Starting phenix.real_space_refine on Wed Mar 4 22:32:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w1y_21518/03_2026/6w1y_21518_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w1y_21518/03_2026/6w1y_21518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w1y_21518/03_2026/6w1y_21518_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w1y_21518/03_2026/6w1y_21518_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w1y_21518/03_2026/6w1y_21518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w1y_21518/03_2026/6w1y_21518.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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 50 5.16 5 C 11070 2.51 5 N 2705 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16845 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3252 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3252 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3252 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3252 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3252 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: 7 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 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: "I" 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: 7 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: "L" 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: 7 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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: "Q" 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: "R" 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: 7 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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: "T" 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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'O7B': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'O7B': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'O7B': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'O7B': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'O7B': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.70, per 1000 atoms: 0.22 Number of scatterers: 16845 At special positions: 0 Unit cell: (102.608, 106.848, 173.84, 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 50 16.00 O 3020 8.00 N 2705 7.00 C 11070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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=5, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG H 1 " - " ASN A 148 " " NAG K 1 " - " ASN B 148 " " NAG N 1 " - " ASN C 148 " " NAG Q 1 " - " ASN D 148 " " NAG T 1 " - " ASN E 148 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 690.9 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3830 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 39.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.680A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.501A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 176' Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.586A pdb=" N ALA A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.528A pdb=" N LEU A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 271 removed outlier: 4.297A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.541A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 4.139A pdb=" N ILE A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 461 removed outlier: 3.592A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 415 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.679A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.502A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 176' Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.586A pdb=" N ALA B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.527A pdb=" N LEU B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 271 removed outlier: 4.297A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 308 removed outlier: 3.541A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 294 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.139A pdb=" N ILE B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 461 removed outlier: 3.592A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 415 " --> pdb=" O HIS B 411 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.679A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.501A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 176' Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.586A pdb=" N ALA C 224 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.527A