: {'peptide': 208} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.38, per 1000 atoms: 0.58 Number of scatterers: 14465 At special positions: 0 Unit cell: (122.485, 115.005, 132.77, 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 82 16.00 O 2671 8.00 N 2360 7.00 C 9352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN H 4 " - " MAN H 5 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " MAN H 6 " - " MAN H 7 " ALPHA1-6 " BMA H 3 " - " MAN H 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG C 501 " - " ASN C 80 " " NAG D 501 " - " ASN D 110 " " NAG E 501 " - " ASN E 208 " " NAG F 1 " - " ASN C 149 " " NAG G 1 " - " ASN A 149 " " NAG H 1 " - " ASN B 111 " " NAG O 1 " - " ASN A 80 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 23 sheets defined 29.7% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.510A pdb=" N VAL A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.693A pdb=" N ALA A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.541A pdb=" N ARG A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 143 " --> pdb=" O LEU A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 143' Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.786A pdb=" N SER A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.846A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 308 removed outlier: 3.611A pdb=" N VAL A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 487 removed outlier: 3.772A pdb=" N ILE A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Proline residue: A 472 - end of helix Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.979A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'B' and resid 244 through 247 removed outlier: 3.519A pdb=" N LEU B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 244 through 247' Processing helix chain 'B' and resid 251 through 273 removed outlier: 3.716A pdb=" N THR B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 310 removed outlier: 3.671A pdb=" N ALA B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 Processing helix chain 'B' and resid 398 through 418 removed outlier: 3.518A pdb=" N PHE B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.034A pdb=" N LYS C 13 " --> pdb=" O MET C 9 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 73 removed outlier: 3.976A pdb=" N ALA C 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.748A pdb=" N ALA C 88 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.723A pdb=" N ILE C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 Processing helix chain 'C' and resid 246 through 269 removed outlier: 3.954A pdb=" N THR C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 308 removed outlier: 3.500A pdb=" N PHE C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 446 removed outlier: 3.532A pdb=" N PHE C 431 " --> pdb=" O SER C 427 " (cutoff:3.500A) Proline residue: C 432 - end of helix removed outlier: 3.508A pdb=" N PHE C 435 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.556A pdb=" N LEU D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 removed outlier: 3.745A pdb=" N ILE D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 242 through 246 removed outlier: 3.635A pdb=" N LEU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 273 removed outlier: 3.555A pdb=" N VAL D 262 " --> pdb=" O GLY D 258 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 309 removed outlier: 3.955A pdb=" N VAL D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 412 removed outlier: 3.604A pdb=" N ARG D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE D 395 " --> pdb=" O ARG D 391 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Proline residue: D 398 - end of helix removed outlier: 3.736A pdb=" N ALA D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR D 412 " --> pdb=" O TYR D 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 99 through 106 removed outlier: 3.671A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS E 105 " --> pdb=" O MET E 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.501A pdb=" N ASP I 82 " --> pdb=" O GLN I 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.515A pdb=" N ASP J 90 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.265A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP A 67 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.233A pdb=" N ASP A 101 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA A 135 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 103 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP A 67 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.869A pdb=" N ILE A 154 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.289A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.289A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.912A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 157 removed outlier: 3.852A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.279A pdb=" N ASP C 101 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA C 135 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR C 62 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE C 44 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN C 64 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 42 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR C 66 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N MET C 40 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ARG C 68 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N VAL C 38 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 167 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.310A pdb=" N TYR C 62 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE C 44 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN C 64 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 42 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR C 66 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N MET C 40 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ARG C 68 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N VAL C 38 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.997A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 203 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.031A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 69 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 132 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU D 58 " --> pdb=" O PRO D 51 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 60 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE D 49 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP D 62 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D 70 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU D 39 " --> pdb=" O LYS D 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.031A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 69 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 132 