Starting phenix.real_space_refine on Thu Jun 12 22:54:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctj_45908/06_2025/9ctj_45908.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctj_45908/06_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_45908/06_2025/9ctj_45908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctj_45908/06_2025/9ctj_45908.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctj_45908/06_2025/9ctj_45908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctj_45908/06_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-5710/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: 8.81, per 1000 atoms: 0.61 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: 3.79 Conformation dependent library (CDL) restraints added in 2.1 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: 1.81 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: 5.05 Time building geometry restraints manager: 4.46 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: 1.140 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.070 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- 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 : 1.558 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: 0.2730 time to fit residues: 241.2181 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 : 1.693 ------------------------------------------------------------------------------- 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 = 0.139763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106660 restraints weight = 29851.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109512 restraints weight = 16009.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.111290 restraints weight = 10774.054| |-----------------------------------------------------------------------------| 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 : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8450 (mmm) cc_final: 0.7698 (mmm) REVERT: A 58 THR cc_start: 0.8943 (m) cc_final: 0.8664 (p) REVERT: A 72 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8835 (mt) REVERT: A 95 ASP cc_start: 0.8366 (t0) cc_final: 0.7724 (t0) REVERT: A 157 TYR cc_start: 0.8151 (t80) cc_final: 0.7941 (t80) REVERT: A 269 ARG cc_start: 0.7261 (ptm160) cc_final: 0.7054 (ptm160) REVERT: A 284 TYR cc_start: 0.8185 (t80) cc_final: 0.7784 (t80) REVERT: A 482 TYR cc_start: 0.6350 (t80) cc_final: 0.6011 (t80) REVERT: B 126 THR cc_start: 0.9008 (m) cc_final: 0.8538 (p) REVERT: B 274 ARG cc_start: 0.7722 (tpt-90) cc_final: 0.7439 (tpt-90) REVERT: C 27 LEU cc_start: 0.8200 (mt) cc_final: 0.7932 (mt) REVERT: C 40 MET cc_start: 0.7628 (mtt) cc_final: 0.7380 (mtt) REVERT: C 95 ASP cc_start: 0.8336 (p0) cc_final: 0.8049 (p0) REVERT: C 190 GLU cc_start: 0.6716 (pm20) cc_final: 0.5983 (pm20) REVERT: C 213 ARG cc_start: 0.7027 (ttp-170) cc_final: 0.6657 (ttp80) REVERT: D 121 GLN cc_start: 0.7867 (tt0) cc_final: 0.7598 (tt0) REVERT: I 86 TYR cc_start: 0.7721 (m-80) cc_final: 0.7295 (m-10) REVERT: I 94 TYR cc_start: 0.8510 (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: 0.8501 (mmp) REVERT: J 52 ASP cc_start: 0.8491 (t0) cc_final: 0.8232 (t0) REVERT: J 67 LYS cc_start: 0.7973 (ptmm) cc_final: 0.7483 (tttp) REVERT: J 95 TYR cc_start: 0.8062 (m-80) cc_final: 0.7532 (m-80) outliers start: 53 outliers final: 28 residues processed: 384 average time/residue: 0.2937 time to fit residues: 168.3903 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 : 2.076 ------------------------------------------------------------------------------- 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: 2.9990 chunk 7 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 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: 5.9990 chunk 53 optimal weight: 6.9990 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 = 0.3805 r_free = 0.3805 target = 0.128622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096254 restraints weight = 31001.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098643 restraints weight = 17504.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100113 restraints weight = 12184.069| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4525 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= 0.281 Angle : 0.773 8.819 20219 Z= 0.390 Chirality : 0.048 0.245 2326 Planarity : 0.005 0.044 2480 Dihedral : 7.670 68.699 2316 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.21 % Allowed : 16.59 % 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: 0.38 (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 0.028 0.002 TRP J 36 HIS 0.007 0.002 HIS E 54 PHE 0.026 0.003 PHE A 221 TYR 0.028 0.002 TYR C 66 ARG 0.006 0.001 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 7) link_NAG-ASN : angle 2.49580 ( 21) link_ALPHA1-6 : bond 0.00403 ( 1) link_ALPHA1-6 : angle 2.55501 ( 3) link_BETA1-4 : bond 0.00234 ( 7) link_BETA1-4 : angle 3.03271 ( 21) link_ALPHA1-2 : bond 0.00304 ( 1) link_ALPHA1-2 : angle 1.89316 ( 3) link_ALPHA1-3 : bond 0.00817 ( 2) link_ALPHA1-3 : angle 2.38127 ( 6) hydrogen