pdb=" N LEU C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 271 removed outlier: 4.298A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 308 removed outlier: 3.541A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 4.139A pdb=" N ILE C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 461 removed outlier: 3.592A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.679A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.501A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 170 through 176' Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.585A pdb=" N ALA D 224 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.527A pdb=" N LEU D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 271 removed outlier: 4.298A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 258 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 308 removed outlier: 3.541A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 294 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.139A pdb=" N ILE D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 461 removed outlier: 3.592A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 415 " --> pdb=" O HIS D 411 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR D 451 " --> pdb=" O ALA D 447 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.680A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.501A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 170 through 176' Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.585A pdb=" N ALA E 224 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 242 removed outlier: 3.528A pdb=" N LEU E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 271 removed outlier: 4.298A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 258 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 308 removed outlier: 3.541A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU E 294 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER E 297 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 removed outlier: 4.139A pdb=" N ILE E 332 " --> pdb=" O ARG E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 461 removed outlier: 3.592A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS E 415 " --> pdb=" O HIS E 411 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG E 420 " --> pdb=" O ARG E 416 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 423 " --> pdb=" O MET E 419 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 458 " --> pdb=" O THR E 454 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.846A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 116 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP A 68 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.287A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 201 " --> pdb=" O ASN A 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 197 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.847A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 116 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP B 68 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN B 50 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.287A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 201 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 197 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.846A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 116 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP C 68 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.287A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 201 " --> pdb=" O ASN C 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 197 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 87 through 89 removed outlier: 6.846A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 116 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP D 68 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.288A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 201 " --> pdb=" O ASN D 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 197 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 89 removed outlier: 6.847A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR E 116 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP E 68 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.287A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE E 201 " --> pdb=" O ASN E 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 197 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1695 