Starting phenix.real_space_refine on Fri Sep 27 22:50:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/09_2024/6x3z_22037.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/09_2024/6x3z_22037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/09_2024/6x3z_22037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/09_2024/6x3z_22037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/09_2024/6x3z_22037.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/09_2024/6x3z_22037.cif" } resolution = 3.23 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= 0.003 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 11211 2.51 5 N 2828 2.21 5 O 3229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17365 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" 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: "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: 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.02, per 1000 atoms: 0.63 Number of scatterers: 17365 At special positions: 0 Unit cell: (134.475, 146.025, 106.425, 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 3229 8.00 N 2828 7.00 C 11211 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=2.02 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 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=2.03 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-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG D 401 " - " ASN D 111 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN E 208 " Time building additional restraints: 5.07 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: 4020 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 28 sheets defined 31.2% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.569A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.559A pdb=" N ARG A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 238 removed outlier: 4.121A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.861A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.698A 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: 3.989A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.987A 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 90 through 94 removed outlier: 3.788A pdb=" N ILE B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 removed outlier: 4.032A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 251 through 274 removed outlier: 3.568A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 345 removed outlier: 4.018A pdb=" N ALA B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.614A pdb=" N LEU B 345 " --> pdb=" O TRP B 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 20 removed outlier: 3.987A pdb=" N VAL C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.524A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 236 removed outlier: 5.042A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 237 through 242 removed outlier: 4.278A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 270 removed outlier: 4.238A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 4.111A 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 339 removed outlier: 3.938A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.789A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 251 through 275 removed outlier: 3.641A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.846A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (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 99 through 106 removed outlier: 4.150A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.097A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.564A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 261 through 285 removed outlier: 3.691A pdb=" N LYS E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 324 removed outlier: 4.313A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 329 removed outlier: 3.539A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 357 removed outlier: 4.624A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix removed outlier: 4.063A pdb=" N LEU E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.717A pdb=" N ASP J 90 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.700A pdb=" N THR K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.523A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.266A 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: 6.877A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.752A