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU D 58 " --> pdb=" O PRO D 51 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 60 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE D 49 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP D 62 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D 70 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU D 39 " --> pdb=" O LYS D 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.865A pdb=" N GLY D 194 " --> pdb=" O HIS D 217 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS D 219 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU D 192 " --> pdb=" O LYS D 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.532A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS E 118 " --> pdb=" O ASP E 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.532A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU E 71 " --> pdb=" O PRO E 64 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 184 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N MET E 57 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N SER E 186 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N VAL E 59 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL E 188 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 12.372A pdb=" N SER E 61 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N VAL E 190 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 13.250A pdb=" N GLY E 63 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.702A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY E 218 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.441A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 18 through 24 Processing sheet with id=AC3, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.456A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.761A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.072A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1959 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: 4.47 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2222 1.31 - 1.44: 4346 1.44 - 1.56: 8115 1.56 - 1.69: 0 1.69 - 1.82: 143 Bond restraints: 14826 Sorted by residual: bond pdb=" CA SER A 209 " pdb=" CB SER A 209 " ideal model delta sigma weight residual 1.530 1.451 0.079 1.69e-02 3.50e+03 2.17e+01 bond pdb=" N ILE A 77 " pdb=" CA ILE A 77 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.12e+01 bond pdb=" CA SER A 156 " pdb=" CB SER A 156 " ideal model delta sigma weight residual 1.530 1.458 0.071 1.55e-02 4.16e+03 2.11e+01 bond pdb=" N PRO D 114 " pdb=" CD PRO D 114 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.09e+01 bond pdb=" C PRO A 206 " pdb=" O PRO A 206 " ideal model delta sigma weight residual 1.232 1.182 0.050 1.20e-02 6.94e+03 1.76e+01 ... (remaining 14821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 19251 2.51 - 5.03: 811 5.03 - 7.54: 76 7.54 - 10.06: 11 10.06 - 12.57: 2 Bond angle restraints: 20151 Sorted by residual: angle pdb=" N ALA B 413 " pdb=" CA ALA B 413 " pdb=" C ALA B 413 " ideal model delta sigma weight residual 112.93 102.62 10.31 1.33e+00 5.65e-01 6.00e+01 angle pdb=" N SER C 10 " pdb=" CA SER C 10 " pdb=" C SER C 10 " ideal model delta sigma weight residual 113.50 106.75 6.75 1.23e+00 6.61e-01 3.02e+01 angle pdb=" O HIS D 109 " pdb=" C HIS D 109 " pdb=" N ASN D 110 " ideal model delta sigma weight residual 123.06 129.55 -6.49 1.20e+00 6.94e-01 2.93e+01 angle pdb=" N MET D 147 " pdb=" CA MET D 147 " pdb=" C MET D 147 " ideal model delta sigma weight residual 112.25 104.91 7.34 1.36e+00 5.41e-01 2.91e+01 angle pdb=" N LYS C 173 " pdb=" CA LYS C 173 " pdb=" C LYS C 173 " ideal model delta sigma weight residual 113.16 106.55 6.61 1.24e+00 6.50e-01 2.84e+01 ... (remaining 20146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 8296 21.24 - 42.48: 556 42.48 - 63.72: 63 63.72 - 84.95: 33 84.95 - 106.19: 12 Dihedral angle restraints: 8960 sinusoidal: 3790 harmonic: 5170 Sorted by residual: dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual 93.00 145.13 -52.13 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA MET B 112 " pdb=" C MET B 112 " pdb=" N THR B 113 " pdb=" CA THR B 113 " ideal model delta harmonic sigma weight residual 0.00 27.88 -27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CD ARG C 169 " pdb=" NE ARG C 169 " pdb=" CZ ARG C 169 " pdb=" NH1 ARG C 169 " ideal model delta sinusoidal sigma weight residual 0.00 44.61 -44.61 1 1.00e+01 1.00e-02 2.77e+01 ... (remaining 8957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1745 0.067 - 0.133: 445 0.133 - 0.200: 100 0.200 - 0.266: 28 0.266 - 0.333: 8 Chirality restraints: 2326 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-02 2.50e+03 2.22e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.44e+02 chirality pdb=" C1 MAN H 4 " pdb=" O3 BMA H 3 " pdb=" C2 MAN H 4 " pdb=" O5 MAN H 4 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.09e+02 ... (remaining 2323 not shown) Planarity restraints: 2487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.308 2.00e-02 2.50e+03 2.70e-01 9.10e+02 pdb=" C7 NAG O 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.111 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.485 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.230 2.00e-02 2.50e+03 1.92e-01 4.61e+02 pdb=" C7 NAG G 1 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.320 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.185 2.00e-02 2.50e+03 1.54e-01 2.95e+02 pdb=" C7 NAG D 501 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " -0.135 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.250 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.016 2.00e-02 2.50e+03 ... (remaining 2484 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 286 2.65 - 3.21: 12394 3.21 - 3.78: 22319 3.78 - 4.34: 31576 4.34 - 4.90: 51678 Nonbonded interactions: 118253 Sorted by model distance: nonbonded pdb=" OD1 ASP E 56 " pdb=" O SER E 187 " model vdw 2.091 3.040 nonbonded pdb=" OH TYR A 57 " pdb=" O THR A 151 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP B 98 " pdb=" O TYR B 160 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 161 " pdb=" O SER A 204 " model vdw 2.231 3.040 nonbonded pdb=" O ALA D 284 " pdb=" OH TYR D 408 " model vdw 2.240 3.040 ... (remaining 118248 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 10 or resid 12 through 17 or resid 19 through 36 \ or resid 38 through 65 or resid 67 through 72 or resid 74 or resid 77 through 1 \ 70 or resid 172 or resid 174 through 178 or resid 181 through 189 or resid 193 o \ r resid 198 through 200 or resid 202 through 203 or resid 205 through 212 or res \ id 214 through 293 or resid 295 through 300 or resid 302 through 309 or resid 46 \ 2 through 469 or resid 471 through 472 or resid 475 through 476 or resid 478 thr \ ough 479 or resid 481 through 487)) selection = (chain 'C' and (resid 8 through 10 or resid 12 through 17 or resid 19 through 