Starting phenix.real_space_refine on Sat Sep 28 00:43:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/09_2024/6x3t_22032.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/09_2024/6x3t_22032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/09_2024/6x3t_22032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/09_2024/6x3t_22032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/09_2024/6x3t_22032.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/09_2024/6x3t_22032.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 97 5.16 5 C 11248 2.51 5 N 2829 2.21 5 O 3241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17415 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2731 Classifications: {'peptide': 334} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} 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: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} 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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" 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: "M" 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: "N" 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: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'PFL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'PFL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.48, per 1000 atoms: 0.60 Number of scatterers: 17415 At special positions: 0 Unit cell: (117.99, 151.11, 130.41, 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 97 16.00 O 3241 8.00 N 2829 7.00 C 11248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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 G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " 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 M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.2 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4018 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 34 sheets defined 32.7% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 239 removed outlier: 4.079A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 246 through 262 removed outlier: 3.579A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.694A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 339 removed outlier: 3.579A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.769A pdb=" N PHE B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.617A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.564A pdb=" N SER B 92 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.830A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 251 through 275 Processing helix chain 'B' and resid 284 through 310 Processing helix chain 'B' and resid 314 through 347 removed outlier: 3.954A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.685A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 246 through 264 removed outlier: 3.998A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 270 removed outlier: 4.092A pdb=" N LEU C 268 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 340 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 87 through 94 removed outlier: 3.513A pdb=" N SER D 92 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.787A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 274 Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 345 removed outlier: 3.699A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 85 through 88 Processing helix chain 'E' and resid 99 through 106 removed outlier: 3.893A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 3.754A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 254 through 257 Processing helix chain 'E' and resid 261 through 285 Processing helix chain 'E' and resid 294 through 321 Processing helix chain 'E' and resid 324 through 356 removed outlier: 3.897A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.821A pdb=" N LEU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.672A pdb=" N THR J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.574A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.436A 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: 6.831A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.698A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 199 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A 205 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS A 197 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG A 207 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A 195 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 209 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 193 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER A 211 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS A 213 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.680A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.235A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N VAL B 180 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 45 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.442A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLN B 204 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR B 210 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE B 202 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 212 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER B 200 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR B 214 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 198 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS B 216 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN B 196 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS B 218 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.423A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.495A pdb=" N ASP C 101 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA C 135 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.750A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 167 through 171 removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N VAL D 180 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.730A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.730A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.000A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 