bonds : bond 0.04313 ( 602) hydrogen bonds : angle 5.16453 ( 1959) SS BOND : bond 0.00435 ( 7) SS BOND : angle 1.12267 ( 14) covalent geometry : bond 0.00645 (14826) covalent geometry : angle 0.76100 (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 400 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 318 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8880 (mmm) cc_final: 0.7257 (mmm) REVERT: A 58 THR cc_start: 0.9107 (m) cc_final: 0.8618 (p) REVERT: A 95 ASP cc_start: 0.8429 (t0) cc_final: 0.7838 (t0) REVERT: A 137 MET cc_start: 0.8401 (mmt) cc_final: 0.8032 (mmm) REVERT: A 157 TYR cc_start: 0.8650 (t80) cc_final: 0.8205 (t80) REVERT: A 237 TRP cc_start: 0.8151 (m-10) cc_final: 0.7549 (m-90) REVERT: A 269 ARG cc_start: 0.7210 (ptm160) cc_final: 0.6662 (ptm160) REVERT: A 274 LYS cc_start: 0.8571 (mttp) cc_final: 0.8152 (ptpt) REVERT: A 284 TYR cc_start: 0.8230 (t80) cc_final: 0.7979 (t80) REVERT: A 298 GLU cc_start: 0.8376 (tp30) cc_final: 0.8032 (tp30) REVERT: A 482 TYR cc_start: 0.6900 (t80) cc_final: 0.6127 (t80) REVERT: B 15 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: B 126 THR cc_start: 0.9019 (m) cc_final: 0.8454 (p) REVERT: B 274 ARG cc_start: 0.8041 (tpt-90) cc_final: 0.7793 (tpt-90) REVERT: C 40 MET cc_start: 0.8093 (mtt) cc_final: 0.7632 (mtt) REVERT: C 57 TYR cc_start: 0.8717 (p90) cc_final: 0.8253 (p90) REVERT: C 95 ASP cc_start: 0.8733 (p0) cc_final: 0.8274 (p0) REVERT: C 190 GLU cc_start: 0.7060 (pm20) cc_final: 0.6068 (pm20) REVERT: C 213 ARG cc_start: 0.7194 (ttp-170) cc_final: 0.6740 (ttp80) REVERT: D 56 ASP cc_start: 0.8572 (m-30) cc_final: 0.8370 (m-30) REVERT: D 165 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: E 102 MET cc_start: 0.7856 (ttt) cc_final: 0.7557 (tpt) REVERT: I 92 TYR cc_start: 0.9488 (t80) cc_final: 0.9259 (t80) REVERT: I 94 TYR cc_start: 0.8620 (m-80) cc_final: 0.8324 (m-80) REVERT: J 29 ILE cc_start: 0.9522 (pt) cc_final: 0.9026 (mt) REVERT: J 52 ASP cc_start: 0.8562 (t0) cc_final: 0.8318 (t0) REVERT: J 67 LYS cc_start: 0.8388 (ptmm) cc_final: 0.7821 (tttp) REVERT: J 82 GLN cc_start: 0.7490 (mp-120) cc_final: 0.7269 (mm-40) outliers start: 82 outliers final: 51 residues processed: 365 average time/residue: 0.2557 time to fit residues: 139.4463 Evaluate side-chains 337 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 48 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.129501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097186 restraints weight = 31060.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099572 restraints weight = 17488.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.101087 restraints weight = 12188.457| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14851 Z= 0.192 Angle : 0.676 8.623 20219 Z= 0.338 Chirality : 0.045 0.193 2326 Planarity : 0.004 0.043 2480 Dihedral : 6.926 63.325 2312 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.32 % Allowed : 18.88 % Favored : 76.80 % 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: -0.69 (0.20), residues: 1733 helix: 0.68 (0.25), residues: 444 sheet: -0.75 (0.21), residues: 570 loop : -0.77 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.001 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 7) link_NAG-ASN : angle 2.33615 ( 21) link_ALPHA1-6 : bond 0.00158 ( 1) link_ALPHA1-6 : angle 2.19448 ( 3) link_BETA1-4 : bond 0.00205 ( 7) link_BETA1-4 : angle 2.70012 ( 21) link_ALPHA1-2 : bond 0.00367 ( 1) link_ALPHA1-2 : angle 1.83250 ( 3) link_ALPHA1-3 : bond 0.00677 ( 2) link_ALPHA1-3 : angle 1.72943 ( 6) hydrogen bonds : bond 0.03752 ( 602) hydrogen bonds : angle 4.80822 ( 1959) SS BOND : bond 0.00369 ( 7) SS BOND : angle 0.70654 ( 14) covalent geometry : bond 0.00436 (14826) covalent geometry : angle 0.66550 (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 370 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 302 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8638 (mmm) cc_final: 0.8017 (mmm) REVERT: A 58 THR cc_start: 0.9110 (m) cc_final: 0.8754 (p) REVERT: A 95 ASP cc_start: 0.8439 (t0) cc_final: 0.7823 (t0) REVERT: A 115 MET cc_start: 0.7472 (ttm) cc_final: 0.7190 (ttt) REVERT: A 157 TYR cc_start: 0.8587 (t80) cc_final: 0.8175 (t80) REVERT: A 237 TRP cc_start: 0.8153 (m-10) cc_final: 0.7557 (m-90) REVERT: A 274 LYS cc_start: 0.8564 (mttp) cc_final: 0.8211 (ptpt) REVERT: A 284 TYR cc_start: 0.8142 (t80) cc_final: 0.7939 (t80) REVERT: A 298 GLU cc_start: 0.8398 (tp30) cc_final: 0.7965 (tp30) REVERT: A 482 TYR cc_start: 0.6748 (t80) cc_final: 0.6122 (t80) REVERT: B 126 THR cc_start: 0.9023 (m) cc_final: 0.8515 (p) REVERT: B 141 MET cc_start: 0.8150 (mtt) cc_final: 0.7928 (mtt) REVERT: C 55 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8293 (mmm) REVERT: C 57 TYR cc_start: 0.8704 (p90) cc_final: 0.8322 (p90) REVERT: C 95 ASP cc_start: 0.8643 (p0) cc_final: 0.8187 (p0) REVERT: C 165 GLU cc_start: 0.7692 (tp30) cc_final: 0.7175 (mm-30) REVERT: C 190 GLU cc_start: 0.6970 (pm20) cc_final: 0.5864 (pm20) REVERT: D 91 SER cc_start: 0.8695 (m) cc_final: 0.8333 (t) REVERT: D 121 GLN cc_start: 0.7874 (tt0) cc_final: 0.7506 (tt0) REVERT: D 147 MET cc_start: 0.8358 (mpp) cc_final: 0.7987 (mpp) REVERT: D 165 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: I 92 TYR cc_start: 0.9421 (t80) cc_final: 0.9197 (t80) REVERT: I 94 TYR cc_start: 0.8501 (m-80) cc_final: 0.8268 (m-80) REVERT: J 34 MET cc_start: 0.8793 (mmm) cc_final: 0.8413 (mmp) REVERT: J 52 ASP cc_start: 0.8562 (t0) cc_final: 0.8332 (t0) REVERT: J 67 LYS cc_start: 0.8245 (ptmm) cc_final: 0.7700 (tttp) REVERT: J 82 GLN cc_start: 0.7602 (mp-120) cc_final: 0.7329 (mm-40) outliers start: 68 outliers final: 50 residues processed: 347 average time/residue: 0.3134 time to fit residues: 161.8617 Evaluate side-chains 333 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 281 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 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 275 ILE 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 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 55 MET 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 151 THR Chi-restraints excluded: chain C residue 160 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 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 73 THR 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 I residue 82 ASP Chi-restraints excluded: chain J residue 11 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 61 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** B 387 ASN C 303 ASN E 60 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3790 r_free = 0.3790 target = 0.127312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095382 restraints weight = 31431.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097701 restraints weight = 17694.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099153 restraints weight = 12335.851| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 14851 Z= 0.240 Angle : 0.708 7.857 20219 Z= 0.354 Chirality : 0.046 0.240 2326 Planarity : 0.005 0.042 2480 Dihedral : 6.724 58.065 2312 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.28 % Allowed : 20.09 % 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: -0.64 (0.20), residues: 1733 helix: 0.78 (0.25), residues: 443 sheet: -0.78 (0.21), residues: 580 loop : -0.72 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 241 HIS 0.012 0.001 HIS C 267 PHE 0.052 0.002 PHE B 404 TYR 0.027 0.002 TYR I 49 ARG 0.008 0.001 ARG C 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 7) link_NAG-ASN : angle 2.44029 ( 21) link_ALPHA1-6 : bond 0.00380 ( 1) link_ALPHA1-6 : angle 2.46496 ( 3) link_BETA1-4 : bond 0.00286 ( 7) link_BETA1-4 : angle 2.64049 ( 21) link_ALPHA1-2 : bond 0.00118 ( 1) link_ALPHA1-2 : angle 1.97583 ( 3) link_ALPHA1-3 : bond 0.00754 ( 2) link_ALPHA1-3 : angle 2.02260 ( 6) hydrogen bonds : bond 0.03765 ( 602) hydrogen bonds : angle 4.78173 ( 1959) SS BOND : bond 0.00306 ( 7) SS BOND : angle 0.81306 ( 14) covalent geometry : bond 0.00546 (14826) covalent geometry : angle 0.69776 (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 378 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 295 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8660 (mmm) cc_final: 0.7310 (mmm) REVERT: A 58 THR cc_start: 0.9116 (m) cc_final: 0.8747 (p) REVERT: A 137 MET cc_start: 0.8269 (mmt) cc_final: 0.8042 (mmm) REVERT: A 237 TRP cc_start: 0.8079 (m-10) cc_final: 0.7748 (m-90) REVERT: A 269 ARG cc_start: 0.7840 (ptm160) cc_final: 0.7472 (ptm160) REVERT: A 274 LYS cc_start: 0.8700 (mttp) cc_final: 0.8367 (ptpt) REVERT: A 284 TYR cc_start: 0.8161 (t80) cc_final: 0.7955 (t80) REVERT: A 298 GLU cc_start: 0.8390 (tp30) cc_final: 0.7965 (tp30) REVERT: A 482 TYR cc_start: 0.6928 (t80) cc_final: 0.6226 (t80) REVERT: B 15 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8081 (m-10) REVERT: B 126 THR cc_start: 0.9011 (m) cc_final: 0.8471 (p) REVERT: B 274 ARG cc_start: 0.7896 (tpt90) cc_final: 0.7596 (tpt-90) REVERT: C 40 MET cc_start: 0.7982 (mtt) cc_final: 0.7453 (mtt) REVERT: C 55 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8353 (mmm) REVERT: C 95 ASP cc_start: 0.8672 (p0) cc_final: 0.8141 (p0) REVERT: C 165 GLU cc_start: 0.7727 (tp30) cc_final: 0.7246 (mm-30) REVERT: C 213 ARG cc_start: 0.7390 (ttp80) cc_final: 0.7085 (ttp80) REVERT: C 444 LEU cc_start: 0.8444 (mm) cc_final: 0.8040 (pp) REVERT: D 91 SER cc_start: 0.8709 (m) cc_final: 0.8371 (t) REVERT: D 121 GLN cc_start: 0.7836 (tt0) cc_final: 0.7352 (tt0) REVERT: D 235 MET cc_start: 0.8101 (ttm) cc_final: 0.7751 (ttt) REVERT: D 241 GLN cc_start: 0.4959 (mt0) cc_final: 0.3943 (tm-30) REVERT: I 4 MET cc_start: 0.8256 (mmp) cc_final: 0.7975 (mmp) REVERT: I 55 TYR cc_start: 0.8264 (t80) cc_final: 0.7991 (t80) REVERT: I 94 TYR cc_start: 0.8559 (m-80) cc_final: 0.8334 (m-80) REVERT: J 67 LYS cc_start: 0.8292 (ptmm) cc_final: 0.7811 (tttp) REVERT: J 82 GLN cc_start: 0.7611 (mp-120) cc_final: 0.7339 (mm-40) outliers start: 83 outliers final: 67 residues processed: 351 average time/residue: 0.2637 time to fit residues: 139.0794 Evaluate side-chains 349 