36 \ or resid 38 through 65 or resid 67 through 72 or resid 74 or resid 77 through 1 \ 70 or resid 172 or resid 174 through 178 or resid 181 through 189 or resid 193 o \ r resid 198 through 200 or resid 202 through 203 or resid 205 through 212 or res \ id 214 through 293 or resid 295 through 300 or resid 302 through 429 or resid 43 \ 1 through 432 or resid 435 through 436 or resid 438 through 439 or resid 441 thr \ ough 447)) } ncs_group { reference = (chain 'B' and (resid 11 or resid 13 or resid 15 through 35 or resid 39 through \ 41 or resid 43 or resid 45 or resid 47 through 55 or resid 57 through 68 or resi \ d 70 through 81 or resid 84 through 121 or resid 124 through 135 or resid 137 th \ rough 151 or resid 153 through 163 or resid 166 through 167 or resid 169 or resi \ d 171 through 172 or resid 178 through 179 or resid 181 through 182 or resid 184 \ through 196 or resid 205 through 210 or resid 212 through 214 or resid 216 thro \ ugh 312 or resid 389 through 394 or resid 396 through 398 or resid 400 through 4 \ 01 or resid 403 through 405 or resid 407 through 417)) selection = (chain 'D' and (resid 10 or resid 12 or resid 14 through 34 or resid 38 through \ 40 or resid 42 or resid 44 or resid 46 through 54 or resid 56 through 67 or resi \ d 69 through 80 or resid 83 through 120 or resid 123 through 134 or resid 136 th \ rough 150 or resid 152 through 162 or resid 165 through 166 or resid 168 or resi \ d 170 through 171 or resid 177 through 178 or resid 180 through 181 or resid 183 \ through 195 or resid 204 through 209 or resid 211 through 213 or resid 215 thro \ ugh 391 or resid 393 through 395 or resid 397 through 398 or resid 400 through 4 \ 02 or resid 404 through 414)) } ncs_group { reference = chain 'F' selection = chain 'G' } 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 group one per residue 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: 1.600 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.800 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 0.007 0.228 14851 Z= 0.464 Angle : 1.092 13.297 20219 Z= 0.687 Chirality : 0.068 0.333 2326 Planarity : 0.018 0.327 2480 Dihedral : 15.104 106.193 5615 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.84 % Allowed : 2.16 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -2.75 (0.18), residues: 1733 helix: -2.56 (0.17), residues: 450 sheet: -1.34 (0.21), residues: 567 loop : -1.49 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 67 HIS 0.010 0.001 HIS C 191 PHE 0.058 0.002 PHE B 258 TYR 0.030 0.002 TYR C 74 ARG 0.015 0.001 ARG C 169 Details of bonding type rmsd link_NAG-ASN : bond 0.08674 ( 7) link_NAG-ASN : angle 2.74743 ( 21) link_ALPHA1-6 : bond 0.01264 ( 1) link_ALPHA1-6 : angle 2.39473 ( 3) link_BETA1-4 : bond 0.00611 ( 7) link_BETA1-4 : angle 4.15882 ( 21) link_ALPHA1-2 : bond 0.00220 ( 1) link_ALPHA1-2 : angle 2.09002 ( 3) link_ALPHA1-3 : bond 0.00968 ( 2) link_ALPHA1-3 : angle 2.05569 ( 6) hydrogen bonds : bond 0.22960 ( 602) hydrogen bonds : angle 9.32083 ( 1959) SS BOND : bond 0.00310 ( 7) SS BOND : angle 0.62809 ( 14) covalent geometry : bond 0.00698 (14826) covalent geometry : angle 1.08051 (20151) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 607 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8764 (m) cc_final: 0.8314 (p) REVERT: A 147 GLU cc_start: 0.7580 (tt0) cc_final: 0.7316 (tt0) REVERT: A 157 TYR cc_start: 0.8389 (t80) cc_final: 0.8163 (t80) REVERT: A 207 ARG cc_start: 0.8659 (ttm170) cc_final: 0.8102 (ttm170) REVERT: A 220 TYR cc_start: 0.6856 (t80) cc_final: 0.6551 (t80) REVERT: A 226 TYR cc_start: 0.8028 (m-80) cc_final: 0.7666 (m-80) REVERT: A 233 THR cc_start: 0.8023 (p) cc_final: 0.7741 (t) REVERT: A 237 TRP cc_start: 0.7935 (m-10) cc_final: 0.7511 (m-90) REVERT: A 284 TYR cc_start: 0.8123 (t80) cc_final: 0.7876 (t80) REVERT: A 297 LEU cc_start: 0.7667 (tt) cc_final: 0.7461 (tt) REVERT: A 299 TYR cc_start: 0.7944 (t80) cc_final: 0.7547 (t80) REVERT: A 482 TYR cc_start: 0.6173 (t80) cc_final: 0.5670 (t80) REVERT: B 130 THR cc_start: 0.8327 (m) cc_final: 0.7889 (p) REVERT: B 194 LEU cc_start: 0.9269 (mt) cc_final: 0.8957 (mp) REVERT: B 215 THR cc_start: 0.8867 (m) cc_final: 0.8378 (p) REVERT: B 386 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6861 (t80) REVERT: C 27 LEU cc_start: 0.8343 (mt) cc_final: 0.8098 (mt) REVERT: C 57 TYR cc_start: 0.8379 (p90) cc_final: 0.7927 (p90) REVERT: C 90 GLN cc_start: 0.8365 (mt0) cc_final: 0.8115 (mp10) REVERT: C 95 ASP cc_start: 0.8359 (p0) cc_final: 0.7681 (p0) REVERT: C 159 TYR cc_start: 0.8347 (m-80) cc_final: 0.7867 (m-80) REVERT: C 211 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7780 (p) REVERT: C 240 PHE cc_start: 0.6959 (m-10) cc_final: 0.6564 (m-10) REVERT: D 57 MET cc_start: 0.8277 (mtt) cc_final: 0.7732 (ttm) REVERT: D 83 LEU cc_start: 0.8582 (mt) cc_final: 0.7933 (mt) REVERT: I 90 GLN cc_start: 0.8525 (pp30) cc_final: 0.8318 (pp30) REVERT: I 102 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8269 (ttmt) REVERT: J 29 ILE cc_start: 0.9440 (pt) cc_final: 0.9216 (mt) REVERT: J 38 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8219 (tttt) REVERT: J 46 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7159 (mm-30) REVERT: J 48 ILE cc_start: 0.9308 (mm) cc_final: 0.8912 (mm) REVERT: J 67 LYS cc_start: 0.8234 (ptmm) cc_final: 0.7620 (tttp) REVERT: J 74 THR cc_start: 0.8407 (m) cc_final: 0.7694 (p) REVERT: J 81 LEU cc_start: 0.6828 (mt) cc_final: 0.6471 (mt) REVERT: J 99 LYS cc_start: 0.8541 (tmtt) cc_final: 0.8336 (tmtt) REVERT: J 103 TRP cc_start: 0.8803 (m100) cc_final: 0.8508 (m100) outliers start: 29 outliers final: 8 residues processed: 619 average time/residue: 0.2691 time to fit residues: 237.5363 Evaluate side-chains 359 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 348 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 386 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain I residue 102 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 119 HIS B 116 ASN B 308 ASN C 65 GLN D 67 GLN D 109 HIS E 60 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.139796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106683 restraints weight = 29852.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109517 restraints weight = 16019.