pdb=" N CYS A 150 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 212 " --> pdb=" O CYS A 150 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A 199 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR A 205 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 197 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG A 207 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR A 195 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 209 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 193 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 211 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 6.655A 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: 4.176A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.219A 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: 7.383A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.075A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 3.749A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.303A 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: 6.847A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.638A pdb=" N CYS C 150 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 212 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.399A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 108 through 109 removed outlier: 7.383A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.804A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.804A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.816A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU E 150 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER E 116 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.816A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS E 184 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR E 55 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER E 186 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N MET E 57 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL E 188 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL E 59 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL E 190 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N SER E 61 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.678A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.589A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.643A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.833A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.902A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.613A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.698A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.549A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.549A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 5.78 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: 4287 1.33 - 1.46: 4733 1.46 - 1.58: 8612 1.58 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 17799 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 1.98e+01 bond pdb=" CD ABU C 405 " pdb=" OE2 ABU C 405 " ideal model delta sigma weight residual 1.250 1.338 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" N GLN A 148 " pdb=" CA GLN A 148 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.21e-02 6.83e+03 7.78e+00 bond pdb=" N ASN E 208 " pdb=" CA ASN E 208 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.64e+00 bond pdb=" N SER C 211 " pdb=" CA SER C 211 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.23e-02 6.61e+03 7.15e+00 ... (remaining 17794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 23922 3.94 - 7.88: 257 7.88 - 11.81: 18 11.81 - 15.75: 6 15.75 - 19.69: 1 Bond angle restraints: 24204 Sorted by residual: angle pdb=" CA ARG C 269 " pdb=" CB ARG C 269 " pdb=" CG ARG C 269 " ideal model delta sigma weight residual 114.10 126.39 -12.29 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA LEU E 345 " pdb=" CB LEU E 345 " pdb=" CG LEU E 345 " ideal model delta sigma weight residual 116.30 135.99 -19.69 3.50e+00 8.16e-02 3.16e+01 angle pdb=" CA THR I 31 " pdb=" CB THR I 31 " pdb=" CG2 THR I 31 " ideal model delta sigma weight residual 110.50 118.08 -7.58 1.70e+00 3.46e-01 1.99e+01 angle pdb=" C CYS C 150 " pdb=" CA CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sigma weight residual 109.35 117.96 -8.61 1.98e+00 2.55e-01 1.89e+01 angle pdb=" C CYS A 150 " pdb=" CA CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sigma