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 280 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 260 THR 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 15 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 155 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 227 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 280 VAL Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 55 MET 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 151 THR 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 166 VAL 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 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 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 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: 9.9990 chunk 1 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN E 60 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 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 = 0.3796 r_free = 0.3796 target = 0.127584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095484 restraints weight = 31517.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.097897 restraints weight = 17477.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099443 restraints weight = 12067.801| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5566 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= 0.205 Angle : 0.686 8.124 20219 Z= 0.342 Chirality : 0.046 0.264 2326 Planarity : 0.004 0.043 2480 Dihedral : 6.455 53.696 2312 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.15 % Allowed : 20.98 % Favored : 73.87 % 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: -0.60 (0.20), residues: 1733 helix: 0.88 (0.25), residues: 445 sheet: -0.79 (0.21), residues: 580 loop : -0.71 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 241 HIS 0.015 0.001 HIS C 267 PHE 0.027 0.002 PHE B 304 TYR 0.035 0.002 TYR C 57 ARG 0.006 0.001 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 7) link_NAG-ASN : angle 2.36962 ( 21) link_ALPHA1-6 : bond 0.00189 ( 1) link_ALPHA1-6 : angle 2.25923 ( 3) link_BETA1-4 : bond 0.00269 ( 7) link_BETA1-4 : angle 2.32740 ( 21) link_ALPHA1-2 : bond 0.00246 ( 1) link_ALPHA1-2 : angle 1.99465 ( 3) link_ALPHA1-3 : bond 0.00709 ( 2) link_ALPHA1-3 : angle 1.80971 ( 6) hydrogen bonds : bond 0.03558 ( 602) hydrogen bonds : angle 4.70363 ( 1959) SS BOND : bond 0.00245 ( 7) SS BOND : angle 0.95372 ( 14) covalent geometry : bond 0.00466 (14826) covalent geometry : angle 0.67702 (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 380 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 299 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9075 (m) cc_final: 0.8701 (p) REVERT: A 76 VAL cc_start: 0.6618 (OUTLIER) cc_final: 0.6336 (t) REVERT: A 90 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: A 95 ASP cc_start: 0.8512 (t0) cc_final: 0.7884 (t0) REVERT: A 157 TYR cc_start: 0.8468 (t80) cc_final: 0.8230 (t80) REVERT: A 237 TRP cc_start: 0.8042 (m-10) cc_final: 0.7712 (m-90) REVERT: A 274 LYS cc_start: 0.8731 (mttp) cc_final: 0.8333 (ptpt) REVERT: A 294 MET cc_start: 0.8769 (mmp) cc_final: 0.7925 (tpt) REVERT: A 482 TYR cc_start: 0.6901 (t80) cc_final: 0.6235 (t80) REVERT: B 15 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: B 126 THR cc_start: 0.9018 (m) cc_final: 0.8484 (p) REVERT: B 213 MET cc_start: 0.7777 (mtp) cc_final: 0.7308 (mtp) REVERT: B 268 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8693 (t) REVERT: B 274 ARG cc_start: 0.7946 (tpt90) cc_final: 0.7599 (tpt-90) REVERT: C 40 MET cc_start: 0.7950 (mtt) cc_final: 0.7424 (mtt) REVERT: C 95 ASP cc_start: 0.8735 (p0) cc_final: 0.8167 (p0) REVERT: C 165 GLU cc_start: 0.7694 (tp30) cc_final: 0.7222 (mm-30) REVERT: C 213 ARG cc_start: 0.7364 (ttp80) cc_final: 0.6966 (ttp80) REVERT: C 444 LEU cc_start: 0.8467 (mm) cc_final: 0.8022 (pp) REVERT: D 91 SER cc_start: 0.8740 (m) cc_final: 0.8381 (t) REVERT: D 121 GLN cc_start: 0.7883 (tt0) cc_final: 0.7475 (tt0) REVERT: D 235 MET cc_start: 0.8157 (ttm) cc_final: 0.7759 (ttt) REVERT: D 241 GLN cc_start: 0.5278 (mt0) cc_final: 0.4269 (tm-30) REVERT: I 35 TRP cc_start: 0.8684 (m100) cc_final: 0.8459 (m-10) REVERT: I 55 TYR cc_start: 0.8307 (t80) cc_final: 0.8089 (t80) REVERT: J 67 LYS cc_start: 0.8278 (ptmm) cc_final: 0.7975 (tptt) REVERT: J 82 GLN cc_start: 0.7616 (mp-120) cc_final: 0.7348 (mm-40) outliers start: 81 outliers final: 64 residues processed: 355 average time/residue: 0.2415 time to fit residues: 128.4401 Evaluate side-chains 354 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 286 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 90 GLN 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 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 15 PHE Chi-restraints excluded: chain B residue 18 ILE 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 113 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 227 VAL 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 280 VAL Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 8 ASN 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 151 THR 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 136 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 151 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 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 = 0.128135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095968 restraints weight = 31164.