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.111297 restraints weight = 10798.653| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14851 Z= 0.178 Angle : 0.740 9.634 20219 Z= 0.371 Chirality : 0.046 0.187 2326 Planarity : 0.006 0.056 2480 Dihedral : 9.035 78.886 2332 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.37 % Allowed : 14.56 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -1.45 (0.19), residues: 1733 helix: -0.36 (0.23), residues: 445 sheet: -0.90 (0.21), residues: 559 loop : -1.22 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 67 HIS 0.006 0.001 HIS B 110 PHE 0.035 0.002 PHE C 221 TYR 0.019 0.002 TYR C 277 ARG 0.007 0.001 ARG E 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 7) link_NAG-ASN : angle 2.58222 ( 21) link_ALPHA1-6 : bond 0.00184 ( 1) link_ALPHA1-6 : angle 1.85915 ( 3) link_BETA1-4 : bond 0.00409 ( 7) link_BETA1-4 : angle 2.99692 ( 21) link_ALPHA1-2 : bond 0.00744 ( 1) link_ALPHA1-2 : angle 1.80027 ( 3) link_ALPHA1-3 : bond 0.00519 ( 2) link_ALPHA1-3 : angle 1.64986 ( 6) hydrogen bonds : bond 0.04637 ( 602) hydrogen bonds : angle 5.57654 ( 1959) SS BOND : bond 0.00875 ( 7) SS BOND : angle 1.18626 ( 14) covalent geometry : bond 0.00395 (14826) covalent geometry : angle 0.72794 (20151) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 357 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8449 (mmm) cc_final: 0.7698 (mmm) REVERT: A 58 THR cc_start: 0.8943 (m) cc_final: 0.8663 (p) REVERT: A 72 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8835 (mt) REVERT: A 95 ASP cc_start: 0.8366 (t0) cc_final: 0.7723 (t0) REVERT: A 157 TYR cc_start: 0.8153 (t80) cc_final: 0.7941 (t80) REVERT: A 269 ARG cc_start: 0.7261 (ptm160) cc_final: 0.7055 (ptm160) REVERT: A 284 TYR cc_start: 0.8185 (t80) cc_final: 0.7782 (t80) REVERT: A 482 TYR cc_start: 0.6350 (t80) cc_final: 0.6010 (t80) REVERT: B 126 THR cc_start: 0.9009 (m) cc_final: 0.8538 (p) REVERT: B 274 ARG cc_start: 0.7721 (tpt-90) cc_final: 0.7439 (tpt-90) REVERT: C 27 LEU cc_start: 0.8200 (mt) cc_final: 0.7931 (mt) REVERT: C 40 MET cc_start: 0.7628 (mtt) cc_final: 0.7381 (mtt) REVERT: C 95 ASP cc_start: 0.8336 (p0) cc_final: 0.8049 (p0) REVERT: C 190 GLU cc_start: 0.6717 (pm20) cc_final: 0.5985 (pm20) REVERT: C 213 ARG cc_start: 0.7028 (ttp-170) cc_final: 0.6658 (ttp80) REVERT: D 121 GLN cc_start: 0.7867 (tt0) cc_final: 0.7599 (tt0) REVERT: I 86 TYR cc_start: 0.7725 (m-80) cc_final: 0.7298 (m-10) REVERT: I 94 TYR cc_start: 0.8511 (m-80) cc_final: 0.8290 (m-80) REVERT: J 29 ILE cc_start: 0.9414 (pt) cc_final: 0.9150 (mt) REVERT: J 34 MET cc_start: 0.8788 (mmm) cc_final: 0.8502 (mmp) REVERT: J 52 ASP cc_start: 0.8492 (t0) cc_final: 0.8231 (t0) REVERT: J 67 LYS cc_start: 0.7976 (ptmm) cc_final: 0.7484 (tttp) REVERT: J 95 TYR cc_start: 0.8064 (m-80) cc_final: 0.7534 (m-80) outliers start: 53 outliers final: 28 residues processed: 384 average time/residue: 0.2386 time to fit residues: 136.1112 Evaluate side-chains 337 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 308 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 106 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 128 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN D 109 HIS D 307 ASN E 60 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.128896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096429 restraints weight = 31026.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098789 restraints weight = 17499.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100284 restraints weight = 12223.637| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 14851 Z= 0.274 Angle : 0.761 8.694 20219 Z= 0.384 Chirality : 0.048 0.245 2326 Planarity : 0.005 0.044 2480 Dihedral : 7.700 69.418 2316 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.15 % Allowed : 16.66 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -0.98 (0.20), residues: 1733 helix: 0.37 (0.24), residues: 442 sheet: -0.87 (0.21), residues: 560 loop : -0.97 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 36 HIS 0.007 0.002 HIS E 54 PHE 0.027 0.002 PHE A 221 TYR 0.028 0.002 TYR C 66 ARG 0.008 0.001 ARG J 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 7) link_NAG-ASN : angle 2.51396 ( 21) link_ALPHA1-6 : bond 0.00442 ( 1) link_ALPHA1-6 : angle 2.52776 ( 3) link_BETA1-4 : bond 0.00374 ( 7) link_BETA1-4 : angle 3.04799 ( 21) link_ALPHA1-2 : bond 0.00163 ( 1) link_ALPHA1-2 : angle 1.82562 ( 3) link_ALPHA1-3 : bond 0.00406 ( 2) link_ALPHA1-3 : angle 2.05185 ( 6) hydrogen bonds : bond 0.04311 ( 602) hydrogen bonds : angle 5.16871 ( 1959) SS BOND : bond 0.00410 ( 7) SS BOND : angle 1.12064 ( 14) covalent geometry : bond 0.00626 (14826) covalent geometry : angle 0.74962 (20151) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 318 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8622 (mmm) cc_final: 0.7137 (mmm) REVERT: A 58 THR cc_start: 0.9064 (m) cc_final: 0.8654 (p) REVERT: A 95 ASP cc_start: 0.8345 (t0) cc_final: 0.7794 (t0) REVERT: A 137 MET cc_start: 0.8260 (mmt) cc_final: 0.7940 (mmm) REVERT: A 157 TYR cc_start: 0.8526 (t80) cc_final: 0.8239 (t80) REVERT: A 237 TRP cc_start: 0.8085 (m-10) cc_final: 0.7552 (m-90) REVERT: A 284 TYR cc_start: 0.8244 (t80) cc_final: 0.8000 (t80) REVERT: A 298 GLU cc_start: 0.8362 (tp30) cc_final: 0.8026 (tp30) REVERT: A 482 TYR cc_start: 0.6866 (t80) cc_final: 0.6161 (t80) REVERT: B 15 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7949 (m-10) REVERT: B 126 THR cc_start: 0.9044 (m) cc_final: 0.8511 (p) REVERT: C 27 LEU cc_start: 0.8310 (mt) cc_final: 0.8103 (mm) REVERT: C 40 MET cc_start: 0.7923 (mtt) cc_final: 0.7510 (mtt) REVERT: C 57 TYR cc_start: 0.8717 (p90) cc_final: 0.8316 (p90) REVERT: C 95 ASP cc_start: 0.8656 (p0) cc_final: 0.8227 (p0) REVERT: C 190 GLU cc_start: 0.6980 (pm20) cc_final: 0.6036 (pm20) REVERT: C 213 ARG cc_start: 0.7138 (ttp-170) cc_final: 0.6740 (ttp80) REVERT: D 68 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8382 (mttt) REVERT: D 121 GLN cc_start: 0.7818 (tt0) cc_final: 0.7400 (tt0) REVERT: D 165 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: E 102 MET cc_start: 0.7780 (ttt) cc_final: 0.7509 (tpt) REVERT: E 189 GLU cc_start: 0.8523 (tp30) cc_final: 0.8317 (tp30) REVERT: I 92 TYR cc_start: 0.9460 (t80) cc_final: 0.9215 (t80) REVERT: I 94 TYR cc_start: 0.8577 (m-80) cc_final: 0.8323 (m-80) REVERT: J 29 ILE cc_start: 0.9497 (pt) cc_final: 0.9015 (mt) REVERT: J 52 ASP cc_start: 0.8541 (t0) cc_final: 0.8307 (t0) REVERT: J 67 LYS cc_start: 0.8185 (ptmm) cc_final: 0.7685 (tttp) outliers start: 81 outliers final: 52 residues processed: 364 average time/residue: 0.2452 time to fit residues: 132.8461 Evaluate side-chains 344 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 289 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 10 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 303 ASN D 135 GLN E 60 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.131044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098868 restraints weight = 30666.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101324 restraints weight = 17106.