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: 2.09 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5030 1.34 - 1.46: 3798 1.46 - 1.57: 8407 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 17315 Sorted by residual: bond pdb=" C18 O7B C 508 " pdb=" C19 O7B C 508 " ideal model delta sigma weight residual 1.551 1.767 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C18 O7B A 508 " pdb=" C19 O7B A 508 " ideal model delta sigma weight residual 1.551 1.767 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C18 O7B E 508 " pdb=" C19 O7B E 508 " ideal model delta sigma weight residual 1.551 1.766 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C18 O7B D 508 " pdb=" C19 O7B D 508 " ideal model delta sigma weight residual 1.551 1.766 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C18 O7B B 508 " pdb=" C19 O7B B 508 " ideal model delta sigma weight residual 1.551 1.766 -0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 17310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.97: 23513 5.97 - 11.95: 132 11.95 - 17.92: 15 17.92 - 23.90: 5 23.90 - 29.87: 5 Bond angle restraints: 23670 Sorted by residual: angle pdb=" C3 NAG M 1 " pdb=" C4 NAG M 1 " pdb=" O4 NAG M 1 " ideal model delta sigma weight residual 107.29 137.16 -29.87 3.00e+00 1.11e-01 9.91e+01 angle pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " pdb=" O4 NAG G 1 " ideal model delta sigma weight residual 107.29 137.15 -29.86 3.00e+00 1.11e-01 9.91e+01 angle pdb=" C3 NAG S 1 " pdb=" C4 NAG S 1 " pdb=" O4 NAG S 1 " ideal model delta sigma weight residual 107.29 137.12 -29.83 3.00e+00 1.11e-01 9.88e+01 angle pdb=" C3 NAG J 1 " pdb=" C4 NAG J 1 " pdb=" O4 NAG J 1 " ideal model delta sigma weight residual 107.29 137.11 -29.82 3.00e+00 1.11e-01 9.88e+01 angle pdb=" C3 NAG P 1 " pdb=" C4 NAG P 1 " pdb=" O4 NAG P 1 " ideal model delta sigma weight residual 107.29 137.09 -29.80 3.00e+00 1.11e-01 9.86e+01 ... (remaining 23665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 10103 21.32 - 42.63: 527 42.63 - 63.94: 75 63.94 - 85.26: 45 85.26 - 106.57: 25 Dihedral angle restraints: 10775 sinusoidal: 4895 harmonic: 5880 Sorted by residual: dihedral pdb=" CA ALA E 277 " pdb=" C ALA E 277 " pdb=" N ILE E 278 " pdb=" CA ILE E 278 " ideal model delta harmonic sigma weight residual -180.00 -137.02 -42.98 0 5.00e+00 4.00e-02 7.39e+01 dihedral pdb=" CA ALA B 277 " pdb=" C ALA B 277 " pdb=" N ILE B 278 " pdb=" CA ILE B 278 " ideal model delta harmonic sigma weight residual -180.00 -137.02 -42.98 0 5.00e+00 4.00e-02 7.39e+01 dihedral pdb=" CA ALA C 277 " pdb=" C ALA C 277 " pdb=" N ILE C 278 " pdb=" CA ILE C 278 " ideal model delta harmonic sigma weight residual -180.00 -137.05 -42.95 0 5.00e+00 4.00e-02 7.38e+01 ... (remaining 10772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.973: 2800 0.973 - 1.947: 5 1.947 - 2.920: 5 2.920 - 3.893: 0 3.893 - 4.867: 5 Chirality restraints: 2815 Sorted by residual: chirality pdb=" C15 O7B A 508 " pdb=" C16 O7B A 508 " pdb=" C20 O7B A 508 " pdb=" N05 O7B A 508 " both_signs ideal model delta sigma weight residual False 2.55 -2.32 4.87 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" C15 O7B D 508 " pdb=" C16 O7B D 508 " pdb=" C20 O7B D 508 " pdb=" N05 O7B D 508 " both_signs ideal model delta sigma weight residual False 2.55 -2.32 4.86 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" C15 O7B E 508 " pdb=" C16 O7B E 508 " pdb=" C20 O7B E 508 " pdb=" N05 O7B E 508 " both_signs ideal model delta sigma weight residual False 2.55 -2.32 4.86 2.00e-01 2.50e+01 5.91e+02 ... (remaining 2812 not shown) Planarity restraints: 2855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " 0.024 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP A 168 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " 0.024 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP D 168 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " 0.024 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP C 168 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.002 2.00e-02 2.50e+03 ... (remaining 2852 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5539 2.84 - 3.36: 14598 3.36 - 3.87: 26453 3.87 - 4.39: 28652 4.39 - 4.90: 48975 Nonbonded interactions: 124217 Sorted by model distance: nonbonded pdb=" O4 NAG F 1 " pdb=" O3 NAG F 2 " model vdw 2.330 2.432 nonbonded pdb=" O4 NAG O 1 " pdb=" O3 NAG O 2 " model vdw 2.331 2.432 nonbonded pdb=" O4 NAG R 1 " pdb=" O3 NAG R 2 " model vdw 2.331 2.432 nonbonded pdb=" O4 NAG L 1 " pdb=" O3 NAG L 2 " model vdw 2.331 2.432 nonbonded pdb=" O4 