179 through 181 removed outlier: 9.048A pdb=" N VAL D 180 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 167 through 171 removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.638A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 69 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 43 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LYS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 41 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N VAL D 180 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.362A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN D 204 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR D 210 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE D 202 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 212 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER D 200 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR D 214 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D 198 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS D 216 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN D 196 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS D 218 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.737A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU E 150 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER E 116 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.737A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU E 71 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL E 65 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR E 73 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE E 77 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL E 59 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA E 79 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N MET E 57 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR E 81 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR E 55 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N TYR E 83 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE E 53 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS E 184 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N MET E 57 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N SER E 186 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N VAL E 59 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N VAL E 188 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 11.790A pdb=" N SER E 61 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N VAL E 190 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 13.434A pdb=" N GLY E 63 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.543A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 218 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.653A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.653A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.697A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.992A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.510A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.510A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.202A pdb=" N LYS K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP K 47 " --> pdb=" O LYS K 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 11 removed outlier: 4.335A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2865 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: 6.54 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3864 1.33 - 1.45: 4357 1.45 - 1.58: 9461 1.58 - 1.70: 0 1.70 - 1.83: 167 Bond restraints: 17849 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE1 ABU A 405 " ideal model delta sigma weight residual 1.247 1.336 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" CD ABU C 405 " pdb=" OE2 ABU C 405 " ideal model delta sigma weight residual 1.250 1.336 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C1 MAN G 7 " pdb=" C2 MAN G 7 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" CD ABU A 405 " pdb=" OE2 ABU A 405 " ideal model delta sigma weight residual 1.250 1.206 0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" C1 PFL D 601 " pdb=" O1 PFL D 601 " ideal model delta sigma weight residual 1.355 1.398 -0.043 2.00e-02 2.50e+03 4.58e+00 ... (remaining 17844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 23600 1.63 - 3.26: 536 3.26 - 4.88: 97 4.88 - 6.51: 35 6.51 - 8.14: 4 Bond angle restraints: 24272 Sorted by residual: angle pdb=" C GLY A 170 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.59e+00 angle pdb=" CA TYR C 299 " pdb=" CB TYR C 299 " pdb=" CG TYR C 299 " ideal model delta sigma weight residual 113.90 108.93 4.97 1.80e+00 3.09e-01 7.61e+00 angle pdb=" C GLY C 170 " pdb=" N ASP C 171 " pdb=" CA ASP C 171 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.07e+00 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 109.15 4.75 1.80e+00 3.09e-01 6.97e+00 angle pdb=" C3 MAN G 7 " pdb=" C2 MAN G 7 " pdb=" O2 MAN G 7 " ideal model delta sigma weight residual 111.77 104.29 7.48 3.00e+00 1.11e-01 6.21e+00 ... (remaining 24267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 10235 21.48 - 42.96: 424 42.96 - 64.44: 84 64.44 - 85.91: 45 85.91 - 107.39: 22 Dihedral angle restraints: 10810 sinusoidal: 4556 harmonic: 6254 Sorted by residual: dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA VAL B 64 " pdb=" C VAL B 64 " pdb=" N PHE B 65 " pdb=" CA PHE B 65 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ILE A 47 " pdb=" C ILE A 47 " pdb=" N ASP A 48 " pdb=" CA ASP A 48 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 10807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2189 0.053 - 0.106: 534 0.106 - 0.159: 76 0.159 - 0.212: 2 0.212 - 0.264: 5 Chirality restraints: 2806 Sorted by residual: chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 208 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2803 not shown) Planarity restraints: 2991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 242 " -0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO E 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 153 