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102827 restraints weight = 11812.310| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14851 Z= 0.153 Angle : 0.656 8.730 20219 Z= 0.326 Chirality : 0.045 0.199 2326 Planarity : 0.004 0.043 2480 Dihedral : 6.808 63.406 2312 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.01 % Allowed : 18.50 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -0.65 (0.20), residues: 1733 helix: 0.66 (0.25), residues: 446 sheet: -0.73 (0.21), residues: 570 loop : -0.70 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 67 HIS 0.009 0.001 HIS C 267 PHE 0.039 0.002 PHE B 404 TYR 0.020 0.002 TYR A 220 ARG 0.006 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 7) link_NAG-ASN : angle 2.23649 ( 21) link_ALPHA1-6 : bond 0.00041 ( 1) link_ALPHA1-6 : angle 2.00458 ( 3) link_BETA1-4 : bond 0.00328 ( 7) link_BETA1-4 : angle 2.60612 ( 21) link_ALPHA1-2 : bond 0.00491 ( 1) link_ALPHA1-2 : angle 1.75211 ( 3) link_ALPHA1-3 : bond 0.00804 ( 2) link_ALPHA1-3 : angle 1.64631 ( 6) hydrogen bonds : bond 0.03611 ( 602) hydrogen bonds : angle 4.78701 ( 1959) SS BOND : bond 0.00414 ( 7) SS BOND : angle 0.60612 ( 14) covalent geometry : bond 0.00344 (14826) covalent geometry : angle 0.64567 (20151) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 312 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9096 (m) cc_final: 0.8765 (p) REVERT: A 95 ASP cc_start: 0.8432 (t0) cc_final: 0.7931 (t0) REVERT: A 115 MET cc_start: 0.7433 (ttm) cc_final: 0.7163 (ttt) REVERT: A 157 TYR cc_start: 0.8453 (t80) cc_final: 0.8112 (t80) REVERT: A 207 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7737 (ttm170) REVERT: A 237 TRP cc_start: 0.8117 (m-10) cc_final: 0.7587 (m-90) REVERT: A 274 LYS cc_start: 0.8530 (mttp) cc_final: 0.8189 (ptpt) REVERT: A 284 TYR cc_start: 0.8120 (t80) cc_final: 0.7866 (t80) REVERT: A 298 GLU cc_start: 0.8397 (tp30) cc_final: 0.7940 (tp30) REVERT: A 482 TYR cc_start: 0.6717 (t80) cc_final: 0.6074 (t80) REVERT: B 34 LEU cc_start: 0.8734 (tp) cc_final: 0.8442 (tp) REVERT: B 126 THR cc_start: 0.8991 (m) cc_final: 0.8498 (p) REVERT: B 141 MET cc_start: 0.8149 (mtt) cc_final: 0.7916 (mtt) REVERT: B 274 ARG cc_start: 0.7917 (tpt-90) cc_final: 0.7488 (tpt-90) REVERT: C 57 TYR cc_start: 0.8630 (p90) cc_final: 0.8250 (p90) REVERT: C 95 ASP cc_start: 0.8652 (p0) cc_final: 0.8202 (p0) REVERT: C 147 GLU cc_start: 0.7942 (pt0) cc_final: 0.7680 (mt-10) REVERT: C 165 GLU cc_start: 0.7681 (tp30) cc_final: 0.7204 (mm-30) REVERT: D 111 MET cc_start: 0.7603 (tpp) cc_final: 0.6748 (tpp) REVERT: D 121 GLN cc_start: 0.7807 (tt0) cc_final: 0.7409 (tt0) REVERT: D 147 MET cc_start: 0.8333 (mpp) cc_final: 0.7993 (mpp) REVERT: D 165 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: E 152 GLN cc_start: 0.6846 (mp10) cc_final: 0.6522 (pm20) REVERT: E 189 GLU cc_start: 0.8487 (tp30) cc_final: 0.8281 (tp30) REVERT: I 37 GLN cc_start: 0.7421 (tm-30) cc_final: 0.7097 (tm-30) REVERT: I 92 TYR cc_start: 0.9410 (t80) cc_final: 0.9124 (t80) REVERT: I 94 TYR cc_start: 0.8511 (m-80) cc_final: 0.8294 (m-80) REVERT: J 29 ILE cc_start: 0.9407 (pt) cc_final: 0.8824 (mt) REVERT: J 52 ASP cc_start: 0.8525 (t0) cc_final: 0.8299 (t0) REVERT: J 67 LYS cc_start: 0.8208 (ptmm) cc_final: 0.7678 (tttp) REVERT: J 82 GLN cc_start: 0.7492 (mp-120) cc_final: 0.7260 (mp10) outliers start: 63 outliers final: 39 residues processed: 354 average time/residue: 0.2597 time to fit residues: 136.4023 Evaluate side-chains 333 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 106 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 61 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 125 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN E 60 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.128189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096142 restraints weight = 31399.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098520 restraints weight = 17631.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100033 restraints weight = 12242.073| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 14851 Z= 0.228 Angle : 0.712 8.196 20219 Z= 0.354 Chirality : 0.046 0.233 2326 Planarity : 0.005 0.041 2480 Dihedral : 6.675 58.087 2312 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.64 % Allowed : 19.83 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -0.63 (0.20), residues: 1733 helix: 0.73 (0.25), residues: 444 sheet: -0.77 (0.21), residues: 577 loop : -0.70 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 241 HIS 0.011 0.001 HIS C 267 PHE 0.053 0.002 PHE B 404 TYR 0.022 0.002 TYR C 66 ARG 0.011 0.001 ARG C 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 7) link_NAG-ASN : angle 2.53930 ( 21) link_ALPHA1-6 : bond 0.00376 ( 1) link_ALPHA1-6 : angle 2.45060 ( 3) link_BETA1-4 : bond 0.00275 ( 7) link_BETA1-4 : angle 2.89644 ( 21) link_ALPHA1-2 : bond 0.00154 ( 1) link_ALPHA1-2 : angle 1.93799 ( 3) link_ALPHA1-3 : bond 0.00471 ( 2) link_ALPHA1-3 : angle 1.85797 ( 6) hydrogen bonds : bond 0.03789 ( 602) hydrogen bonds : angle 4.78092 ( 1959) SS BOND : bond 0.00249 ( 7) SS BOND : angle 0.79021 ( 14) covalent geometry : bond 0.00520 (14826) covalent geometry : angle 0.70025 (20151) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 293 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8605 (mmm) cc_final: 0.8041 (mmm) REVERT: A 58 THR cc_start: 0.9097 (m) cc_final: 0.8730 (p) REVERT: A 95 ASP cc_start: 0.8496 (t0) cc_final: 0.7847 (t0) REVERT: A 157 TYR cc_start: 0.8699 (t80) cc_final: 0.8272 (t80) REVERT: A 274 LYS cc_start: 0.8615 (mttp) cc_final: 0.8273 (ptpt) REVERT: A 284 TYR cc_start: 0.8049 (t80) cc_final: 0.7793 (t80) REVERT: A 298 GLU cc_start: 0.8363 (tp30) cc_final: 0.7932 (tp30) REVERT: A 482 TYR cc_start: 0.6830 (t80) cc_final: 0.6236 (t80) REVERT: B 126 THR cc_start: 0.9008 (m) cc_final: 0.8467 (p) REVERT: C 40 MET cc_start: 0.7977 (mtt) cc_final: 0.7427 (mtt) REVERT: C 95 ASP cc_start: 0.8663 (p0) cc_final: 0.8152 (p0) REVERT: C 165 GLU cc_start: 0.7703 (tp30) cc_final: 0.7231 (mm-30) REVERT: D 91 SER cc_start: 0.8741 (m) cc_final: 0.8342 (t) REVERT: D 121 GLN cc_start: 0.7806 (tt0) cc_final: 0.7420 (tt0) REVERT: D 147 MET cc_start: 0.8432 (mpp) cc_final: 0.8150 (mpp) REVERT: D 235 MET cc_start: 0.8164 (ttm) cc_final: 0.7804 (ttt) REVERT: D 241 GLN cc_start: 0.4608 (mt0) cc_final: 0.3787 (tm-30) REVERT: E 130 MET cc_start: 0.7674 (ttp) cc_final: 0.7427 (ptm) REVERT: E 189 GLU cc_start: 0.8569 (tp30) cc_final: 0.8355 (tp30) REVERT: I 92 TYR cc_start: 0.9406 (t80) cc_final: 0.9193 (t80) REVERT: I 94 TYR cc_start: 0.8562 (m-80) cc_final: 0.8353 (m-80) REVERT: J 34 MET cc_start: 0.8790 (mmm) cc_final: 0.8357 (mmp) REVERT: J 67 LYS cc_start: 0.8196 (ptmm) cc_final: 0.7774 (tttp) REVERT: J 82 GLN cc_start: 0.7512 (mp-120) cc_final: 0.7263 (mm-40) outliers start: 73 outliers final: 59 residues processed: 338 average time/residue: 0.2495 time to fit residues: 124.8871 Evaluate side-chains 337 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 278 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 ASN C 303 ASN E 60 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.127683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.095268 restraints weight = 31790.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097692 restraints weight = 17698.