NAG I 1 " pdb=" O3 NAG I 2 " model vdw 2.331 2.432 ... (remaining 124212 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'F' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'H' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'I' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'K' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'L' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'N' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'O' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'Q' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) selection = (chain 'R' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )) or resid 2)) selection = (chain 'T' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 o \ r name O6 or name O7 )))) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.920 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 : 0.012 0.216 17345 Z= 0.548 Angle : 1.420 32.027 23740 Z= 0.640 Chirality : 0.248 4.867 2815 Planarity : 0.006 0.052 2850 Dihedral : 14.817 106.575 6930 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.82 % Allowed : 7.42 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.17 (0.14), residues: 1950 helix: -4.27 (0.09), residues: 705 sheet: -2.70 (0.19), residues: 430 loop : -2.81 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 315 TYR 0.030 0.003 TYR A 207 PHE 0.023 0.003 PHE D 199 TRP 0.056 0.003 TRP A 168 HIS 0.005 0.002 HIS D 158 Details of bonding type rmsd covalent geometry : bond 0.01189 (17315) covalent geometry : angle 1.31789 (23670) SS BOND : bond 0.00362 ( 5) SS BOND : angle 1.23325 ( 10) hydrogen bonds : bond 0.29518 ( 580) hydrogen bonds : angle 9.43025 ( 1695) Misc. bond : bond 0.00074 ( 5) link_BETA1-4 : bond 0.04077 ( 15) link_BETA1-4 : angle 12.09654 ( 45) link_NAG-ASN : bond 0.01155 ( 5) link_NAG-ASN : angle 3.50691 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8869 (p0) cc_final: 0.8632 (p0) REVERT: A 405 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8670 (mm-30) REVERT: A 419 MET cc_start: 0.9103 (mmm) cc_final: 0.8656 (mmm) REVERT: A 456 TRP cc_start: 0.6520 (t60) cc_final: 0.5801 (t60) REVERT: B 418 GLU cc_start: 0.8701 (tt0) cc_final: 0.8491 (tm-30) REVERT: B 427 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8249 (tt) REVERT: B 456 TRP cc_start: 0.6567 (t60) cc_final: 0.6042 (t60) REVERT: C 286 TYR cc_start: 0.8042 (m-10) cc_final: 0.7827 (m-10) REVERT: C 405 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8700 (mm-30) REVERT: C 411 HIS cc_start: 0.9032 (t70) cc_final: 0.8587 (t-170) REVERT: C 427 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8184 (tt) REVERT: C 456 TRP cc_start: 0.6763 (t60) cc_final: 0.6100 (t60) REVERT: D 411 HIS cc_start: 0.9184 (t70) cc_final: 0.8864 (t-170) REVERT: D 419 MET cc_start: 0.9185 (mmm) cc_final: 0.8635 (mmm) REVERT: D 421 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8325 (tm-30) REVERT: D 427 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7881 (tt) REVERT: D 456 TRP cc_start: 0.6701 (t60) cc_final: 0.6025 (t60) REVERT: E 45 MET cc_start: 0.9143 (mmm) cc_final: 0.8916 (tpt) REVERT: E 235 MET cc_start: 0.9040 (mmt) cc_final: 0.8767 (mmt) REVERT: E 456 TRP cc_start: 0.6617 (t60) cc_final: 0.5804 (t60) outliers start: 15 outliers final: 0 residues processed: 241 average time/residue: 0.1526 time to fit residues: 52.7580 Evaluate side-chains 160 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 427 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 411 HIS B 82 ASN B 411 HIS C 82 ASN D 82 ASN E 82 ASN E 411 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.069119 restraints weight = 32461.348| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.31 r_work: 0.2707 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17345 Z= 0.148 Angle : 0.816 20.410 23740 Z= 0.369 Chirality : 0.054 0.506 2815 Planarity : 0.004 0.036 2850 Dihedral : 12.269 65.972 3096 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 1.76 % Allowed : 11.87 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.16), residues: 1950 helix: -2.09 (0.15), residues: 705 sheet: -2.43 (0.20), residues: 445 loop : -2.13 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 400 TYR 0.015 0.001 TYR C 126 PHE 0.011 0.001 PHE B 242 TRP 0.030 0.002 TRP C 168 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00292 (17315) covalent geometry : angle 0.74647 (23670) SS BOND : bond 0.00468 ( 5) SS BOND : angle 1.09665 ( 10) hydrogen bonds : bond 0.06259 ( 580) hydrogen bonds : angle 5.30778 ( 1695) Misc. bond : bond 