weight residual 109.70 117.49 -7.79 1.81e+00 3.05e-01 1.85e+01 ... (remaining 24199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 10079 21.85 - 43.71: 592 43.71 - 65.56: 46 65.56 - 87.41: 37 87.41 - 109.26: 14 Dihedral angle restraints: 10768 sinusoidal: 4512 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -7.40 -78.60 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -13.57 -72.43 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS C 136 " pdb=" SG CYS C 136 " pdb=" SG CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sinusoidal sigma weight residual -86.00 -19.82 -66.18 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 10765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.914: 2795 0.914 - 1.827: 0 1.827 - 2.741: 0 2.741 - 3.655: 0 3.655 - 4.569: 2 Chirality restraints: 2797 Sorted by residual: chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.47e+03 chirality pdb=" C1 MAN G 6 " pdb=" O2 MAN G 5 " pdb=" C2 MAN G 6 " pdb=" O5 MAN G 6 " both_signs ideal model delta sigma weight residual False 2.40 1.66 0.74 2.00e-02 2.50e+03 1.37e+03 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.22e+03 ... (remaining 2794 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.289 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG M 2 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.414 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.150 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C7 NAG M 1 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.202 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.146 2.00e-02 2.50e+03 1.20e-01 1.81e+02 pdb=" C7 NAG F 2 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.195 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.020 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2920 2.77 - 3.30: 15374 3.30 - 3.83: 29493 3.83 - 4.37: 35165 4.37 - 4.90: 62034 Nonbonded interactions: 144986 Sorted by model distance: nonbonded pdb=" O VAL B 257 " pdb=" OG1 THR B 261 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR C 226 " pdb=" OH TYR C 335 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.286 3.040 nonbonded pdb=" O THR C 256 " pdb=" OG1 THR C 260 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR E 111 " pdb=" OH TYR E 181 " model vdw 2.308 3.040 ... (remaining 144981 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' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.760 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 41.910 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 17799 Z= 0.474 Angle : 1.089 19.690 24204 Z= 0.573 Chirality : 0.142 4.569 2797 Planarity : 0.009 0.243 2981 Dihedral : 14.388 109.265 6721 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.69 % Allowed : 5.63 % Favored : 93.68 % Cbeta Deviations : 0.10 % 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: -2.07 (0.16), residues: 2103 helix: -0.27 (0.20), residues: 564 sheet: -0.96 (0.19), residues: 632 loop : -2.37 (0.17), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 336 HIS 0.005 0.002 HIS B 151 PHE 0.045 0.004 PHE B 258 TYR 0.042 0.003 TYR C 157 ARG 0.010 0.001 ARG C 269 *********************** 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 422 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 409 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LEU cc_start: 0.8493 (mt) cc_final: 0.8217 (mp) REVERT: A 319 TRP cc_start: 0.7432 (t60) cc_final: 0.6880 (t-100) REVERT: B 24 ASP cc_start: 0.7732 (t0) cc_final: 0.7253 (p0) REVERT: B 71 LYS cc_start: 0.8337 (tttp) cc_final: 0.8092 (tttp) REVERT: B 73 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7826 (mm-30) REVERT: B 98 ASP cc_start: 0.7600 (p0) cc_final: 0.7227 (p0) REVERT: B 335 ILE cc_start: 0.8155 (pt) cc_final: 0.7906 (mp) REVERT: C 41 ASN cc_start: 0.7848 (m110) cc_final: 0.7347 (t0) REVERT: C 54 ASN cc_start: 0.8106 (m110) cc_final: 0.7851 (m110) REVERT: C 137 MET cc_start: 0.8279 (mmm) cc_final: 0.7985 (mmm) REVERT: D 93 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7734 (tptp) REVERT: E 33 ASN cc_start: 0.8174 (m-40) cc_final: 0.7907 (m-40) REVERT: I 13 MET cc_start: 0.7054 (ppp) cc_final: 0.6479 (ppp) REVERT: I 60 ASP cc_start: 0.8418 (t70) cc_final: 0.8206 (t0) REVERT: J 46 GLU cc_start: 0.8170 (tt0) cc_final: 0.7871 (tt0) REVERT: J 63 LYS cc_start: 0.8741 (mttp) cc_final: 0.8529 (ttpt) REVERT: J 65 GLN cc_start: 0.8115 (tp40) cc_final: 0.7882 (tp40) REVERT: J 80 TYR cc_start: 0.8792 (m-80) cc_final: 0.8368 (m-80) REVERT: K 73 ASP cc_start: 0.8170 (t0) cc_final: 0.7765 (t0) outliers start: 13 outliers final: 3 residues processed: 417 average time/residue: 0.3362 time to fit residues: 205.0497 Evaluate side-chains 323 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 320 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 187 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 54 ASN A 65 GLN A 185 GLN B 68 GLN B 242 GLN C 65 GLN C 303 ASN C 309 GLN D 68 GLN D 102 HIS D 116 ASN D 189 ASN D 275 ASN D 308 ASN D 314 GLN D 346 ASN E 128 ASN I 38 GLN J 6 GLN K 6 GLN K 110 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17799 Z= 0.210 Angle : 0.639 10.204 24204 Z= 0.317 Chirality : 0.053 1.054 2797 Planarity : 0.004 0.043 2981 Dihedral : 8.727 78.804 2787 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.33 % Allowed : 11.68 % Favored : 86.99 % 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: -1.28 (0.17), residues: 2103 helix: 0.58 (0.21), residues: 558 sheet: -0.75 (0.19), residues: 646 loop : -1.80 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 252 HIS 0.003 0.001 HIS A 267 PHE 0.027 0.002 PHE E 158 TYR 0.018 0.001 TYR E 314 ARG 0.007 0.001 ARG I 61 *********************** 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 366 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 341 time to evaluate : 1.802 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7823 (mtp-110) REVERT: A 304 TYR cc_start: 0.6989 (t80) cc_final: 0.6755 (t80) REVERT: A 319 TRP cc_start: 0.7467 (t60) cc_final: 0.6940 (t-100) REVERT: B 24 ASP cc_start: 0.7588 (t0) cc_final: 0.7146 (p0) REVERT: B 71 LYS cc_start: 0.8181 (tttp) cc_final: 0.7926 (tptm) REVERT: B 98 ASP cc_start: 0.7511 (p0) cc_final: 0.7109 (p0) REVERT: B 246 TRP cc_start: 0.7064 (m100) cc_final: 0.6713 (m-10) REVERT: C 41 ASN cc_start: 0.7936 (m110) cc_final: 0.7395 (t0) REVERT: C 54 ASN cc_start: 0.8197 (m110) cc_final: 0.7935 (m110) REVERT: C 68 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.7993 (ttt-90) REVERT: C 323 PHE cc_start: 0.5947 (m-10) cc_final: 0.5680 (m-10) REVERT: D 58 MET cc_start: 0.8351 (mmm) cc_final: 0.7789 (mtm) REVERT: D 93 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7832 (tptp) REVERT: D 112 MET cc_start: 0.8110 (tpp) cc_final: 0.7236 (tpp) REVERT: E 117 LYS cc_start: 0.8976 (mttm) cc_final: 0.8755 (mttt) REVERT: I 13 MET cc_start: 0.7123 (ppp) cc_final: 0.6546 (ppp) REVERT: I 60 ASP cc_start: 0.8399 (t70) cc_final: 0.8143 (t0) REVERT: J 65 GLN cc_start: 0.8088 (tp40) cc_final: 0.7840 (tp40) REVERT: J 80 TYR cc_start: 0.8960 (m-80) cc_final: 0.8581 (m-80) REVERT: K 73 ASP cc_start: 0.8185 (t0) cc_final: 0.7885 (t0) outliers start: 25 outliers final: 16 residues processed: 349 average time/residue: 0.2983 time to fit residues: 155.3499 Evaluate side-chains 322 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 306 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 116 ASN D 151 HIS E 69 ASN L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17799 Z= 0.326 Angle : 0.641 10.293 24204 Z= 0.317 Chirality : 0.046 0.264 2797 Planarity : 0.004 0.051 2981 Dihedral : 7.068 65.724 2783 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.71 % Allowed : 13.17 % Favored : 84.12 % 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: -0.87 (0.18), residues: 2103 helix: 0.97 (0.21), residues: 558 sheet: -0.60 (0.20), residues: 605 loop : -1.49 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 252 HIS 0.004 0.001 HIS A 119 PHE 0.024 0.002 PHE E 304 TYR 0.015 0.002 TYR C 157 ARG 0.004 0.000 ARG J 50 *********************** 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 374 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 323 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.7982 (p0) cc_final: 0.7766 (p0) REVERT: A 142 ARG cc_start: 0.8144 (mtp180) cc_final: 0.7915 (mtp-110) REVERT: A 227 MET cc_start: 0.7146 (ttp) cc_final: 0.6277 (ttp) REVERT: A 319 TRP cc_start: 0.7472 (t60) cc_final: 0.6873 (t-100) REVERT: B 24 ASP cc_start: 0.7720 (t0) cc_final: 0.7242 (p0) REVERT: B 58 MET cc_start: 0.8413 (mmm) cc_final: 0.8170 (mmt) REVERT: B 71 LYS cc_start: 0.8328 (tttp) cc_final: 0.8060 (tptm) REVERT: B 98 ASP cc_start: 0.7720 (p0) cc_final: 0.7341 (p0) REVERT: B 294 TYR cc_start: 0.6969 (t80) cc_final: 0.6721 (t80) REVERT: B 335 ILE cc_start: 0.8188 (pt) cc_final: 0.7985 (mp) REVERT: C 9 MET cc_start: 0.8225 (tpp) cc_final: 0.7983 (tpp) REVERT: C 54 ASN cc_start: 0.8280 (m110) cc_final: 0.8021 (m110) REVERT: C 289 PHE cc_start: 0.7466 (t80) cc_final: 0.6770 (t80) REVERT: D 58 MET cc_start: 0.8411 (mmm) cc_final: 0.7879 (mtm) REVERT: D 93 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7955 (tptp) REVERT: D 112 MET cc_start: 0.8202 (tpp) cc_final: 0.7277 (tpp) REVERT: D 138 GLU cc_start: 0.7559 (pt0) cc_final: 0.7347 (pt0) REVERT: D 236 MET cc_start: 0.6516 (mtt) cc_final: 0.6294 (mtp) REVERT: E 34 LEU cc_start: 0.8453 (mt) cc_final: 0.8252 (mp) REVERT: I 13 MET cc_start: 0.7262 (ppp) cc_final: 0.6785 (ppp) REVERT: I 60 ASP cc_start: 0.8390 (t70) cc_final: 0.8185 (t0) REVERT: J 19 LYS cc_start: 0.8957 (tptt) cc_final: 0.8665 (tptp) REVERT: J 65 GLN cc_start: 0.8131 (tp40) cc_final: 0.7887 (tp40) REVERT: K 73 ASP cc_start: 0.8244 (t0) cc_final: 0.7907 (t0) REVERT: K 110 GLN cc_start: 0.8460 (pm20) cc_final: 0.8014 (pm20) outliers start: 51 outliers final: 30 residues processed: 351 average time/residue: 0.2855 time to fit residues: 151.9822 Evaluate side-chains 335 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 305 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 53 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 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN D 216 HIS E 80 GLN E 258 ASN I 1 ASN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17799 Z= 0.381 Angle : 0.648 9.839 24204 Z= 0.324 Chirality : 0.046 0.308 2797 Planarity : 0.004 0.049 2981 Dihedral : 6.518 57.550 2783 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.45 % Allowed : 14.92 % Favored : 81.63 % 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: -0.66 (0.18), residues: 2103 helix: 1.14 (0.21), residues: 557 sheet: -0.62 (0.20), residues: 611 loop : -1.24 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 252 HIS 0.005 0.001 HIS E 122 PHE 0.030 0.002 PHE E 346 TYR 0.022 0.002 TYR A 338 ARG 0.012 0.001 ARG C 141 *********************** 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 382 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 317 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8013 (p0) cc_final: 0.7811 (p0) REVERT: A 319 TRP cc_start: 0.7490 (t60) cc_final: 0.6875 (t-100) REVERT: A 338 TYR cc_start: 0.7551 (t80) cc_final: 0.7244 (t80) REVERT: B 24 ASP cc_start: 0.7844 (t0) cc_final: 0.7378 (p0) REVERT: B 58 MET cc_start: 0.8511 (mmm) cc_final: 0.8272 (mmm) REVERT: B 98 ASP cc_start: 0.7853 (p0) cc_final: 0.7494 (p0) REVERT: B 294 TYR cc_start: 0.7086 (t80) cc_final: 0.6753 (t80) REVERT: C 41 ASN cc_start: 0.8141 (m110) cc_final: 0.7760 (m-40) REVERT: C 54 ASN cc_start: 0.8428 (m110) cc_final: 0.8163 (m110) REVERT: C 59 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8506 (pt) REVERT: C 68 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.7972 (ttt-90) REVERT: D 58 MET cc_start: 0.8472 (mmm) cc_final: 0.7947 (mtm) REVERT: D 112 MET cc_start: 0.8253 (tpp) cc_final: 0.7410 (tpp) REVERT: E 34 LEU cc_start: 0.8490 (mt) cc_final: 0.8283 (mp) REVERT: I 13 MET cc_start: 0.7330 (ppp) cc_final: 0.6936 (ppp) REVERT: J 65 GLN cc_start: 0.8130 (tp40) cc_final: 0.7916 (tp40) REVERT: K 73 ASP cc_start: 0.8275 (t0) cc_final: 0.7883 (t0) outliers start: 65 outliers final: 46 residues processed: 355 average time/residue: 0.2990 time to fit residues: 161.1539 Evaluate side-chains 353 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 306 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 179 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17799 Z= 0.254 Angle : 0.593 9.552 24204 Z= 0.297 Chirality : 0.044 0.273 2797 Planarity : 0.004 0.041 2981 Dihedral : 6.234 59.498 2783 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.03 % Allowed : 16.09 % Favored : 80.88 % 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: -0.44 (0.18), residues: 2103 helix: 1.29 (0.22), residues: 560 sheet: -0.49 (0.20), residues: 611 loop : -1.08 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 252 HIS 0.003 0.001 HIS B 142 PHE 0.028 0.002 PHE E 346 TYR 0.014 0.001 TYR A 338 ARG 0.010 0.000 ARG I 61 *********************** 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 381 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 324 time to evaluate : 1.906 Fit side-chains revert: symmetry clash REVERT: A 95 ASP cc_start: 0.7926 (p0) cc_final: 0.7722 (p0) REVERT: A 319 TRP cc_start: 