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099217 restraints weight = 12262.907| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14851 Z= 0.229 Angle : 0.700 8.210 20219 Z= 0.351 Chirality : 0.046 0.303 2326 Planarity : 0.005 0.050 2480 Dihedral : 6.532 53.818 2312 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.40 % Allowed : 19.96 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -0.62 (0.20), residues: 1733 helix: 0.84 (0.25), residues: 443 sheet: -0.81 (0.20), residues: 583 loop : -0.69 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 245 HIS 0.014 0.001 HIS C 267 PHE 0.029 0.002 PHE B 404 TYR 0.034 0.002 TYR C 57 ARG 0.006 0.001 ARG E 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 7) link_NAG-ASN : angle 2.43531 ( 21) link_ALPHA1-6 : bond 0.00337 ( 1) link_ALPHA1-6 : angle 2.34966 ( 3) link_BETA1-4 : bond 0.00214 ( 7) link_BETA1-4 : angle 2.41438 ( 21) link_ALPHA1-2 : bond 0.00183 ( 1) link_ALPHA1-2 : angle 1.99827 ( 3) link_ALPHA1-3 : bond 0.00702 ( 2) link_ALPHA1-3 : angle 1.87247 ( 6) hydrogen bonds : bond 0.03637 ( 602) hydrogen bonds : angle 4.72747 ( 1959) SS BOND : bond 0.00262 ( 7) SS BOND : angle 1.01185 ( 14) covalent geometry : bond 0.00521 (14826) covalent geometry : angle 0.69040 (20151) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 292 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9041 (m) cc_final: 0.8669 (p) REVERT: A 237 TRP cc_start: 0.8029 (m-10) cc_final: 0.7262 (m-90) REVERT: A 270 GLU cc_start: 0.7636 (pm20) cc_final: 0.7375 (pm20) REVERT: A 274 LYS cc_start: 0.8688 (mttp) cc_final: 0.8310 (ptpt) REVERT: A 284 TYR cc_start: 0.8162 (t80) cc_final: 0.7934 (t80) REVERT: A 482 TYR cc_start: 0.6848 (t80) cc_final: 0.6201 (t80) REVERT: B 126 THR cc_start: 0.9017 (m) cc_final: 0.8479 (p) REVERT: B 148 MET cc_start: 0.8173 (ptp) cc_final: 0.7953 (ptm) REVERT: B 268 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8683 (t) REVERT: B 274 ARG cc_start: 0.8000 (tpt-90) cc_final: 0.7573 (tpt-90) REVERT: C 40 MET cc_start: 0.7972 (mtt) cc_final: 0.7413 (mtt) REVERT: C 90 GLN cc_start: 0.8663 (mp10) cc_final: 0.8177 (mt0) REVERT: C 95 ASP cc_start: 0.8747 (p0) cc_final: 0.8197 (p0) REVERT: C 165 GLU cc_start: 0.7696 (tp30) cc_final: 0.7210 (mm-30) REVERT: C 240 PHE cc_start: 0.7150 (m-80) cc_final: 0.6291 (m-10) REVERT: C 444 LEU cc_start: 0.8442 (mm) cc_final: 0.8018 (pp) REVERT: D 91 SER cc_start: 0.8751 (m) cc_final: 0.8381 (t) REVERT: D 111 MET cc_start: 0.7753 (tpp) cc_final: 0.6908 (tpp) REVERT: D 121 GLN cc_start: 0.7920 (tt0) cc_final: 0.7513 (tt0) REVERT: D 235 MET cc_start: 0.8074 (ttm) cc_final: 0.7751 (ttt) REVERT: D 241 GLN cc_start: 0.5081 (mt0) cc_final: 0.4248 (tm-30) REVERT: E 189 GLU cc_start: 0.8522 (tp30) cc_final: 0.8184 (tp30) REVERT: I 85 ASP cc_start: 0.7490 (m-30) cc_final: 0.7020 (m-30) REVERT: I 102 LYS cc_start: 0.8904 (tptt) cc_final: 0.8662 (tptt) REVERT: J 67 LYS cc_start: 0.8298 (ptmm) cc_final: 0.7809 (tttp) outliers start: 85 outliers final: 66 residues processed: 348 average time/residue: 0.2346 time to fit residues: 122.9909 Evaluate side-chains 342 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 257 PHE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 136 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.128728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096325 restraints weight = 31238.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.098763 restraints weight = 17332.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100312 restraints weight = 12007.382| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14851 Z= 0.171 Angle : 0.691 11.396 20219 Z= 0.339 Chirality : 0.046 0.356 2326 Planarity : 0.004 0.047 2480 Dihedral : 6.249 51.199 2312 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.96 % Allowed : 21.23 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -0.51 (0.20), residues: 1733 helix: 0.97 (0.25), residues: 441 sheet: -0.76 (0.20), residues: 588 loop : -0.64 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 245 HIS 0.018 0.001 HIS C 267 PHE 0.018 0.002 PHE A 221 TYR 0.028 0.002 TYR I 49 ARG 0.007 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 7) link_NAG-ASN : angle 2.39162 ( 21) link_ALPHA1-6 : bond 0.00010 ( 1) link_ALPHA1-6 : angle 2.13072 ( 3) link_BETA1-4 : bond 0.00244 ( 7) link_BETA1-4 : angle 2.30320 ( 21) link_ALPHA1-2 : bond 0.00251 ( 1) link_ALPHA1-2 : angle 2.00078 ( 3) link_ALPHA1-3 : bond 0.00805 ( 2) link_ALPHA1-3 : angle 1.69779 ( 6) hydrogen bonds : bond 0.03402 ( 602) hydrogen bonds : angle 4.65464 ( 1959) SS BOND : bond 0.00212 ( 7) SS BOND : angle 0.94161 ( 14) covalent geometry : bond 0.00389 (14826) covalent geometry : angle 0.68195 (20151) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 298 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8568 (mmm) cc_final: 0.8148 (mmm) REVERT: A 58 THR cc_start: 0.9001 (m) cc_final: 0.8605 (p) REVERT: A 237 TRP cc_start: 0.8055 (m-10) cc_final: 0.7298 (m-90) REVERT: A 270 GLU cc_start: 0.7563 (pm20) cc_final: 0.7273 (pm20) REVERT: A 274 LYS cc_start: 0.8731 (mttp) cc_final: 0.8362 (ptpt) REVERT: B 126 THR cc_start: 0.9015 (m) cc_final: 0.8479 (p) REVERT: B 148 MET cc_start: 0.8224 (ptp) cc_final: 0.7983 (ptm) REVERT: B 236 MET cc_start: 0.8264 (mmp) cc_final: 0.8054 (mmp) REVERT: B 268 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8691 (t) REVERT: C 40 MET cc_start: 0.7889 (mtt) cc_final: 0.7336 (mtt) REVERT: C 95 ASP cc_start: 0.8672 (p0) cc_final: 0.8112 (p0) REVERT: C 165 GLU cc_start: 0.7639 (tp30) cc_final: 0.7218 (mm-30) REVERT: C 240 PHE cc_start: 0.7049 (m-80) cc_final: 0.6251 (m-10) REVERT: C 444 LEU cc_start: 0.8450 (mm) cc_final: 0.8020 (pp) REVERT: D 91 SER cc_start: 0.8760 (m) cc_final: 0.8369 (t) REVERT: D 111 MET cc_start: 0.7738 (tpp) cc_final: 0.6938 (tpp) REVERT: D 121 GLN cc_start: 0.7900 (tt0) cc_final: 0.7498 (tt0) REVERT: D 235 MET cc_start: 0.8077 (ttm) cc_final: 0.7745 (ttt) REVERT: D 241 GLN cc_start: 0.5204 (mt0) cc_final: 0.4344 (tm-30) REVERT: E 60 ASN cc_start: 0.7642 (m-40) cc_final: 0.7245 (m110) REVERT: E 189 GLU cc_start: 0.8474 (tp30) cc_final: 0.8124 (tp30) REVERT: I 29 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8494 (m) REVERT: I 35 TRP cc_start: 0.8637 (m100) cc_final: 0.8374 (m-10) REVERT: J 34 MET cc_start: 0.8750 (mmm) cc_final: 0.8319 (mmp) REVERT: J 38 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8050 (tppt) REVERT: J 67 LYS cc_start: 0.8174 (ptmm) cc_final: 0.7837 (tttp) outliers start: 78 outliers final: 67 residues processed: 348 average time/residue: 0.2371 time to fit residues: 124.2991 Evaluate side-chains 357 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 287 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 257 PHE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 33 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 50 optimal weight: 0.0030 chunk 157 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097572 restraints weight = 31333.