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.098383 restraints weight = 17257.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099924 restraints weight = 11921.233| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14851 Z= 0.182 Angle : 0.677 8.503 20219 Z= 0.336 Chirality : 0.046 0.367 2326 Planarity : 0.004 0.050 2480 Dihedral : 6.192 50.589 2312 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.34 % Allowed : 21.23 % Favored : 73.43 % 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: -0.54 (0.20), residues: 1733 helix: 0.96 (0.25), residues: 446 sheet: -0.76 (0.21), residues: 585 loop : -0.70 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 67 HIS 0.017 0.001 HIS C 267 PHE 0.026 0.002 PHE D 288 TYR 0.021 0.002 TYR B 294 ARG 0.007 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 7) link_NAG-ASN : angle 2.35278 ( 21) link_ALPHA1-6 : bond 0.00122 ( 1) link_ALPHA1-6 : angle 2.19724 ( 3) link_BETA1-4 : bond 0.00315 ( 7) link_BETA1-4 : angle 2.20113 ( 21) link_ALPHA1-2 : bond 0.00316 ( 1) link_ALPHA1-2 : angle 2.06678 ( 3) link_ALPHA1-3 : bond 0.00689 ( 2) link_ALPHA1-3 : angle 1.70176 ( 6) hydrogen bonds : bond 0.03416 ( 602) hydrogen bonds : angle 4.63950 ( 1959) SS BOND : bond 0.00220 ( 7) SS BOND : angle 0.91225 ( 14) covalent geometry : bond 0.00415 (14826) covalent geometry : angle 0.66757 (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 386 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 302 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8691 (mmm) cc_final: 0.8389 (mmm) REVERT: A 58 THR cc_start: 0.9045 (m) cc_final: 0.8639 (p) REVERT: A 76 VAL cc_start: 0.6554 (OUTLIER) cc_final: 0.6326 (t) REVERT: A 90 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: A 226 TYR cc_start: 0.7748 (m-80) cc_final: 0.7427 (m-80) REVERT: A 237 TRP cc_start: 0.7970 (m-10) cc_final: 0.7236 (m-90) REVERT: A 269 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7831 (ptm160) REVERT: A 270 GLU cc_start: 0.7518 (pm20) cc_final: 0.7257 (pm20) REVERT: A 274 LYS cc_start: 0.8767 (mttp) cc_final: 0.8289 (ptpt) REVERT: A 284 TYR cc_start: 0.7871 (t80) cc_final: 0.7534 (t80) REVERT: A 482 TYR cc_start: 0.6892 (t80) cc_final: 0.6281 (t80) REVERT: B 126 THR cc_start: 0.9020 (m) cc_final: 0.8483 (p) REVERT: B 148 MET cc_start: 0.8222 (ptp) cc_final: 0.8003 (ptm) REVERT: B 190 GLN cc_start: 0.8690 (tp40) cc_final: 0.8304 (tp40) REVERT: B 268 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8694 (t) REVERT: B 274 ARG cc_start: 0.8029 (tpt90) cc_final: 0.7664 (tpt-90) REVERT: B 400 PHE cc_start: 0.7459 (m-80) cc_final: 0.7254 (m-80) REVERT: C 40 MET cc_start: 0.7943 (mtt) cc_final: 0.7396 (mtt) REVERT: C 95 ASP cc_start: 0.8736 (p0) cc_final: 0.8132 (p0) REVERT: C 165 GLU cc_start: 0.7729 (tp30) cc_final: 0.7292 (mm-30) REVERT: C 213 ARG cc_start: 0.7331 (ttp80) cc_final: 0.6900 (ttp80) REVERT: C 240 PHE cc_start: 0.7009 (m-80) cc_final: 0.6260 (m-10) REVERT: C 444 LEU cc_start: 0.8459 (mm) cc_final: 0.8013 (pp) REVERT: D 91 SER cc_start: 0.8769 (m) cc_final: 0.8379 (t) REVERT: D 111 MET cc_start: 0.7789 (tpp) cc_final: 0.6961 (tpp) REVERT: D 121 GLN cc_start: 0.7902 (tt0) cc_final: 0.7511 (tt0) REVERT: D 235 MET cc_start: 0.8129 (ttm) cc_final: 0.7820 (ttt) REVERT: D 241 GLN cc_start: 0.5314 (mt0) cc_final: 0.4532 (tm-30) REVERT: I 29 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8518 (m) REVERT: I 37 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7203 (tm-30) REVERT: I 85 ASP cc_start: 0.7595 (m-30) cc_final: 0.7211 (m-30) REVERT: J 67 LYS cc_start: 0.8288 (ptmm) cc_final: 0.7976 (tptt) REVERT: J 82 GLN cc_start: 0.7566 (mp-120) cc_final: 0.7300 (mm-40) outliers start: 84 outliers final: 68 residues processed: 364 average time/residue: 0.2419 time to fit residues: 132.5985 Evaluate side-chains 363 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 291 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 87 VAL Chi-restraints excluded: chain A residue 90 GLN 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 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 113 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 SER 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 8 ASN Chi-restraints excluded: chain C residue 83 LEU 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 151 THR 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 166 VAL 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 73 THR 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 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 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 72 THR Chi-restraints excluded: chain I residue 78 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 33 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 139 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN C 224 GLN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 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 = 0.3830 r_free = 0.3830 target = 0.130060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097694 restraints weight = 31156.