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO B 154 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " -0.017 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR A 299 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " -0.004 2.00e-02 2.50e+03 ... (remaining 2988 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 640 2.72 - 3.26: 16781 3.26 - 3.81: 29412 3.81 - 4.35: 37646 4.35 - 4.90: 63131 Nonbonded interactions: 147610 Sorted by model distance: nonbonded pdb=" OG1 THR B 122 " pdb=" OD1 ASP B 124 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASP B 63 " pdb=" OG1 THR B 134 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP D 10 " pdb=" OG1 THR D 12 " model vdw 2.185 3.040 nonbonded pdb=" OG SER L 65 " pdb=" OG1 THR L 72 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP C 101 " pdb=" OG SER C 104 " model vdw 2.219 3.040 ... (remaining 147605 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' selection = (chain 'C' and (resid 7 through 173 or (resid 174 and (name N or name CA or name \ C or name O )) or resid 175 through 340 or resid 404 through 405)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.280 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.005 0.089 17849 Z= 0.306 Angle : 0.662 8.142 24272 Z= 0.348 Chirality : 0.046 0.264 2806 Planarity : 0.004 0.040 2984 Dihedral : 14.711 107.393 6765 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.28 % Allowed : 7.65 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2103 helix: 0.51 (0.20), residues: 582 sheet: -0.37 (0.19), residues: 652 loop : -1.26 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 103 HIS 0.003 0.001 HIS E 122 PHE 0.015 0.002 PHE E 236 TYR 0.022 0.002 TYR A 299 ARG 0.006 0.001 ARG K 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 325 time to evaluate : 2.048 Fit side-chains REVERT: A 14 GLU cc_start: 0.7180 (tt0) cc_final: 0.6679 (tp30) REVERT: A 318 ARG cc_start: 0.6230 (mtm110) cc_final: 0.5468 (ppt170) REVERT: A 323 PHE cc_start: 0.6019 (t80) cc_final: 0.5480 (m-80) REVERT: B 24 ASP cc_start: 0.6922 (t0) cc_final: 0.6524 (p0) REVERT: B 141 MET cc_start: 0.8444 (mtt) cc_final: 0.7962 (mtt) REVERT: B 204 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7921 (tp-100) REVERT: B 271 ILE cc_start: 0.7482 (mt) cc_final: 0.7259 (mm) REVERT: B 275 ASN cc_start: 0.5850 (m-40) cc_final: 0.5607 (m-40) REVERT: B 286 MET cc_start: 0.8281 (ttp) cc_final: 0.7824 (ttp) REVERT: B 317 ARG cc_start: 0.6685 (ttt180) cc_final: 0.6373 (ttt-90) REVERT: C 90 GLN cc_start: 0.8109 (mt0) cc_final: 0.7758 (mp10) REVERT: C 182 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6971 (tp30) REVERT: C 227 MET cc_start: 0.7395 (mmt) cc_final: 0.7148 (mmt) REVERT: C 286 MET cc_start: 0.8338 (mtt) cc_final: 0.8056 (mtt) REVERT: C 303 ASN cc_start: 0.8402 (t0) cc_final: 0.8100 (t0) REVERT: C 304 TYR cc_start: 0.8049 (t80) cc_final: 0.7717 (t80) REVERT: D 24 ASP cc_start: 0.7248 (t70) cc_final: 0.6907 (p0) REVERT: D 73 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: D 248 ASN cc_start: 0.6912 (t0) cc_final: 0.6648 (t0) REVERT: D 286 MET cc_start: 0.7738 (ttp) cc_final: 0.7535 (ttm) REVERT: D 320 LYS cc_start: 0.6816 (ttpt) cc_final: 0.6465 (ttmm) REVERT: D 324 LEU cc_start: 0.6874 (mt) cc_final: 0.6659 (mp) REVERT: E 66 ASN cc_start: 0.7678 (t0) cc_final: 0.7468 (t0) REVERT: E 168 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7487 (mt-10) REVERT: E 189 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7356 (mt-10) REVERT: E 236 PHE cc_start: 0.7911 (m-80) cc_final: 0.7645 (m-80) REVERT: I 61 ARG cc_start: 0.6766 (ptt-90) cc_final: 0.6522 (ptt90) REVERT: I 72 THR cc_start: 0.8285 (m) cc_final: 0.8062 (t) REVERT: J 19 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7015 (mttm) REVERT: J 114 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7169 (p) REVERT: L 21 LEU cc_start: 0.7874 (mp) cc_final: 0.7653 (mt) REVERT: L 24 LYS cc_start: 0.8364 (mttt) cc_final: 0.7968 (mttp) REVERT: L 82 ASP cc_start: 0.6323 (m-30) cc_final: 0.5739 (m-30) REVERT: K 25 SER cc_start: 0.7521 (m) cc_final: 0.7045 (t) REVERT: K 61 ASP cc_start: 0.7618 (t0) cc_final: 0.7371 (t0) outliers start: 43 outliers final: 21 residues processed: 358 average time/residue: 1.3920 time to fit residues: 553.0435 Evaluate side-chains 296 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 272 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 102 HIS B 190 GLN B 229 GLN C 224 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 258 ASN K 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17849 Z= 0.313 Angle : 0.644 8.507 24272 Z= 0.336 Chirality : 0.046 0.176 2806 Planarity : 0.005 0.055 2984 Dihedral : 10.263 83.252 2868 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.09 % Allowed : 12.21 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.10 (0.18), residues: 2103 helix: 1.49 (0.21), residues: 588 sheet: -0.15 (0.19), residues: 666 loop : -0.67 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.017 0.002 PHE E 236 TYR 0.035 0.002 TYR A 299 ARG 0.005 0.001 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 272 time to evaluate : 2.053 Fit side-chains REVERT: A 14 GLU cc_start: 0.7220 (tt0) cc_final: 0.6715 (tp30) REVERT: A 21 LYS cc_start: 0.7160 (mttp) cc_final: 0.6810 (mttt) REVERT: A 40 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7020 (mpt) REVERT: A 86 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7527 (mtm-85) REVERT: A 101 ASP cc_start: 0.7924 (p0) cc_final: 0.7574 (p0) REVERT: A 244 TYR cc_start: 0.6477 (p90) cc_final: 0.6235 (p90) REVERT: A 306 PHE cc_start: 0.5524 (t80) cc_final: 0.5245 (t80) REVERT: A 318 ARG cc_start: 0.6228 (mtm110) cc_final: 0.5880 (mtm-85) REVERT: A 323 PHE cc_start: 0.6055 (t80) cc_final: 0.5466 (m-80) REVERT: B 24 ASP cc_start: 0.6938 (t0) cc_final: 0.6551 (p0) REVERT: B 141 MET cc_start: 0.8421 (mtt) cc_final: 0.7928 (mtt) REVERT: B 204 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7979 (tp-100) REVERT: B 271 ILE cc_start: 0.7499 (mt) cc_final: 0.7268 (mm) REVERT: B 275 ASN cc_start: 0.5883 (m-40) cc_final: 0.5619 (m-40) REVERT: B 286 MET cc_start: 0.8244 (ttp) cc_final: 0.7825 (ttp) REVERT: C 90 GLN cc_start: 0.8017 (mt0) cc_final: 0.7667 (mp10) REVERT: C 182 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6996 (tp30) REVERT: C 227 MET cc_start: 0.7456 (mmt) cc_final: 0.7212 (mmt) REVERT: C 283 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6667 (tpt) REVERT: C 286 MET cc_start: 0.8342 (mtt) cc_final: 0.8053 (mtt) REVERT: C 303 ASN cc_start: 0.8392 (t0) cc_final: 0.8096 (t0) REVERT: C 304 TYR cc_start: 0.8034 (t80) cc_final: 0.7710 (t80) REVERT: D 24 ASP cc_start: 0.7195 (t70) cc_final: 0.6853 (p0) REVERT: D 40 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: D 73 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: D 141 MET cc_start: 0.8358 (mtt) cc_final: 0.8106 (mtp) REVERT: D 248 ASN cc_start: 0.6878 (t0) cc_final: 0.6583 (t0) REVERT: D 286 MET cc_start: 0.7739 (ttp) cc_final: 0.7534 (ttm) REVERT: D 320 LYS cc_start: 0.6946 (ttpt) cc_final: 0.6543 (ttmm) REVERT: D 324 LEU cc_start: 0.7000 (mt) cc_final: 0.6762 (mp) REVERT: D 331 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7838 (tp) REVERT: E 66 ASN cc_start: 0.7745 (t0) cc_final: 0.7497 (t0) REVERT: E 168 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7550 (mt-10) REVERT: E 189 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7506 (mt-10) REVERT: E 236 PHE cc_start: 0.7940 (m-80) cc_final: 0.7692 (m-80) REVERT: E 282 ILE cc_start: 0.7859 (mm) cc_final: 0.7592 (OUTLIER) REVERT: E 331 MET cc_start: 0.6739 (ttm) cc_final: 0.6338 (ptp) REVERT: I 72 THR cc_start: 0.8286 (m) cc_final: 0.8043 (t) REVERT: J 19 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6990 (mttm) REVERT: J 114 VAL cc_start: 0.7377 (OUTLIER) cc_final: 0.7155 (p) REVERT: L 18 ARG cc_start: 0.6660 (mtp85) cc_final: 0.6339 (ttm-80) REVERT: L 24 LYS cc_start: 0.8376 (mttt) cc_final: 0.7968 (mttp) REVERT: L 61 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7179 (ptp90) REVERT: L 82 ASP cc_start: 0.6245 (m-30) cc_final: 0.5747 (m-30) REVERT: K 25 SER cc_start: 0.7588 (m) cc_final: 0.7052 (t) REVERT: K 61 ASP cc_start: 0.7546 (t0) cc_final: 0.7299 (t0) REVERT: K 89 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5342 (pp20) outliers start: 77 outliers final: 42 residues processed: 325 average time/residue: 1.3484 time to fit residues: 486.2195 Evaluate side-chains 316 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 266 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 167 optimal weight: 0.5980 chunk 186 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 190 GLN C 185 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17849 Z= 0.268 Angle : 0.613 7.876 24272 Z= 0.319 Chirality : 0.045 0.171 2806 Planarity : 0.005 0.052 2984 Dihedral : 8.917 79.337 2860 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.67 % Allowed : 12.69 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.49 (0.18), residues: 2103 helix: 1.88 (0.22), residues: 593 sheet: 0.01 (0.19), residues: 663 loop : -0.43 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.016 0.002 PHE E 236 TYR 0.037 0.002 TYR A 299 ARG 0.004 0.001 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 271 time to evaluate : 1.884 Fit side-chains REVERT: A 14 GLU cc_start: 0.7228 (tt0) cc_final: 0.6714 (tp30) REVERT: A 21 LYS cc_start: 0.7026 (mttp) cc_final: 0.6689 (mttt) REVERT: A 40 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7024 (mpt) REVERT: A 86 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7545 (mtm-85) REVERT: A 101 ASP cc_start: 0.7911 (p0) cc_final: 0.7541 (p0) REVERT: A 244 TYR cc_start: 0.6498 (p90) cc_final: 0.6198 (p90) REVERT: A 253 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7090 (tp) REVERT: A 306 PHE cc_start: 0.5472 (t80) cc_final: 0.5161 (t80) REVERT: A 318 ARG cc_start: 0.6194 (mtm110) cc_final: 0.5465 (ppt170) REVERT: A 323 PHE cc_start: 0.5891 (t80) cc_final: 0.5466 (m-80) REVERT: B 24 ASP cc_start: 0.6870 (t0) cc_final: 0.6596 (p0) REVERT: B 141 MET cc_start: 0.8420 (mtt) cc_final: 0.7915 (mtt) REVERT: B 204 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7960 (tp-100) REVERT: B 286 MET cc_start: 0.8228 (ttp) cc_final: 0.7698 (ttp) REVERT: C 90 GLN cc_start: 0.8043 (mt0) cc_final: 0.7668 (mp10) REVERT: C 182 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6998 (tp30) REVERT: C 227 MET cc_start: 0.7493 (mmt) cc_final: 0.7248 (mmt) REVERT: C 245 ASP cc_start: 0.6662 (p0) cc_final: 0.6205 (p0) REVERT: C 272 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6848 (mm) REVERT: C 303 ASN cc_start: 0.8315 (t0) cc_final: 0.8049 (t0) REVERT: C 304 TYR cc_start: 0.8015 (t80) cc_final: 0.7714 (t80) REVERT: D 24 ASP cc_start: 0.7219 (t70) cc_final: 0.6808 (p0) REVERT: D 40 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: D 73 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: D 248 ASN cc_start: 0.6968 (t0) cc_final: 0.6649 (t0) REVERT: D 286 MET cc_start: 0.7706 (ttp) cc_final: 0.7505 (ttm) REVERT: D 320 LYS cc_start: 0.6958 (ttpt) cc_final: 0.6643 (ttmm) REVERT: D 331 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7815 (tp) REVERT: E 168 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7642 (mt-10) REVERT: E 189 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7496 (mt-10) REVERT: E 233 MET cc_start: 0.6434 (OUTLIER) cc_final: 0.5757 (ttm) REVERT: E 236 PHE cc_start: 0.7917 (m-80) cc_final: 0.7663 (m-80) REVERT: E 331 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6340 (ptp) REVERT: I 61 ARG cc_start: 0.6834 (ptt90) cc_final: 0.6549 (ptt90) REVERT: I 72 THR cc_start: 0.8271 (m) cc_final: 0.8037 (t) REVERT: L 61 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7053 (ptp90) REVERT: L 82 ASP cc_start: 0.6392 (m-30) cc_final: 0.5891 (m-30) REVERT: K 61 ASP cc_start: 0.7486 (t0) cc_final: 0.7236 (t0) REVERT: K 89 GLU cc_start: 0.5813 (pp20) cc_final: 0.5467 (pp20) outliers start: 88 outliers final: 53 residues processed: 329 average time/residue: 1.2833 time to fit residues: 471.0619 Evaluate side-chains 327 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 264 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.0170 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 0.4980 chunk 188 