0.00009 ( 5) link_BETA1-4 : bond 0.02575 ( 15) link_BETA1-4 : angle 7.53236 ( 45) link_NAG-ASN : bond 0.00267 ( 5) link_NAG-ASN : angle 1.96355 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.9046 (p0) cc_final: 0.8822 (p0) REVERT: A 326 LEU cc_start: 0.8844 (mt) cc_final: 0.8641 (tt) REVERT: A 421 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8429 (tm-30) REVERT: B 315 ARG cc_start: 0.7836 (ppt170) cc_final: 0.7519 (ppt170) REVERT: B 456 TRP cc_start: 0.5659 (t60) cc_final: 0.5414 (t60) REVERT: B 459 TRP cc_start: 0.6839 (t60) cc_final: 0.6564 (t60) REVERT: C 311 GLN cc_start: 0.5880 (pm20) cc_final: 0.5659 (pm20) REVERT: C 326 LEU cc_start: 0.8798 (mt) cc_final: 0.8468 (tt) REVERT: C 411 HIS cc_start: 0.9096 (t70) cc_final: 0.8794 (t-170) REVERT: C 419 MET cc_start: 0.9129 (tpp) cc_final: 0.8904 (tpp) REVERT: C 456 TRP cc_start: 0.5694 (t60) cc_final: 0.5385 (t60) REVERT: D 421 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8446 (tm-30) REVERT: E 265 PHE cc_start: 0.8396 (t80) cc_final: 0.8117 (t80) REVERT: E 421 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8440 (tm-30) REVERT: E 456 TRP cc_start: 0.5736 (t60) cc_final: 0.5495 (t60) outliers start: 32 outliers final: 9 residues processed: 197 average time/residue: 0.1262 time to fit residues: 38.0015 Evaluate side-chains 158 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 84 optimal weight: 0.4980 chunk 180 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS D 309 HIS D 411 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.066303 restraints weight = 32928.131| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.35 r_work: 0.2641 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17345 Z= 0.208 Angle : 0.766 19.832 23740 Z= 0.351 Chirality : 0.053 0.450 2815 Planarity : 0.004 0.039 2850 Dihedral : 10.289 59.930 3090 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.57 % Allowed : 11.37 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.17), residues: 1950 helix: -0.82 (0.18), residues: 705 sheet: -2.11 (0.21), residues: 440 loop : -1.86 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.014 0.001 TYR E 448 PHE 0.014 0.001 PHE E 412 TRP 0.020 0.002 TRP D 168 HIS 0.006 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00481 (17315) covalent geometry : angle 0.69955 (23670) SS BOND : bond 0.00502 ( 5) SS BOND : angle 1.20021 ( 10) hydrogen bonds : bond 0.05514 ( 580) hydrogen bonds : angle 4.79402 ( 1695) Misc. bond : bond 0.00005 ( 5) link_BETA1-4 : bond 0.02220 ( 15) link_BETA1-4 : angle 7.14096 ( 45) link_NAG-ASN : bond 0.00424 ( 5) link_NAG-ASN : angle 1.77657 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 155 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.9104 (p0) cc_final: 0.8852 (p0) REVERT: A 315 ARG cc_start: 0.7708 (ppt170) cc_final: 0.7466 (ppt170) REVERT: A 405 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8930 (mm-30) REVERT: A 418 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 421 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8505 (tm-30) REVERT: C 78 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8677 (tm-30) REVERT: C 326 LEU cc_start: 0.8828 (mt) cc_final: 0.8497 (tt) REVERT: C 411 HIS cc_start: 0.8977 (t70) cc_final: 0.8721 (t-170) REVERT: C 446 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7915 (mt) REVERT: D 421 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8486 (tm-30) REVERT: E 421 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8465 (tm-30) outliers start: 65 outliers final: 27 residues processed: 211 average time/residue: 0.1176 time to fit residues: 38.9951 Evaluate side-chains 172 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 3 optimal weight: 0.2980 chunk 175 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.0870 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.065515 restraints weight = 32933.023| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.31 r_work: 0.2640 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17345 Z= 0.179 Angle : 0.725 18.617 23740 Z= 0.330 Chirality : 0.051 0.427 2815 Planarity : 0.003 0.034 2850 Dihedral : 9.142 59.977 3090 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.52 % Allowed : 12.25 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 1950 helix: 0.03 (0.19), residues: 705 sheet: -2.08 (0.21), residues: 450 loop : -1.60 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 217 TYR 0.016 0.001 TYR D 262 PHE 0.008 0.001 PHE E 438 TRP 0.028 0.001 TRP C 456 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00404 (17315) covalent geometry : angle 0.66105 (23670) SS BOND : bond 0.00449 ( 5) SS BOND : angle 1.12857 ( 10) hydrogen bonds : bond 0.04811 ( 580) hydrogen bonds : angle 4.49981 ( 1695) Misc. bond : bond 0.00010 ( 5) link_BETA1-4 : bond 0.02229 ( 15) link_BETA1-4 : angle 6.78574 ( 45) link_NAG-ASN : bond 0.00225 ( 5) link_NAG-ASN : angle 1.67913 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 152 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.9135 (p0) cc_final: 0.8893 (p0) REVERT: A 418 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 421 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8523 (tm-30) REVERT: B 459 TRP cc_start: 0.6903 (t60) cc_final: 0.6641 (t60) REVERT: C 49 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9263 (mt) REVERT: C 78 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8664 (tm-30) REVERT: C 326 LEU cc_start: 0.8842 (mt) cc_final: 0.8503 (tt) REVERT: C 411 HIS cc_start: 0.8917 (t70) cc_final: 0.8666 (t-170) REVERT: E 149 CYS cc_start: 0.8092 (m) cc_final: 0.7710 (m) REVERT: E 421 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8478 (tm-30) outliers start: 64 outliers final: 35 residues processed: 211 average time/residue: 0.1144 time to fit residues: 38.1015 Evaluate side-chains 187 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 176 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 136 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.066116 restraints weight = 32660.109| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.30 r_work: 0.2640 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17345 Z= 0.165 Angle : 0.710 18.229 23740 Z= 0.319 Chirality : 0.050 0.417 2815 Planarity : 0.003 0.034 2850 Dihedral : 8.420 59.089 3090 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.46 % Allowed : 13.35 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.19), residues: 1950 helix: 0.77 (0.20), residues: 705 sheet: -1.99 (0.22), residues: 450 loop : -1.52 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 251 TYR 0.013 0.001 TYR D 67 PHE 0.028 0.001 PHE A 233 TRP 0.037 0.002 TRP C 320 HIS 0.004 0.001 HIS A 460 Details of bonding type rmsd covalent geometry : bond 0.00371 (17315) covalent geometry : angle 0.64927 (23670) SS BOND : bond 0.00390 ( 5) SS BOND : angle 0.98535 ( 10) hydrogen bonds : bond 0.04423 ( 580) hydrogen bonds : angle 4.27901 ( 1695) Misc. bond : bond 0.00019 ( 5) link_BETA1-4 : bond 0.02227 ( 15) link_BETA1-4 : angle 6.57590 ( 45) link_NAG-ASN : bond 0.00237 ( 5) link_NAG-ASN : angle 1.62053 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 152 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.9118 (p0) cc_final: 0.8893 (p0) REVERT: A 149 CYS cc_start: 0.8049 (m) cc_final: 0.7630 (m) REVERT: A 418 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 421 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8562 (tm-30) REVERT: C 49 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9300 (mt) REVERT: C 78 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8673 (tm-30) REVERT: C 326 LEU cc_start: 0.8824 (mt) cc_final: 0.8483 (tt) REVERT: C 411 HIS cc_start: 0.8895 (t70) cc_final: 0.8651 (t-170) REVERT: D 404 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8761 (tm-30) REVERT: E 202 ASP cc_start: 0.8610 (t0) cc_final: 0.8375 (t0) REVERT: E 326 LEU cc_start: 0.8712 (mt) cc_final: 0.8341 (tt) REVERT: E 421 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8455 (tm-30) outliers start: 63 outliers final: 41 residues processed: 211 average time/residue: 0.1112 time to fit residues: 37.0967 Evaluate side-chains 183 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 183 optimal weight: 0.0570 chunk 148 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 159 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.067686 restraints weight = 32426.421| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.32 r_work: 0.2686 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17345 Z= 0.116 Angle : 0.674 17.378 23740 Z= 0.299 Chirality : 0.048 0.402 2815 Planarity : 0.003 0.028 2850 Dihedral : 7.800 56.986 3090 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.75 % Allowed : 14.40 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 1950 helix: 1.26 (0.20), residues: 705 sheet: -1.81 (0.22), residues: 445 loop : -1.42 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 251 TYR 0.011 0.001 TYR E 448 PHE 0.022 0.001 PHE A 233 TRP 0.037 0.001 TRP D 320 HIS 0.002 0.000 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00234 (17315) covalent