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.100169 restraints weight = 17239.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.101734 restraints weight = 11883.251| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5848 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= 0.129 Angle : 0.677 12.398 20219 Z= 0.331 Chirality : 0.045 0.348 2326 Planarity : 0.004 0.048 2480 Dihedral : 5.838 47.043 2312 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.69 % Allowed : 23.39 % Favored : 72.92 % 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: -0.41 (0.21), residues: 1733 helix: 1.10 (0.25), residues: 446 sheet: -0.73 (0.21), residues: 584 loop : -0.59 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP J 36 HIS 0.020 0.001 HIS C 267 PHE 0.026 0.001 PHE C 221 TYR 0.028 0.001 TYR I 55 ARG 0.008 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 7) link_NAG-ASN : angle 2.20702 ( 21) link_ALPHA1-6 : bond 0.00311 ( 1) link_ALPHA1-6 : angle 1.81487 ( 3) link_BETA1-4 : bond 0.00313 ( 7) link_BETA1-4 : angle 2.00553 ( 21) link_ALPHA1-2 : bond 0.00347 ( 1) link_ALPHA1-2 : angle 1.96816 ( 3) link_ALPHA1-3 : bond 0.00909 ( 2) link_ALPHA1-3 : angle 1.54778 ( 6) hydrogen bonds : bond 0.03220 ( 602) hydrogen bonds : angle 4.55714 ( 1959) SS BOND : bond 0.00265 ( 7) SS BOND : angle 1.69108 ( 14) covalent geometry : bond 0.00295 (14826) covalent geometry : angle 0.66853 (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 369 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 311 time to evaluate : 1.467 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: 0.8640 (mmm) cc_final: 0.8017 (mmm) REVERT: A 58 THR cc_start: 0.9040 (m) cc_final: 0.8650 (p) REVERT: A 95 ASP cc_start: 0.8502 (t0) cc_final: 0.7832 (t0) REVERT: A 157 TYR cc_start: 0.8403 (t80) cc_final: 0.8146 (t80) REVERT: A 226 TYR cc_start: 0.7628 (m-80) cc_final: 0.7315 (m-80) REVERT: A 274 LYS cc_start: 0.8682 (mttp) cc_final: 0.8392 (mmtp) REVERT: A 284 TYR cc_start: 0.7725 (t80) cc_final: 0.7447 (t80) REVERT: A 294 MET cc_start: 0.8821 (mmp) cc_final: 0.8008 (tpt) REVERT: A 482 TYR cc_start: 0.6751 (t80) cc_final: 0.6269 (t80) REVERT: B 126 THR cc_start: 0.8999 (m) cc_final: 0.8481 (p) REVERT: B 148 MET cc_start: 0.8222 (ptp) cc_final: 0.7963 (ptm) REVERT: B 268 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8687 (t) REVERT: B 274 ARG cc_start: 0.8034 (tpt90) cc_final: 0.7637 (tpt-90) REVERT: C 40 MET cc_start: 0.7727 (mtt) cc_final: 0.7157 (mtt) REVERT: C 90 GLN cc_start: 0.8552 (mp10) cc_final: 0.8126 (mt0) REVERT: C 95 ASP cc_start: 0.8641 (p0) cc_final: 0.8007 (p0) REVERT: C 165 GLU cc_start: 0.7715 (tp30) cc_final: 0.7327 (mm-30) REVERT: C 213 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6872 (ttp80) REVERT: C 240 PHE cc_start: 0.6842 (m-80) cc_final: 0.6147 (m-10) REVERT: C 444 LEU cc_start: 0.8453 (mm) cc_final: 0.8022 (pp) REVERT: D 111 MET cc_start: 0.7646 (tpp) cc_final: 0.6968 (tpp) REVERT: D 121 GLN cc_start: 0.7863 (tt0) cc_final: 0.7502 (tt0) REVERT: D 235 MET cc_start: 0.8100 (ttm) cc_final: 0.7814 (ttt) REVERT: D 241 GLN cc_start: 0.5203 (mt0) cc_final: 0.4460 (tm-30) REVERT: E 60 ASN cc_start: 0.7766 (m-40) cc_final: 0.7442 (m-40) REVERT: E 130 MET cc_start: 0.7586 (ttp) cc_final: 0.7256 (ptm) REVERT: I 24 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8427 (mmmt) REVERT: I 29 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8480 (m) REVERT: I 37 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7220 (tm-30) REVERT: I 94 TYR cc_start: 0.8505 (m-80) cc_final: 0.8217 (m-80) REVERT: J 6 GLN cc_start: 0.7451 (mp10) cc_final: 0.6297 (mp10) REVERT: J 52 ASP cc_start: 0.8579 (t0) cc_final: 0.8284 (t0) REVERT: J 67 LYS cc_start: 0.8169 (ptmm) cc_final: 0.7809 (tttp) outliers start: 58 outliers final: 49 residues processed: 352 average time/residue: 0.2400 time to fit residues: 127.2141 Evaluate side-chains 347 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 296 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 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 181 ILE Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 159 SER 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 8 ASN 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 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 166 VAL 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 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 29 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 160 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.131420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099073 restraints weight = 30757.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101562 restraints weight = 17039.