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN C 243 ASN D 87 ASN E 69 ASN E 258 ASN J 65 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17849 Z= 0.189 Angle : 0.556 7.297 24272 Z= 0.289 Chirality : 0.043 0.162 2806 Planarity : 0.004 0.048 2984 Dihedral : 8.048 74.219 2859 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.04 % Allowed : 14.60 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2103 helix: 2.24 (0.22), residues: 589 sheet: 0.25 (0.19), residues: 650 loop : -0.38 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.014 0.002 PHE E 338 TYR 0.035 0.002 TYR A 299 ARG 0.004 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 285 time to evaluate : 2.026 Fit side-chains REVERT: A 14 GLU cc_start: 0.7212 (tt0) cc_final: 0.6721 (tp30) REVERT: A 21 LYS cc_start: 0.7032 (mttp) cc_final: 0.6740 (mttp) REVERT: A 40 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.6965 (mpt) REVERT: A 86 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7470 (mtm-85) REVERT: A 101 ASP cc_start: 0.7834 (p0) cc_final: 0.7438 (p0) REVERT: A 244 TYR cc_start: 0.6379 (p90) cc_final: 0.6121 (p90) REVERT: A 253 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7095 (tp) REVERT: A 306 PHE cc_start: 0.5479 (t80) cc_final: 0.5208 (t80) REVERT: A 318 ARG cc_start: 0.6200 (mtm110) cc_final: 0.5464 (ppt170) REVERT: A 323 PHE cc_start: 0.5969 (t80) cc_final: 0.5545 (m-80) REVERT: B 24 ASP cc_start: 0.6891 (t0) cc_final: 0.6649 (p0) REVERT: B 141 MET cc_start: 0.8405 (mtt) cc_final: 0.7910 (mtt) REVERT: B 286 MET cc_start: 0.8164 (ttp) cc_final: 0.7803 (ttp) REVERT: C 90 GLN cc_start: 0.7991 (mt0) cc_final: 0.7580 (mp10) REVERT: C 182 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7012 (tp30) REVERT: C 272 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6673 (mm) REVERT: C 286 MET cc_start: 0.8350 (mtt) cc_final: 0.8123 (mtt) REVERT: C 303 ASN cc_start: 0.8304 (t0) cc_final: 0.8042 (t0) REVERT: C 304 TYR cc_start: 0.8002 (t80) cc_final: 0.7727 (t80) REVERT: D 24 ASP cc_start: 0.7192 (t70) cc_final: 0.6811 (p0) REVERT: D 40 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: D 73 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: D 87 ASN cc_start: 0.5191 (OUTLIER) cc_final: 0.4932 (t0) REVERT: D 248 ASN cc_start: 0.6982 (t0) cc_final: 0.6639 (t0) REVERT: D 286 MET cc_start: 0.7672 (ttp) cc_final: 0.7469 (ttm) REVERT: D 320 LYS cc_start: 0.6971 (ttpt) cc_final: 0.6668 (ttmm) REVERT: D 331 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7723 (tp) REVERT: E 71 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: E 120 ASP cc_start: 0.7496 (t0) cc_final: 0.7106 (t70) REVERT: E 168 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7502 (mt-10) REVERT: E 233 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5770 (ttm) REVERT: E 236 PHE cc_start: 0.7742 (m-80) cc_final: 0.7532 (m-80) REVERT: E 282 ILE cc_start: 0.7758 (mm) cc_final: 0.7491 (OUTLIER) REVERT: E 331 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6283 (ptp) REVERT: I 72 THR cc_start: 0.8292 (m) cc_final: 0.8060 (t) REVERT: L 61 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6916 (ptp90) REVERT: L 82 ASP cc_start: 0.6335 (m-30) cc_final: 0.5822 (m-30) REVERT: K 61 ASP cc_start: 0.7612 (t0) cc_final: 0.7331 (t0) outliers start: 76 outliers final: 43 residues processed: 329 average time/residue: 1.3501 time to fit residues: 492.9043 Evaluate side-chains 324 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 271 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN D 229 GLN E 258 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17849 Z= 0.320 Angle : 0.636 8.160 24272 Z= 0.330 Chirality : 0.046 0.189 2806 Planarity : 0.005 0.064 2984 Dihedral : 8.134 76.049 2846 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.78 % Allowed : 15.14 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2103 helix: 2.14 (0.22), residues: 589 sheet: 0.09 (0.19), residues: 666 loop : -0.30 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.018 0.002 PHE E 236 TYR 0.039 0.002 TYR A 299 ARG 0.005 0.001 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 273 time to evaluate : 2.250 Fit side-chains REVERT: A 14 GLU cc_start: 0.7239 (tt0) cc_final: 0.6689 (tp30) REVERT: A 21 LYS cc_start: 0.7094 (mttp) cc_final: 0.6738 (mttp) REVERT: A 40 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7059 (mpt) REVERT: A 86 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: A 101 ASP cc_start: 0.7927 (p0) cc_final: 0.7543 (p0) REVERT: A 253 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7118 (tp) REVERT: A 318 ARG cc_start: 0.6205 (mtm110) cc_final: 0.5458 (ppt170) REVERT: A 323 PHE cc_start: 0.5859 (t80) cc_final: 0.5520 (m-80) REVERT: B 24 ASP cc_start: 0.6898 (t0) cc_final: 0.6622 (p0) REVERT: B 141 MET cc_start: 0.8410 (mtt) cc_final: 0.7890 (mtt) REVERT: B 286 MET cc_start: 0.8223 (ttp) cc_final: 0.7742 (ttp) REVERT: C 90 GLN cc_start: 0.8028 (mt0) cc_final: 0.7563 (mp10) REVERT: C 182 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7009 (tp30) REVERT: C 272 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6854 (mm) REVERT: C 303 ASN cc_start: 0.8309 (t0) cc_final: 0.8045 (t0) REVERT: C 304 TYR cc_start: 0.7992 (t80) cc_final: 0.7700 (t80) REVERT: D 24 ASP cc_start: 0.7179 (t70) cc_final: 0.6850 (p0) REVERT: D 40 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: D 73 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: D 88 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6720 (p0) REVERT: D 248 ASN cc_start: 0.6995 (t0) cc_final: 0.6663 (t0) REVERT: D 286 MET cc_start: 0.7718 (ttp) cc_final: 0.7515 (ttm) REVERT: D 320 LYS cc_start: 0.6955 (ttpt) cc_final: 0.6655 (ttmm) REVERT: D 331 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7816 (tp) REVERT: E 71 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: E 150 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: E 168 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7609 (mt-10) REVERT: E 233 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.5800 (ttm) REVERT: E 236 PHE cc_start: 0.7841 (m-80) cc_final: 0.7613 (m-80) REVERT: E 282 ILE cc_start: 0.7773 (mm) cc_final: 0.7557 (OUTLIER) REVERT: E 331 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6251 (ptp) REVERT: I 72 THR cc_start: 0.8270 (m) cc_final: 0.8027 (t) REVERT: J 46 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: L 61 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7086 (ptp90) REVERT: L 82 ASP cc_start: 0.6447 (m-30) cc_final: 0.5962 (m-30) REVERT: K 11 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6539 (tp) REVERT: K 61 ASP cc_start: 0.7645 (t0) cc_final: 0.7332 (t0) outliers start: 90 outliers final: 54 residues processed: 332 average time/residue: 1.3096 time to fit residues: 484.5531 Evaluate side-chains 330 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 263 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN E 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17849 Z= 0.205 Angle : 0.566 7.277 24272 Z= 0.294 Chirality : 0.043 0.167 2806 Planarity : 0.004 0.044 2984 Dihedral : 7.681 73.019 2846 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.41 % Allowed : 15.83 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2103 helix: 2.33 (0.22), residues: 589 sheet: 0.32 (0.19), residues: 651 loop : -0.24 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.017 0.002 PHE E 338 TYR 0.037 0.002 TYR A 299 ARG 0.005 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 273 time to evaluate : 2.090 Fit side-chains REVERT: A 14 GLU cc_start: 0.7219 (tt0) cc_final: 0.6664 (tp30) REVERT: A 21 LYS cc_start: 0.6934 (mttp) cc_final: 0.6632 (mttp) REVERT: A 40 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7008 (mpt) REVERT: A 86 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7458 (mtm-85) REVERT: A 101 ASP cc_start: 0.7841 (p0) cc_final: 0.7425 (p0) REVERT: A 253 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7087 (tp) REVERT: A 318 ARG cc_start: 0.6183 (mtm110) cc_final: 0.5460 (ppt170) REVERT: A 323 PHE cc_start: 0.5926 (t80) cc_final: 0.5576 (m-80) REVERT: B 24 ASP cc_start: 0.6905 (t0) cc_final: 0.6665 (p0) REVERT: B 141 MET cc_start: 0.8394 (mtt) cc_final: 0.7913 (mtt) REVERT: B 286 MET cc_start: 0.8152 (ttp) cc_final: 0.7817 (ttp) REVERT: C 90 GLN cc_start: 0.7976 (mt0) cc_final: 0.7565 (mp10) REVERT: C 180 LYS cc_start: 0.7344 (mtmt) cc_final: 0.6981 (mppt) REVERT: C 182 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6995 (tp30) REVERT: C 272 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6772 (mm) REVERT: C 303 ASN cc_start: 0.8254 (t0) cc_final: 0.7993 (t0) REVERT: C 304 TYR cc_start: 0.7965 (t80) cc_final: 0.7686 (t80) REVERT: D 24 ASP cc_start: 0.7116 (t70) cc_final: 0.6812 (p0) REVERT: D 40 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: D 73 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: D 248 ASN cc_start: 0.7017 (t0) cc_final: 0.6638 (t0) REVERT: D 286 MET cc_start: 0.7673 (ttp) cc_final: 0.7469 (ttm) REVERT: D 320 LYS cc_start: 0.6919 (ttpt) cc_final: 0.6612 (ttmm) REVERT: D 331 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7717 (tp) REVERT: E 71 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: E 168 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7582 (mt-10) REVERT: E 233 MET cc_start: 0.6454 (OUTLIER) cc_final: 0.5811 (ttm) REVERT: E 313 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7432 (tm-30) REVERT: E 331 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6293 (ptp) REVERT: I 72 THR cc_start: 0.8242 (m) cc_final: 0.8029 (t) REVERT: J 46 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: J 98 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7724 (ttp-170) REVERT: L 61 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6927 (ptp90) REVERT: L 82 ASP cc_start: 0.6345 (m-30) cc_final: 0.5847 (m-30) REVERT: K 11 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6515 (tp) REVERT: K 25 SER cc_start: 0.7644 (m) cc_final: 0.7377 (p) REVERT: K 61 ASP cc_start: 0.7614 (t0) cc_final: 0.7294 (t0) outliers start: 83 outliers final: 51 residues processed: 325 average time/residue: 1.3866 time to fit residues: 500.8283 Evaluate side-chains 330 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 267 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN E 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17849 Z= 0.227 Angle : 0.579 7.125 24272 Z= 0.300 Chirality : 0.044 0.175 2806 Planarity : 0.004 0.045 2984 Dihedral : 7.660 71.621 2846 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.30 % Allowed : 15.99 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.99 (0.18), residues: 2103 helix: 2.34 (0.21), residues: 589 sheet: 0.33 (0.19), residues: 651 loop : -0.20 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.017 0.002 PHE E 338 TYR 0.038 0.002 TYR A 299 ARG 0.006 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 265 time to evaluate : 2.043 Fit side-chains REVERT: A 14 GLU cc_start: 0.7222 (tt0) cc_final: 0.6695 (tp30) REVERT: A 40 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7016 (mpt) REVERT: A 86 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7458 (mtm-85) REVERT: A 101 ASP cc_start: 0.7896 (p0) cc_final: 0.7478 (p0) REVERT: A 253 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7174 (tp) REVERT: A 306 PHE cc_start: 0.5264 (t80) cc_final: 0.5060 (t80) REVERT: A 318 ARG cc_start: 0.6176 (mtm110) cc_final: 0.5448 (ppt170) REVERT: B 24 ASP cc_start: 0.6921 (t0) cc_final: 0.6665 (p0) REVERT: B 141 MET cc_start: 0.8399 (mtt) cc_final: 0.7928 (mtt) REVERT: B 286 MET cc_start: 0.8160 (ttp) cc_final: 0.7835 (ttp) REVERT: C 68 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7330 (tpp80) REVERT: C 90 GLN cc_start: 0.7996 (mt0) cc_final: 0.7577 (mp10) REVERT: C 180 LYS cc_start: 0.7523 (mtmt) cc_final: 0.7125 (mppt) REVERT: C 182 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7009 (tp30) REVERT: C 272 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6772 (mm) REVERT: C 303 ASN cc_start: 0.8254 (t0) cc_final: 0.7994 (t0) REVERT: C 304 TYR cc_start: 0.7962 (t80) cc_final: 0.7672 (t80) REVERT: D 24 ASP cc_start: 0.7181 (t70) cc_final: 0.6780 (p0) REVERT: D 40 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: D 73 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: D 248 ASN cc_start: 0.7110 (t0) cc_final: 0.6726 (t0) REVERT: D 286 MET cc_start: 0.7676 (ttp) cc_final: 0.7473 (ttm) REVERT: D 320 LYS cc_start: 0.6963 (ttpt) cc_final: 0.6660 (ttmm) REVERT: D 331 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7729 (tp) REVERT: E 71 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: E 168 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7608 (mt-10) REVERT: E 282 ILE cc_start: 0.7640 (mm) cc_final: 0.7439 (mm) REVERT: E 313 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7447 (tm-30) REVERT: E 331 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6285 (ptp) REVERT: I 72 THR cc_start: 0.8224 (m) cc_final: 0.8008 (t) REVERT: J 46 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: L 61 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6935 (ptp90) REVERT: L 82 ASP cc_start: 0.6409 (m-30) cc_final: 0.5916 (m-30) REVERT: K 11 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6519 (tp) REVERT: K 25 SER cc_start: 0.7655 (m) cc_final: 0.7380 (p) REVERT: K 61 ASP cc_start: 0.7529 (t0) cc_final: 0.7228 (t0) outliers start: 81 outliers final: 56 residues processed: 317 average time/residue: 1.3681 time to fit residues: 482.2911 Evaluate side-chains 332 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 264 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 3.9990 chunk 79 optimal weight: 0.0050 chunk 119 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN E 258 ASN L 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17849 Z= 0.275 Angle : 0.613 8.290 24272 Z= 0.317 Chirality : 0.045 0.184 2806 Planarity : 0.005 0.050 2984 Dihedral : 7.884 73.268 2846 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.83 % Allowed : 15.83 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.92 (0.18), residues: 2103 helix: 2.26 (0.21), residues: 589 sheet: 0.23 (0.19), residues: 667 loop : -0.17 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.018 0.002 PHE E 338 TYR 0.041 0.002 TYR A 299 ARG 0.006 0.001 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 274 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7224 (tt0) cc_final: 0.6669 (tp30) REVERT: A 21 LYS cc_start: 0.7281 (mttp) cc_final: 0.6664 (mttp) REVERT: A 40 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7029 (mpt) REVERT: A 86 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7478 (mtm-85) REVERT: A 101 ASP cc_start: 0.7889 (p0) cc_final: 0.7470 (p0) REVERT: A 253 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7095 (tp) REVERT: A 318 ARG cc_start: 0.6204 (mtm110) cc_final: 0.5453 (ppt170) REVERT: A 323 PHE cc_start: 0.5164 (OUTLIER) cc_final: 0.4459 (t80) REVERT: B 24 ASP cc_start: 0.6901 (t0) cc_final: 0.6636 (p0) REVERT: B 123 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: B 131 MET cc_start: 0.8699 (ptm) cc_final: 0.8461 (ptp) REVERT: B 141 MET cc_start: 0.8408 (mtt) cc_final: 0.7888 (mtt) REVERT: B 286 MET cc_start: 0.8187 (ttp) cc_final: 0.7728 (ttp) REVERT: C 68 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7348 (tpp80) REVERT: C 90 GLN cc_start: 0.8032 (mt0) cc_final: 0.7592 (mp10) REVERT: C 182 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6977 (tp30) REVERT: C 303 ASN cc_start: 0.8263 (t0) cc_final: 0.8001 (t0) REVERT: C 304 TYR cc_start: 0.7964 (t80) cc_final: 0.7675 (t80) REVERT: D 24 ASP cc_start: 0.7168 (t70) cc_final: 0.6845 (p0) REVERT: D 40 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: D 73 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: D 248 ASN cc_start: 0.7137 (t0) cc_final: 0.6761 (t0) REVERT: D 286 MET cc_start: 0.7699 (ttp) cc_final: 0.7497 (ttm) REVERT: D 320 LYS cc_start: 0.6981 (ttpt) cc_final: 0.6648 (ttmm) REVERT: D 331 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7814 (tp) REVERT: E 71 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: E 168 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7606 (mt-10) REVERT: E 313 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7429 (tm-30) REVERT: E 331 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6272 (ptp) REVERT: I 72 THR cc_start: 0.8234 (m) cc_final: 0.8003 (t) REVERT: J 46 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: L 61 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7171 (ptp90) REVERT: L 82 ASP cc_start: 0.6444 (m-30) cc_final: 0.5985 (m-30) REVERT: K 11 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6533 (tp) REVERT: K 61 ASP cc_start: 0.7514 (t0) cc_final: 0.7254 (t0) outliers start: 91 outliers final: 61 residues processed: 333 average time/residue: 1.2887 time to fit residues: 477.4128 Evaluate side-chains 341 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 267 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN E 258 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17849 Z= 0.270 Angle : 0.615 9.621 24272 Z= 0.317 Chirality : 0.045 0.182 2806 Planarity : 0.005 0.046 2984 Dihedral : 7.904 74.086 2846 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.46 % Allowed : 16.20 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2103 helix: 2.25 (0.21), residues: 589 sheet: 0.23 (0.19), residues: 667 loop : -0.15 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.019 0.002 PHE E 338 TYR 0.042 0.002 TYR A 299 ARG 0.006 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 266 time to evaluate : 2.139 Fit side-chains REVERT: A 14 GLU cc_start: 0.7229 (tt0) cc_final: 0.6689 (tp30) REVERT: A 21 LYS cc_start: 0.7205 (mttp) cc_final: 0.6663 (mttp) REVERT: A 40 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7054 (mpt) REVERT: A 86 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7469 (mtm-85) REVERT: A 101 ASP cc_start: 0.7889 (p0) cc_final: 0.7465 (p0) REVERT: A 253 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7089 (tp) REVERT: A 318 ARG cc_start: 0.6206 (mtm110) cc_final: 0.5457 (ppt170) REVERT: A 323 PHE cc_start: 0.5197 (OUTLIER) cc_final: 0.4470 (t80) REVERT: B 24 ASP cc_start: 0.6908 (t0) cc_final: 0.6647 (p0) REVERT: B 123 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: B 131 MET cc_start: 0.8693 (ptm) cc_final: 0.8465 (ptp) REVERT: B 141 MET cc_start: 0.8408 (mtt) cc_final: 0.7917 (mtt) REVERT: B 286 MET cc_start: 0.8143 (ttp) cc_final: 