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100058 restraints weight = 17402.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101565 restraints weight = 12015.171| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14851 Z= 0.140 Angle : 0.678 12.415 20219 Z= 0.332 Chirality : 0.046 0.377 2326 Planarity : 0.004 0.044 2480 Dihedral : 5.925 47.395 2312 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.13 % Allowed : 22.50 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -0.37 (0.20), residues: 1733 helix: 1.10 (0.25), residues: 442 sheet: -0.67 (0.21), residues: 582 loop : -0.59 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 35 HIS 0.018 0.001 HIS C 267 PHE 0.026 0.001 PHE B 304 TYR 0.028 0.002 TYR A 299 ARG 0.007 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 7) link_NAG-ASN : angle 2.30781 ( 21) link_ALPHA1-6 : bond 0.00204 ( 1) link_ALPHA1-6 : angle 1.86784 ( 3) link_BETA1-4 : bond 0.00309 ( 7) link_BETA1-4 : angle 2.12292 ( 21) link_ALPHA1-2 : bond 0.00290 ( 1) link_ALPHA1-2 : angle 1.98210 ( 3) link_ALPHA1-3 : bond 0.00870 ( 2) link_ALPHA1-3 : angle 1.59256 ( 6) hydrogen bonds : bond 0.03238 ( 602) hydrogen bonds : angle 4.54202 ( 1959) SS BOND : bond 0.00279 ( 7) SS BOND : angle 1.39833 ( 14) covalent geometry : bond 0.00323 (14826) covalent geometry : angle 0.66947 (20151) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 303 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8988 (m) cc_final: 0.8605 (p) REVERT: A 95 ASP cc_start: 0.8514 (t0) cc_final: 0.7848 (t0) REVERT: A 139 ASP cc_start: 0.7524 (t0) cc_final: 0.7283 (p0) REVERT: A 270 GLU cc_start: 0.7646 (pm20) cc_final: 0.7383 (pm20) REVERT: A 274 LYS cc_start: 0.8680 (mttp) cc_final: 0.8303 (mmtp) REVERT: A 294 MET cc_start: 0.8868 (mmp) cc_final: 0.8005 (tpt) REVERT: A 482 TYR cc_start: 0.6507 (t80) cc_final: 0.6064 (t80) REVERT: B 126 THR cc_start: 0.8996 (m) cc_final: 0.8460 (p) REVERT: B 148 MET cc_start: 0.8274 (ptp) cc_final: 0.8009 (ptm) REVERT: B 268 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8670 (t) REVERT: B 274 ARG cc_start: 0.8007 (tpt-90) cc_final: 0.7612 (tpt-90) REVERT: B 400 PHE cc_start: 0.7497 (m-80) cc_final: 0.7284 (m-80) REVERT: C 40 MET cc_start: 0.7842 (mtt) cc_final: 0.7280 (mtt) REVERT: C 49 MET cc_start: 0.8474 (ppp) cc_final: 0.7725 (ppp) REVERT: C 90 GLN cc_start: 0.8590 (mp10) cc_final: 0.8154 (mt0) REVERT: C 95 ASP cc_start: 0.8679 (p0) cc_final: 0.8081 (p0) REVERT: C 165 GLU cc_start: 0.7734 (tp30) cc_final: 0.7327 (mm-30) REVERT: C 240 PHE cc_start: 0.7069 (m-80) cc_final: 0.6340 (m-10) REVERT: C 444 LEU cc_start: 0.8467 (mm) cc_final: 0.8039 (pp) REVERT: D 111 MET cc_start: 0.7717 (tpp) cc_final: 0.6970 (tpp) REVERT: D 121 GLN cc_start: 0.7883 (tt0) cc_final: 0.7473 (tt0) REVERT: D 235 MET cc_start: 0.8040 (ttm) cc_final: 0.7706 (ttt) REVERT: D 241 GLN cc_start: 0.5204 (mt0) cc_final: 0.4417 (tm-30) REVERT: E 60 ASN cc_start: 0.7665 (m-40) cc_final: 0.7272 (m110) REVERT: E 189 GLU cc_start: 0.8449 (tp30) cc_final: 0.8127 (tp30) REVERT: I 29 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8537 (m) REVERT: I 94 TYR cc_start: 0.8507 (m-80) cc_final: 0.8211 (m-80) REVERT: J 34 MET cc_start: 0.8767 (mmm) cc_final: 0.8543 (mmm) REVERT: J 36 TRP cc_start: 0.7935 (m100) cc_final: 0.7710 (m100) REVERT: J 38 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8117 (tppt) REVERT: J 52 ASP cc_start: 0.8625 (t0) cc_final: 0.8335 (t0) REVERT: J 67 LYS cc_start: 0.8208 (ptmm) cc_final: 0.7851 (tttp) outliers start: 65 outliers final: 57 residues processed: 349 average time/residue: 0.2417 time to fit residues: 128.2853 Evaluate side-chains 348 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 289 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 257 PHE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN B 88 ASN J 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.130287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098101 restraints weight = 30841.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.100522 restraints weight = 17052.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102109 restraints weight = 11796.935| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14851 Z= 0.138 Angle : 0.689 13.441 20219 Z= 0.336 Chirality : 0.046 0.381 2326 Planarity : 0.004 0.047 2480 Dihedral : 5.724 44.660 2312 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.26 % Allowed : 23.14 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -0.35 (0.21), residues: 1733 helix: 1.18 (0.25), residues: 442 sheet: -0.67 (0.21), residues: 586 loop : -0.59 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP I 35 HIS 0.022 0.001 HIS C 267 PHE 0.013 0.001 PHE A 221 TYR 0.029 0.002 TYR A 299 ARG 0.007 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 7) link_NAG-ASN : angle 2.26138 ( 21) link_ALPHA1-6 : bond 0.00356 ( 1) link_ALPHA1-6 : angle 1.78507 ( 3) link_BETA1-4 : bond 0.00288 ( 7) link_BETA1-4 : angle 2.05190 ( 21) link_ALPHA1-2 : bond 0.00274 ( 1) link_ALPHA1-2 : angle 1.93468 ( 3) link_ALPHA1-3 : bond 0.00993 ( 2) link_ALPHA1-3 : angle 1.59849 ( 6) hydrogen bonds : bond 0.03190 ( 602) hydrogen bonds : angle 4.53166 ( 1959) SS BOND : bond 0.00211 ( 7) SS BOND : angle 1.36524 ( 14) covalent geometry : bond 0.00318 (14826) covalent geometry : angle 0.68056 (20151) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8989 (m) cc_final: 0.8615 (p) REVERT: A 61 MET cc_start: 0.8084 (ptp) cc_final: 0.7860 (ptp) REVERT: A 95 ASP cc_start: 0.8491 (t0) cc_final: 0.7851 (t0) REVERT: A 139 ASP cc_start: 0.7518 (t0) cc_final: 0.7180 (p0) REVERT: A 237 TRP cc_start: 0.7956 (m-10) cc_final: 0.7599 (m-90) REVERT: A 270 GLU cc_start: 0.7643 (pm20) cc_final: 0.7403 (pm20) REVERT: A 274 LYS cc_start: 0.8703 (mttp) cc_final: 0.8310 (mmtp) REVERT: A 294 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.7996 (tpt) REVERT: B 126 THR cc_start: 0.8993 (m) cc_final: 0.8470 (p) REVERT: B 148 MET cc_start: 0.8299 (ptp) cc_final: 0.8064 (ptm) REVERT: B 268 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8692 (t) REVERT: B 282 TYR cc_start: 0.7710 (p90) cc_final: 0.7475 (p90) REVERT: C 40 MET cc_start: 0.7750 (mtt) cc_final: 0.7266 (mtt) REVERT: C 49 MET cc_start: 0.8346 (ppp) cc_final: 0.7830 (ppp) REVERT: C 90 GLN cc_start: 0.8556 (mp10) cc_final: 0.8106 (mt0) REVERT: C 95 ASP cc_start: 0.8657 (p0) cc_final: 0.8000 (p0) REVERT: C 165 GLU cc_start: 0.7623 (tp30) cc_final: 0.7306 (mm-30) REVERT: C 240 PHE cc_start: 0.7001 (m-80) cc_final: 0.6248 (m-10) REVERT: C 444 LEU cc_start: 0.8432 (mm) cc_final: 0.8044 (pp) REVERT: D 56 ASP cc_start: 0.8725 (m-30) cc_final: 0.8130 (m-30) REVERT: D 111 MET cc_start: 0.7642 (tpp) cc_final: 0.6943 (tpp) REVERT: D 121 GLN cc_start: 0.7842 (tt0) cc_final: 0.7468 (tt0) REVERT: D 235 MET cc_start: 0.8030 (ttm) cc_final: 0.7715 (ttt) REVERT: D 241 GLN cc_start: 0.5346 (mt0) cc_final: 0.4536 (tm-30) REVERT: E 60 ASN cc_start: 0.7589 (m-40) cc_final: 