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103144 restraints weight = 11747.408| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5988 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 : 0.691 10.492 20219 Z= 0.337 Chirality : 0.045 0.356 2326 Planarity : 0.004 0.056 2480 Dihedral : 5.533 43.030 2312 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.56 % Allowed : 24.28 % Favored : 72.16 % 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: 1.19 (0.25), residues: 447 sheet: -0.63 (0.21), residues: 582 loop : -0.59 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP I 35 HIS 0.022 0.001 HIS C 267 PHE 0.028 0.001 PHE D 288 TYR 0.023 0.002 TYR A 299 ARG 0.010 0.000 ARG E 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 7) link_NAG-ASN : angle 2.09944 ( 21) link_ALPHA1-6 : bond 0.00565 ( 1) link_ALPHA1-6 : angle 1.64307 ( 3) link_BETA1-4 : bond 0.00276 ( 7) link_BETA1-4 : angle 1.86590 ( 21) link_ALPHA1-2 : bond 0.00324 ( 1) link_ALPHA1-2 : angle 1.90373 ( 3) link_ALPHA1-3 : bond 0.01118 ( 2) link_ALPHA1-3 : angle 1.53321 ( 6) hydrogen bonds : bond 0.03118 ( 602) hydrogen bonds : angle 4.51543 ( 1959) SS BOND : bond 0.00250 ( 7) SS BOND : angle 1.59640 ( 14) covalent geometry : bond 0.00279 (14826) covalent geometry : angle 0.68387 (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 363 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 1.562 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: 0.8723 (mmm) cc_final: 0.8474 (mmm) REVERT: A 58 THR cc_start: 0.9001 (m) cc_final: 0.8656 (p) REVERT: A 61 MET cc_start: 0.8142 (ptp) cc_final: 0.7885 (ptp) REVERT: A 95 ASP cc_start: 0.8519 (t0) cc_final: 0.7828 (t0) REVERT: A 157 TYR cc_start: 0.8409 (t80) cc_final: 0.8175 (t80) REVERT: A 237 TRP cc_start: 0.7942 (m-10) cc_final: 0.7580 (m-90) REVERT: A 274 LYS cc_start: 0.8656 (mttp) cc_final: 0.8396 (ptpt) REVERT: A 294 MET cc_start: 0.8830 (mmp) cc_final: 0.8042 (tpt) REVERT: A 482 TYR cc_start: 0.6772 (t80) cc_final: 0.6227 (t80) REVERT: B 148 MET cc_start: 0.8278 (ptp) cc_final: 0.8026 (ptm) REVERT: B 268 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8674 (t) REVERT: C 40 MET cc_start: 0.7696 (mtt) cc_final: 0.7179 (mtt) REVERT: C 49 MET cc_start: 0.8298 (ppp) cc_final: 0.7817 (ppp) REVERT: C 56 ASP cc_start: 0.8340 (p0) cc_final: 0.7774 (p0) REVERT: C 90 GLN cc_start: 0.8579 (mp10) cc_final: 0.8114 (mt0) REVERT: C 95 ASP cc_start: 0.8624 (p0) cc_final: 0.7965 (p0) REVERT: C 165 GLU cc_start: 0.7634 (tp30) cc_final: 0.7348 (mm-30) REVERT: C 226 TYR cc_start: 0.7472 (m-80) cc_final: 0.7219 (m-80) REVERT: C 240 PHE cc_start: 0.6809 (m-80) cc_final: 0.6157 (m-10) REVERT: C 444 LEU cc_start: 0.8469 (mm) cc_final: 0.8072 (pp) REVERT: D 111 MET cc_start: 0.7690 (tpp) cc_final: 0.6985 (tpp) REVERT: D 121 GLN cc_start: 0.7828 (tt0) cc_final: 0.7488 (tt0) REVERT: D 235 MET cc_start: 0.8068 (ttm) cc_final: 0.7744 (ttt) REVERT: D 241 GLN cc_start: 0.5064 (mt0) cc_final: 0.4419 (tm-30) REVERT: E 60 ASN cc_start: 0.7740 (m-40) cc_final: 0.7394 (m110) REVERT: E 130 MET cc_start: 0.7538 (ttp) cc_final: 0.7288 (ptm) REVERT: I 29 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8508 (m) REVERT: I 94 TYR cc_start: 0.8472 (m-80) cc_final: 0.8241 (m-80) REVERT: J 52 ASP cc_start: 0.8546 (t0) cc_final: 0.8243 (t0) REVERT: J 67 LYS cc_start: 0.8252 (ptmm) cc_final: 0.7826 (tttp) outliers start: 56 outliers final: 43 residues processed: 346 average time/residue: 0.2371 time to fit residues: 122.8732 Evaluate side-chains 337 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL 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 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 159 SER 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 268 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET 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 141 HIS Chi-restraints excluded: chain D residue 166 VAL 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 5 THR 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 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: 6.9990 chunk 116 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.131851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099564 restraints weight = 30991.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102028 restraints weight = 17095.