0.7671 (ttp) REVERT: C 68 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7565 (tpp80) REVERT: C 90 GLN cc_start: 0.7987 (mt0) cc_final: 0.7550 (mp10) REVERT: C 180 LYS cc_start: 0.7525 (mtmt) cc_final: 0.7201 (mppt) REVERT: C 182 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6981 (tp30) REVERT: C 303 ASN cc_start: 0.8255 (t0) cc_final: 0.7993 (t0) REVERT: C 304 TYR cc_start: 0.7963 (t80) cc_final: 0.7675 (t80) REVERT: D 24 ASP cc_start: 0.7153 (t70) cc_final: 0.6831 (p0) REVERT: D 40 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: D 73 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: D 248 ASN cc_start: 0.7100 (t0) cc_final: 0.6721 (t0) REVERT: D 286 MET cc_start: 0.7697 (ttp) cc_final: 0.7497 (ttm) REVERT: D 320 LYS cc_start: 0.6977 (ttpt) cc_final: 0.6682 (ttmm) REVERT: D 331 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7802 (tp) REVERT: E 71 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: E 168 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7604 (mt-10) REVERT: E 313 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7430 (tm-30) REVERT: E 331 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6275 (ptp) REVERT: I 72 THR cc_start: 0.8234 (m) cc_final: 0.8003 (t) REVERT: J 46 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: L 61 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7171 (ptp90) REVERT: L 82 ASP cc_start: 0.6438 (m-30) cc_final: 0.5910 (m-30) REVERT: K 11 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6542 (tp) REVERT: K 25 SER cc_start: 0.7661 (m) cc_final: 0.7382 (p) REVERT: K 61 ASP cc_start: 0.7517 (t0) cc_final: 0.7225 (t0) outliers start: 84 outliers final: 60 residues processed: 322 average time/residue: 1.3699 time to fit residues: 493.6082 Evaluate side-chains 338 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 265 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 130 optimal weight: 9.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN E 258 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17849 Z= 0.371 Angle : 0.678 9.113 24272 Z= 0.351 Chirality : 0.048 0.198 2806 Planarity : 0.006 0.100 2984 Dihedral : 8.195 77.843 2843 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.51 % Allowed : 16.36 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.74 (0.18), residues: 2103 helix: 2.05 (0.21), residues: 591 sheet: -0.01 (0.19), residues: 682 loop : -0.09 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.024 0.003 PHE A 306 TYR 0.045 0.002 TYR A 299 ARG 0.012 0.001 ARG C 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 268 time to evaluate : 2.166 Fit side-chains REVERT: A 14 GLU cc_start: 0.7247 (tt0) cc_final: 0.6695 (tp30) REVERT: A 21 LYS cc_start: 0.7181 (mttp) cc_final: 0.6642 (mttp) REVERT: A 40 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7138 (mpt) REVERT: A 86 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: A 101 ASP cc_start: 0.7914 (p0) cc_final: 0.7506 (p0) REVERT: A 253 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7249 (tt) REVERT: A 318 ARG cc_start: 0.6242 (mtm110) cc_final: 0.5458 (ppt170) REVERT: A 323 PHE cc_start: 0.5117 (OUTLIER) cc_final: 0.4835 (t80) REVERT: B 24 ASP cc_start: 0.6937 (t0) cc_final: 0.6649 (p0) REVERT: B 123 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: B 131 MET cc_start: 0.8739 (ptm) cc_final: 0.8529 (ptp) REVERT: B 141 MET cc_start: 0.8411 (mtt) cc_final: 0.7885 (mtt) REVERT: B 286 MET cc_start: 0.8201 (ttp) cc_final: 0.7911 (ttp) REVERT: C 68 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7386 (tpp80) REVERT: C 90 GLN cc_start: 0.8134 (mt0) cc_final: 0.7740 (mp-120) REVERT: C 180 LYS cc_start: 0.7413 (mtmt) cc_final: 0.7096 (mppt) REVERT: C 182 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6971 (tp30) REVERT: C 303 ASN cc_start: 0.8266 (t0) cc_final: 0.8026 (t0) REVERT: C 304 TYR cc_start: 0.7970 (t80) cc_final: 0.7667 (t80) REVERT: D 24 ASP cc_start: 0.7189 (t70) cc_final: 0.6837 (p0) REVERT: D 40 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: D 73 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: D 248 ASN cc_start: 0.7113 (t0) cc_final: 0.6735 (t0) REVERT: D 286 MET cc_start: 0.7752 (ttp) cc_final: 0.7545 (ttm) REVERT: D 320 LYS cc_start: 0.6957 (ttpt) cc_final: 0.6662 (ttmm) REVERT: D 331 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7833 (tp) REVERT: E 71 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: E 168 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7660 (mt-10) REVERT: E 282 ILE cc_start: 0.7665 (mm) cc_final: 0.7458 (mm) REVERT: E 331 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6219 (ptp) REVERT: I 72 THR cc_start: 0.8266 (m) cc_final: 0.8012 (t) REVERT: J 46 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: L 82 ASP cc_start: 0.6470 (m-30) cc_final: 0.5983 (m-30) REVERT: K 11 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6566 (tp) REVERT: K 61 ASP cc_start: 0.7538 (t0) cc_final: 0.7217 (t0) outliers start: 85 outliers final: 62 residues processed: 324 average time/residue: 1.2781 time to fit residues: 461.5225 Evaluate side-chains 337 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 264 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 185 GLN E 258 ASN ** L 42 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 = 0.3633 r_free = 0.3633 target = 0.134057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106605 restraints weight = 21387.833| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.93 r_work: 0.3042 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17849 Z= 0.204 Angle : 0.586 9.461 24272 Z= 0.303 Chirality : 0.044 0.180 2806 Planarity : 0.004 0.043 2984 Dihedral : 7.684 74.147 2843 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.56 % Allowed : 17.79 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 1.02 (0.18), residues: 2103 helix: 2.32 (0.21), residues: 593 sheet: 0.32 (0.19), residues: 651 loop : -0.13 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.023 0.002 PHE A 306 TYR 0.040 0.002 TYR A 299 ARG 0.016 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7637.65 seconds wall clock time: 133 minutes 43.32 seconds (8023.32 seconds total)