0.7205 (m110) REVERT: E 189 GLU cc_start: 0.8431 (tp30) cc_final: 0.8091 (tp30) REVERT: I 29 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8505 (m) REVERT: I 37 GLN cc_start: 0.7329 (tp40) cc_final: 0.7090 (tp40) REVERT: I 94 TYR cc_start: 0.8526 (m-80) cc_final: 0.8242 (m-80) REVERT: J 6 GLN cc_start: 0.7444 (mp10) cc_final: 0.6120 (mp10) REVERT: J 34 MET cc_start: 0.8744 (mmm) cc_final: 0.8421 (mmp) REVERT: J 36 TRP cc_start: 0.7909 (m100) cc_final: 0.7646 (m100) REVERT: J 52 ASP cc_start: 0.8562 (t0) cc_final: 0.8259 (t0) REVERT: J 67 LYS cc_start: 0.8209 (ptmm) cc_final: 0.7839 (tttp) REVERT: J 82 GLN cc_start: 0.7242 (mp-120) cc_final: 0.6990 (mp10) outliers start: 67 outliers final: 57 residues processed: 344 average time/residue: 0.2280 time to fit residues: 119.3729 Evaluate side-chains 344 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 257 PHE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 24 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.131758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099554 restraints weight = 30915.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102073 restraints weight = 17027.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103624 restraints weight = 11638.670| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14851 Z= 0.123 Angle : 0.711 13.752 20219 Z= 0.344 Chirality : 0.046 0.383 2326 Planarity : 0.004 0.079 2480 Dihedral : 5.498 41.338 2312 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.24 % Allowed : 24.28 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -0.31 (0.21), residues: 1733 helix: 1.24 (0.25), residues: 447 sheet: -0.64 (0.21), residues: 583 loop : -0.62 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP I 35 HIS 0.024 0.001 HIS C 267 PHE 0.022 0.001 PHE I 62 TYR 0.021 0.001 TYR I 49 ARG 0.009 0.001 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 7) link_NAG-ASN : angle 2.16278 ( 21) link_ALPHA1-6 : bond 0.00466 ( 1) link_ALPHA1-6 : angle 1.56723 ( 3) link_BETA1-4 : bond 0.00330 ( 7) link_BETA1-4 : angle 1.92158 ( 21) link_ALPHA1-2 : bond 0.00329 ( 1) link_ALPHA1-2 : angle 1.88596 ( 3) link_ALPHA1-3 : bond 0.00955 ( 2) link_ALPHA1-3 : angle 1.43873 ( 6) hydrogen bonds : bond 0.03093 ( 602) hydrogen bonds : angle 4.52328 ( 1959) SS BOND : bond 0.00228 ( 7) SS BOND : angle 1.28536 ( 14) covalent geometry : bond 0.00283 (14826) covalent geometry : angle 0.70448 (20151) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 289 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8981 (m) cc_final: 0.8654 (p) REVERT: A 61 MET cc_start: 0.8136 (ptp) cc_final: 0.7933 (ptp) REVERT: A 95 ASP cc_start: 0.8507 (t0) cc_final: 0.7865 (t0) REVERT: A 139 ASP cc_start: 0.7567 (t0) cc_final: 0.7073 (p0) REVERT: A 226 TYR cc_start: 0.7921 (m-80) cc_final: 0.7693 (m-80) REVERT: A 237 TRP cc_start: 0.7937 (m-10) cc_final: 0.7581 (m-90) REVERT: A 274 LYS cc_start: 0.8675 (mttp) cc_final: 0.8230 (ptpt) REVERT: A 294 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8020 (tpt) REVERT: B 148 MET cc_start: 0.8326 (ptp) cc_final: 0.8107 (ptm) REVERT: B 268 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8678 (t) REVERT: C 40 MET cc_start: 0.7664 (mtt) cc_final: 0.7228 (mtt) REVERT: C 49 MET cc_start: 0.8273 (ppp) cc_final: 0.7826 (ppp) REVERT: C 55 MET cc_start: 0.8638 (mtt) cc_final: 0.8260 (mtt) REVERT: C 56 ASP cc_start: 0.8366 (p0) cc_final: 0.7808 (p0) REVERT: C 90 GLN cc_start: 0.8528 (mp10) cc_final: 0.8076 (mt0) REVERT: C 95 ASP cc_start: 0.8626 (p0) cc_final: 0.7972 (p0) REVERT: C 157 TYR cc_start: 0.8646 (t80) cc_final: 0.8445 (t80) REVERT: C 165 GLU cc_start: 0.7622 (tp30) cc_final: 0.7344 (mm-30) REVERT: C 226 TYR cc_start: 0.7480 (m-80) cc_final: 0.7204 (m-80) REVERT: C 240 PHE cc_start: 0.6926 (m-80) cc_final: 0.6279 (m-10) REVERT: C 444 LEU cc_start: 0.8411 (mm) cc_final: 0.8063 (pp) REVERT: D 111 MET cc_start: 0.7670 (tpp) cc_final: 0.7003 (tpp) REVERT: D 121 GLN cc_start: 0.7817 (tt0) cc_final: 0.7413 (tt0) REVERT: D 235 MET cc_start: 0.8010 (ttm) cc_final: 0.7695 (ttt) REVERT: D 241 GLN cc_start: 0.5172 (mt0) cc_final: 0.4439 (tm-30) REVERT: E 60 ASN cc_start: 0.7582 (m-40) cc_final: 0.7194 (m110) REVERT: E 189 GLU cc_start: 0.8398 (tp30) cc_final: 0.8154 (tp30) REVERT: I 29 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8487 (m) REVERT: I 37 GLN cc_start: 0.7316 (tp40) cc_final: 0.7115 (tp40) REVERT: I 94 TYR cc_start: 0.8477 (m-80) cc_final: 0.8225 (m-80) REVERT: I 102 LYS cc_start: 0.8696 (tptt) cc_final: 0.8480 (tptt) REVERT: J 6 GLN cc_start: 0.7372 (mp10) cc_final: 0.5421 (mt0) REVERT: J 34 MET cc_start: 0.8695 (mmm) cc_final: 0.8399 (mmp) REVERT: J 36 TRP cc_start: 0.7843 (m100) cc_final: 0.7499 (m100) REVERT: J 52 ASP cc_start: 0.8524 (t0) cc_final: 0.8223 (t0) REVERT: J 67 LYS cc_start: 0.8275 (ptmm) cc_final: 0.7895 (tttp) outliers start: 51 outliers final: 40 residues processed: 321 average time/residue: 0.2286 time to fit residues: 112.2811 Evaluate side-chains 323 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 257 PHE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 4 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 122 optimal weight: 30.0000 chunk 152 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN J 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.132238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099917 restraints weight = 30932.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102426 restraints weight = 17069.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103983 restraints weight = 11731.162| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14851 Z= 0.121 Angle : 0.702 13.751 20219 Z= 0.339 Chirality : 0.046 0.389 2326 Planarity : 0.004 0.071 2480 Dihedral : 5.340 39.480 2312 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.18 % Allowed : 24.54 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.30 % 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: -0.20 (0.21), residues: 1733 helix: 1.37 (0.26), residues: 442 sheet: -0.54 (0.21), residues: 575 loop : -0.60 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 35 HIS 0.022 0.001 HIS C 267 PHE 0.021 0.001 PHE B 304 TYR 0.021 0.001 TYR I 49 ARG 0.008 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 7) link_NAG-ASN : angle 2.13248 ( 21) link_ALPHA1-6 : bond 0.00614 ( 1) link_ALPHA1-6 : angle 1.55857 ( 3) link_BETA1-4 : bond 0.00336 ( 7) link_BETA1-4 : angle 1.86259 ( 21) link_ALPHA1-2 : bond 0.00283 ( 1) link_ALPHA1-2 : angle 1.87806 ( 3) link_ALPHA1-3 : bond 0.01002 ( 2) link_ALPHA1-3 : angle 1.46675 ( 6) hydrogen bonds : bond 0.03067 ( 602) hydrogen bonds : angle 4.49121 ( 1959) SS BOND : bond 0.00271 ( 7) SS BOND : angle 1.27826 ( 14) covalent geometry : bond 0.00281 (14826) covalent geometry : angle 0.69574 (20151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4915.51 seconds wall clock time: 86 minutes 49.16 seconds (5209.16 seconds total)