0.7434 (t60) cc_final: 0.6769 (t-100) REVERT: A 338 TYR cc_start: 0.7503 (t80) cc_final: 0.7274 (t80) REVERT: B 24 ASP cc_start: 0.7815 (t0) cc_final: 0.7363 (p0) REVERT: B 58 MET cc_start: 0.8379 (mmm) cc_final: 0.7964 (mmm) REVERT: B 71 LYS cc_start: 0.8355 (tttp) cc_final: 0.8011 (tttp) REVERT: B 73 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 98 ASP cc_start: 0.7738 (p0) cc_final: 0.7396 (p0) REVERT: B 222 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8338 (mtmt) REVERT: B 294 TYR cc_start: 0.7103 (t80) cc_final: 0.6823 (t80) REVERT: C 41 ASN cc_start: 0.8066 (m110) cc_final: 0.7789 (m-40) REVERT: C 54 ASN cc_start: 0.8383 (m110) cc_final: 0.8100 (m-40) REVERT: C 59 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8513 (pt) REVERT: C 68 ARG cc_start: 0.8234 (ttt-90) cc_final: 0.7976 (ttt-90) REVERT: C 162 ASP cc_start: 0.8155 (p0) cc_final: 0.7858 (p0) REVERT: D 112 MET cc_start: 0.8263 (tpp) cc_final: 0.7436 (tpp) REVERT: I 13 MET cc_start: 0.7277 (ppp) cc_final: 0.7028 (ppp) REVERT: J 65 GLN cc_start: 0.8132 (tp40) cc_final: 0.7927 (tp40) REVERT: K 73 ASP cc_start: 0.8259 (t0) cc_final: 0.7848 (t0) outliers start: 57 outliers final: 40 residues processed: 356 average time/residue: 0.2970 time to fit residues: 159.0247 Evaluate side-chains 356 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 315 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN D 189 ASN L 53 ASN ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17799 Z= 0.213 Angle : 0.580 9.576 24204 Z= 0.289 Chirality : 0.044 0.269 2797 Planarity : 0.004 0.045 2981 Dihedral : 6.046 59.563 2783 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.03 % Allowed : 17.31 % Favored : 79.66 % 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: -0.29 (0.18), residues: 2103 helix: 1.43 (0.22), residues: 560 sheet: -0.41 (0.21), residues: 609 loop : -0.98 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 252 HIS 0.002 0.001 HIS D 110 PHE 0.026 0.001 PHE E 346 TYR 0.013 0.001 TYR C 299 ARG 0.013 0.000 ARG I 61 *********************** 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 377 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 320 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.7913 (p0) cc_final: 0.7698 (p0) REVERT: A 319 TRP cc_start: 0.7372 (t60) cc_final: 0.6777 (t-100) REVERT: A 338 TYR cc_start: 0.7508 (t80) cc_final: 0.7251 (t80) REVERT: B 24 ASP cc_start: 0.7863 (t0) cc_final: 0.7397 (p0) REVERT: B 71 LYS cc_start: 0.8347 (tttp) cc_final: 0.8002 (tttp) REVERT: B 73 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 98 ASP cc_start: 0.7759 (p0) cc_final: 0.7408 (p0) REVERT: B 222 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8323 (mtmt) REVERT: C 41 ASN cc_start: 0.8020 (m110) cc_final: 0.7578 (m110) REVERT: C 54 ASN cc_start: 0.8357 (m110) cc_final: 0.8090 (m-40) REVERT: C 59 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8499 (pt) REVERT: C 68 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7971 (ttt-90) REVERT: C 162 ASP cc_start: 0.8101 (p0) cc_final: 0.7764 (p0) REVERT: D 112 MET cc_start: 0.8215 (tpp) cc_final: 0.7437 (tpp) REVERT: E 306 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: K 73 ASP cc_start: 0.8247 (t0) cc_final: 0.7839 (t0) outliers start: 57 outliers final: 42 residues processed: 355 average time/residue: 0.2870 time to fit residues: 153.5864 Evaluate side-chains 354 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 310 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 0.0870 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN A 332 ASN B 189 ASN D 189 ASN E 101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17799 Z= 0.350 Angle : 0.630 9.687 24204 Z= 0.313 Chirality : 0.045 0.282 2797 Planarity : 0.004 0.043 2981 Dihedral : 6.128 59.843 2783 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.56 % Allowed : 17.74 % Favored : 78.70 % 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: -0.28 (0.18), residues: 2103 helix: 1.41 (0.22), residues: 560 sheet: -0.46 (0.21), residues: 617 loop : -0.92 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 252 HIS 0.004 0.001 HIS D 110 PHE 0.017 0.002 PHE E 158 TYR 0.014 0.002 TYR C 157 ARG 0.010 0.000 ARG I 61 *********************** 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 381 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 314 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.7989 (p0) cc_final: 0.7788 (p0) REVERT: A 319 TRP cc_start: 0.7346 (t60) cc_final: 0.6801 (t-100) REVERT: A 338 TYR cc_start: 0.7544 (t80) cc_final: 0.7293 (t80) REVERT: B 58 MET cc_start: 0.8247 (mmm) cc_final: 0.7807 (mmm) REVERT: B 98 ASP cc_start: 0.7842 (p0) cc_final: 0.7492 (p0) REVERT: C 41 ASN cc_start: 0.8100 (m110) cc_final: 0.7827 (m-40) REVERT: C 54 ASN cc_start: 0.8433 (m110) cc_final: 0.8154 (m-40) REVERT: C 59 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8517 (pt) REVERT: C 68 ARG cc_start: 0.8249 (ttt-90) cc_final: 0.7983 (ttt-90) REVERT: C 162 ASP cc_start: 0.8158 (p0) cc_final: 0.7836 (p0) REVERT: D 112 MET cc_start: 0.8216 (tpp) cc_final: 0.7430 (tpp) REVERT: D 133 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8553 (pt) REVERT: E 256 TRP cc_start: 0.8256 (m-90) cc_final: 0.7842 (m-10) REVERT: E 306 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6844 (m-10) REVERT: K 73 ASP cc_start: 0.8294 (t0) cc_final: 0.7865 (t0) outliers start: 67 outliers final: 54 residues processed: 358 average time/residue: 0.2966 time to fit residues: 161.3181 Evaluate side-chains 363 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 306 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 308 ASN E 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17799 Z= 0.188 Angle : 0.579 9.548 24204 Z= 0.288 Chirality : 0.043 0.263 2797 Planarity : 0.004 0.044 2981 Dihedral : 5.874 58.424 2783 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.81 % Allowed : 18.11 % Favored : 79.08 % 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: -0.12 (0.19), residues: 2103 helix: 1.51 (0.22), residues: 560 sheet: -0.37 (0.21), residues: 617 loop : -0.80 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 252 HIS 0.002 0.000 HIS E 163 PHE 0.029 0.001 PHE C 289 TYR 0.013 0.001 TYR C 143 ARG 0.008 0.000 ARG I 61 *********************** 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 376 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 323 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8366 (mtm110) cc_final: 0.8160 (mtm110) REVERT: A 95 ASP cc_start: 0.7913 (p0) cc_final: 0.7696 (p0) REVERT: A 319 TRP cc_start: 0.7342 (t60) cc_final: 0.6769 (t-100) REVERT: B 24 ASP cc_start: 0.7874 (t0) cc_final: 0.7454 (p0) REVERT: B 71 LYS cc_start: 0.8360 (tttp) cc_final: 0.8133 (tptm) REVERT: B 98 ASP cc_start: 0.7711 (p0) cc_final: 0.7405 (p0) REVERT: B 222 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8278 (mtmt) REVERT: C 41 ASN cc_start: 0.7927 (m110) cc_final: 0.7641 (m110) REVERT: C 54 ASN cc_start: 0.8356 (m110) cc_final: 0.8096 (m-40) REVERT: C 68 ARG cc_start: 0.8216 (ttt-90) cc_final: 0.7961 (ttt-90) REVERT: C 212 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: D 112 MET cc_start: 0.8215 (tpp) cc_final: 0.7447 (tpp) REVERT: E 306 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6839 (m-10) REVERT: J 19 LYS cc_start: 0.8712 (tptp) cc_final: 0.8391 (tptp) REVERT: K 65 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7742 (mm-40) REVERT: K 73 ASP cc_start: 0.8241 (t0) cc_final: 0.7826 (t0) outliers start: 53 outliers final: 41 residues processed: 355 average time/residue: 0.2936 time to fit residues: 158.0120 Evaluate side-chains 354 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 311 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 185 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 0.0030 chunk 57 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN D 189 ASN L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17799 Z= 0.196 Angle : 0.579 9.725 24204 Z= 0.288 Chirality : 0.043 0.262 2797 Planarity : 0.004 0.047 2981 Dihedral : 5.769 58.817 2783 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.76 % Allowed : 18.37 % Favored : 78.86 % 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: -0.01 (0.19), residues: 2103 helix: 1.55 (0.22), residues: 565 sheet: -0.29 (0.21), residues: 611 loop : -0.71 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 252 HIS 0.002 0.001 HIS E 122 PHE 0.016 0.001 PHE E 158 TYR 0.018 0.001 TYR A 226 ARG 0.013 0.000 ARG I 61 *********************** 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 365 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 313 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8329 (mtm110) cc_final: 0.8092 (ptp90) REVERT: A 95 ASP cc_start: 0.7915 (p0) cc_final: 0.7712 (p0) REVERT: A 261 MET cc_start: 0.7377 (tpp) cc_final: 0.7173 (mtp) REVERT: A 319 TRP cc_start: 0.7350 (t60) cc_final: 0.6778 (t-100) REVERT: B 24 ASP cc_start: 0.7878 (t0) cc_final: 0.7448 (p0) REVERT: B 71 LYS cc_start: 0.8324 (tttp) cc_final: 0.8092 (tptm) REVERT: B 98 ASP cc_start: 0.7750 (p0) cc_final: 0.7422 (p0) REVERT: B 246 TRP cc_start: 0.6842 (m100) cc_final: 0.6463 (m-10) REVERT: C 14 GLU cc_start: 0.7761 (tp30) cc_final: 0.7477 (tp30) REVERT: C 41 ASN cc_start: 0.7930 (m110) cc_final: 0.7645 (m110) REVERT: C 54 ASN cc_start: 0.8369 (m110) cc_final: 0.8135 (m-40) REVERT: C 68 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7969 (ttt-90) REVERT: C 162 ASP cc_start: 0.8057 (p0) cc_final: 0.7676 (p0) REVERT: C 212 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: D 112 MET cc_start: 0.8212 (tpp) cc_final: 0.7464 (tpp) REVERT: E 306 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6685 (m-10) REVERT: K 65 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7792 (mm-40) REVERT: K 73 ASP cc_start: 0.8266 (t0) cc_final: 0.7855 (t0) outliers start: 52 outliers final: 46 residues processed: 345 average time/residue: 0.2805 time to fit residues: 146.5509 Evaluate side-chains 351 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 303 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 136 optimal weight: 0.0970 chunk 206 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 332 ASN B 189 ASN L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17799 Z= 0.177 Angle : 0.572 9.529 24204 Z= 0.284 Chirality : 0.043 0.268 2797 Planarity : 0.004 0.048 2981 Dihedral : 5.678 59.041 2783 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.60 % Allowed : 18.48 % Favored : 78.92 % 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: 0.08 (0.19), residues: 2103 helix: 1.63 (0.22), residues: 565 sheet: -0.20 (0.21), residues: 613 loop : -0.69 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 252 HIS 0.003 0.001 HIS E 163 PHE 0.022 0.001 PHE E 346 TYR 0.017 0.001 TYR B 294 ARG 0.012 0.000 ARG I 61 ********************** 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 360 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 311 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8316 (mtm110) cc_final: 0.8098 (ptp90) REVERT: A 95 ASP cc_start: 0.7869 (p0) cc_final: 0.7657 (p0) REVERT: A 261 MET cc_start: 0.7347 (tpp) cc_final: 0.7083 (mtp) REVERT: A 319 TRP cc_start: 0.7332 (t60) cc_final: 0.6754 (t-100) REVERT: B 24 ASP cc_start: 0.7863 (t0) cc_final: 0.7432 (p0) REVERT: B 71 LYS cc_start: 0.8325 (tttp) cc_final: 0.8092 (tptm) REVERT: B 98 ASP cc_start: 0.7707 (p0) cc_final: 0.7399 (p0) REVERT: B 246 TRP cc_start: 0.6913 (m100) cc_final: 0.6470 (m-10) REVERT: C 41 ASN cc_start: 0.7859 (m110) cc_final: 0.7616 (m110) REVERT: C 54 ASN cc_start: 0.8346 (m110) cc_final: 0.8107 (m-40) REVERT: C 68 ARG cc_start: 0.8214 (ttt-90) cc_final: 0.7964 (ttt-90) REVERT: C 212 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: D 112 MET cc_start: 0.8197 (tpp) cc_final: 0.7448 (tpp) REVERT: E 306 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6601 (m-10) REVERT: J 107 TYR cc_start: 0.8389 (m-80) cc_final: 0.8130 (m-80) REVERT: K 65 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7827 (mm-40) REVERT: K 73 ASP cc_start: 0.8289 (t0) cc_final: 0.7852 (t0) outliers start: 49 outliers final: 43 residues processed: 340 average time/residue: 0.2814 time to fit residues: 146.0164 Evaluate side-chains 351 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 306 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 144 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114451 restraints weight = 21834.501| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.37 r_work: 0.3103 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17799 Z= 0.177 Angle : 0.577 10.011 24204 Z= 0.286 Chirality : 0.043 0.270 2797 Planarity : 0.004 0.043 2981 Dihedral : 5.617 59.199 2783 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.66 % Allowed : 18.85 % Favored : 78.49 % 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: 0.16 (0.19), residues: 2103 helix: 1.62 (0.22), residues: 567 sheet: -0.11 (0.21), residues: 625 loop : -0.62 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 252 HIS 0.002 0.001 HIS B 102 PHE 0.016 0.001 PHE E 158 TYR 0.016 0.001 TYR E 241 ARG 0.010 0.000 ARG I 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4310.89 seconds wall clock time: 77 minutes 26.32 seconds (4646.32 seconds total)