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103648 restraints weight = 11801.394| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.680 10.873 20219 Z= 0.332 Chirality : 0.045 0.299 2326 Planarity : 0.005 0.078 2480 Dihedral : 5.298 39.887 2312 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.86 % Allowed : 24.86 % 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: -0.27 (0.21), residues: 1733 helix: 1.18 (0.25), residues: 447 sheet: -0.57 (0.21), residues: 582 loop : -0.59 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J 36 HIS 0.022 0.001 HIS C 267 PHE 0.026 0.002 PHE D 288 TYR 0.029 0.001 TYR A 299 ARG 0.011 0.000 ARG A 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 7) link_NAG-ASN : angle 2.03846 ( 21) link_ALPHA1-6 : bond 0.00608 ( 1) link_ALPHA1-6 : angle 1.56740 ( 3) link_BETA1-4 : bond 0.00315 ( 7) link_BETA1-4 : angle 1.80303 ( 21) link_ALPHA1-2 : bond 0.00285 ( 1) link_ALPHA1-2 : angle 1.88846 ( 3) link_ALPHA1-3 : bond 0.00940 ( 2) link_ALPHA1-3 : angle 1.46558 ( 6) hydrogen bonds : bond 0.03103 ( 602) hydrogen bonds : angle 4.47936 ( 1959) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.31970 ( 14) covalent geometry : bond 0.00282 (14826) covalent geometry : angle 0.67373 (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 350 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8638 (mmm) cc_final: 0.8039 (mmm) REVERT: A 58 THR cc_start: 0.8980 (m) cc_final: 0.8660 (p) REVERT: A 61 MET cc_start: 0.8108 (ptp) cc_final: 0.7879 (ptp) REVERT: A 95 ASP cc_start: 0.8511 (t0) cc_final: 0.7837 (t0) REVERT: A 139 ASP cc_start: 0.7361 (t0) cc_final: 0.7139 (p0) REVERT: A 157 TYR cc_start: 0.8361 (t80) cc_final: 0.8125 (t80) REVERT: A 237 TRP cc_start: 0.7923 (m-10) cc_final: 0.7532 (m-90) REVERT: A 274 LYS cc_start: 0.8711 (mttp) cc_final: 0.8215 (ptpt) REVERT: A 294 MET cc_start: 0.8828 (mmp) cc_final: 0.8048 (tpt) REVERT: A 482 TYR cc_start: 0.6772 (t80) cc_final: 0.6302 (t80) REVERT: B 148 MET cc_start: 0.8279 (ptp) cc_final: 0.8025 (ptm) REVERT: B 190 GLN cc_start: 0.8561 (tp40) cc_final: 0.8343 (tp40) REVERT: B 282 TYR cc_start: 0.7838 (p90) cc_final: 0.7540 (p90) REVERT: C 40 MET cc_start: 0.7610 (mtt) cc_final: 0.7168 (mtt) REVERT: C 49 MET cc_start: 0.8251 (ppp) cc_final: 0.7839 (ppp) REVERT: C 55 MET cc_start: 0.8558 (mtt) cc_final: 0.8297 (mtt) REVERT: C 56 ASP cc_start: 0.8346 (p0) cc_final: 0.7718 (p0) REVERT: C 59 LEU cc_start: 0.7407 (tt) cc_final: 0.6228 (tt) REVERT: C 90 GLN cc_start: 0.8498 (mp10) cc_final: 0.8045 (mt0) REVERT: C 95 ASP cc_start: 0.8546 (p0) cc_final: 0.7922 (p0) REVERT: C 165 GLU cc_start: 0.7574 (tp30) cc_final: 0.7321 (mm-30) REVERT: C 173 LYS cc_start: 0.8493 (pttt) cc_final: 0.8149 (pttm) REVERT: C 240 PHE cc_start: 0.6730 (m-80) cc_final: 0.6156 (m-10) REVERT: C 444 LEU cc_start: 0.8392 (mm) cc_final: 0.8058 (pp) REVERT: D 111 MET cc_start: 0.7587 (tpp) cc_final: 0.6930 (tpp) REVERT: D 121 GLN cc_start: 0.7778 (tt0) cc_final: 0.7450 (tt0) REVERT: D 235 MET cc_start: 0.8089 (ttm) cc_final: 0.7803 (ttt) REVERT: D 241 GLN cc_start: 0.5182 (mt0) cc_final: 0.4388 (tm-30) REVERT: E 60 ASN cc_start: 0.7646 (m-40) cc_final: 0.7331 (m110) REVERT: E 130 MET cc_start: 0.7521 (ttp) cc_final: 0.7311 (ptm) REVERT: I 94 TYR cc_start: 0.8474 (m-80) cc_final: 0.8238 (m-80) REVERT: J 6 GLN cc_start: 0.7393 (mp10) cc_final: 0.5351 (mt0) REVERT: J 52 ASP cc_start: 0.8497 (t0) cc_final: 0.8265 (t0) outliers start: 45 outliers final: 40 residues processed: 335 average time/residue: 0.2482 time to fit residues: 125.3214 Evaluate side-chains 327 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 110 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 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 159 SER 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 271 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 166 VAL 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 5 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 81 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 4 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** D 67 GLN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.130492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098341 restraints weight = 31090.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100797 restraints weight = 17143.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102325 restraints weight = 11804.309| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14851 Z= 0.151 Angle : 0.700 13.137 20219 Z= 0.343 Chirality : 0.046 0.361 2326 Planarity : 0.005 0.070 2480 Dihedral : 5.337 39.215 2312 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.99 % Allowed : 25.30 % Favored : 71.71 % 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: -0.24 (0.20), residues: 1733 helix: 1.19 (0.25), residues: 447 sheet: -0.51 (0.21), residues: 572 loop : -0.60 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 35 HIS 0.022 0.001 HIS C 267 PHE 0.029 0.002 PHE B 304 TYR 0.034 0.002 TYR A 299 ARG 0.009 0.001 ARG E 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 7) link_NAG-ASN : angle 2.07389 ( 21) link_ALPHA1-6 : bond 0.00540 ( 1) link_ALPHA1-6 : angle 1.70302 ( 3) link_BETA1-4 : bond 0.00293 ( 7) link_BETA1-4 : angle 1.85895 ( 21) link_ALPHA1-2 : bond 0.00115 ( 1) link_ALPHA1-2 : angle 1.93778 ( 3) link_ALPHA1-3 : bond 0.00814 ( 2) link_ALPHA1-3 : angle 1.57207 ( 6) hydrogen bonds : bond 0.03193 ( 602) hydrogen bonds : angle 4.49878 ( 1959) SS BOND : bond 0.00223 ( 7) SS BOND : angle 1.22561 ( 14) covalent geometry : bond 0.00352 (14826) covalent geometry : angle 0.69311 (20151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5331.47 seconds wall clock time: 94 minutes 8.65 seconds (5648.65 seconds total)