geometry : angle 0.61598 (23670) SS BOND : bond 0.00273 ( 5) SS BOND : angle 0.81799 ( 10) hydrogen bonds : bond 0.03859 ( 580) hydrogen bonds : angle 3.97995 ( 1695) Misc. bond : bond 0.00039 ( 5) link_BETA1-4 : bond 0.02247 ( 15) link_BETA1-4 : angle 6.23303 ( 45) link_NAG-ASN : bond 0.00122 ( 5) link_NAG-ASN : angle 1.52974 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.9100 (p0) cc_final: 0.8845 (p0) REVERT: A 418 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8118 (tm-30) REVERT: A 421 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8516 (tm-30) REVERT: C 149 CYS cc_start: 0.7913 (m) cc_final: 0.7499 (m) REVERT: C 326 LEU cc_start: 0.8823 (mt) cc_final: 0.8499 (tt) REVERT: C 411 HIS cc_start: 0.8805 (t70) cc_final: 0.8584 (t-170) REVERT: D 404 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8812 (tm-30) REVERT: D 419 MET cc_start: 0.9184 (tpp) cc_final: 0.8965 (mmm) REVERT: E 202 ASP cc_start: 0.8597 (t0) cc_final: 0.8391 (t0) REVERT: E 326 LEU cc_start: 0.8707 (mt) cc_final: 0.8344 (tt) REVERT: E 421 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8471 (tm-30) outliers start: 50 outliers final: 34 residues processed: 195 average time/residue: 0.1165 time to fit residues: 35.4614 Evaluate side-chains 169 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 411 HIS E 411 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.066685 restraints weight = 32500.617| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.30 r_work: 0.2687 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17345 Z= 0.155 Angle : 0.690 17.782 23740 Z= 0.309 Chirality : 0.049 0.401 2815 Planarity : 0.003 0.031 2850 Dihedral : 7.684 59.045 3090 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.30 % Allowed : 14.01 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 1950 helix: 1.48 (0.21), residues: 705 sheet: -1.82 (0.22), residues: 450 loop : -1.29 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 217 TYR 0.012 0.001 TYR A 262 PHE 0.023 0.001 PHE A 233 TRP 0.032 0.002 TRP A 320 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00350 (17315) covalent geometry : angle 0.63213 (23670) SS BOND : bond 0.00359 ( 5) SS BOND : angle 0.83206 ( 10) hydrogen bonds : bond 0.03984 ( 580) hydrogen bonds : angle 4.00696 ( 1695) Misc. bond : bond 0.00026 ( 5) link_BETA1-4 : bond 0.02252 ( 15) link_BETA1-4 : angle 6.30544 ( 45) link_NAG-ASN : bond 0.00242 ( 5) link_NAG-ASN : angle 1.50227 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.9111 (p0) cc_final: 0.8866 (p0) REVERT: A 418 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 421 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8602 (tm-30) REVERT: C 326 LEU cc_start: 0.8836 (mt) cc_final: 0.8470 (tt) REVERT: C 411 HIS cc_start: 0.8835 (t70) cc_final: 0.8611 (t-170) REVERT: D 202 ASP cc_start: 0.8605 (t0) cc_final: 0.8402 (t0) REVERT: D 404 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: E 326 LEU cc_start: 0.8691 (mt) cc_final: 0.8322 (tt) REVERT: E 421 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8530 (tm-30) outliers start: 60 outliers final: 48 residues processed: 198 average time/residue: 0.1201 time to fit residues: 36.4008 Evaluate side-chains 183 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 158 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.100230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.067168 restraints weight = 32484.131| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.29 r_work: 0.2682 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17345 Z= 0.121 Angle : 0.680 17.431 23740 Z= 0.303 Chirality : 0.048 0.397 2815 Planarity : 0.003 0.045 2850 Dihedral : 7.386 59.864 3090 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.86 % Allowed : 14.84 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1950 helix: 1.66 (0.21), residues: 710 sheet: -1.67 (0.22), residues: 445 loop : -1.23 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 120 TYR 0.013 0.001 TYR C 262 PHE 0.020 0.001 PHE A 233 TRP 0.042 0.002 TRP A 320 HIS 0.002 0.001 HIS C 119 Details of bonding type rmsd covalent geometry : bond 0.00257 (17315) covalent geometry : angle 0.62400 (23670) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.77060 ( 10) hydrogen bonds : bond 0.03701 ( 580) hydrogen bonds : angle 3.87961 ( 1695) Misc. bond : bond 0.00037 ( 5) link_BETA1-4 : bond 0.02278 ( 15) link_BETA1-4 : angle 6.18235 ( 45) link_NAG-ASN : bond 0.00023 ( 5) link_NAG-ASN : angle 1.45566 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8590 (t0) cc_final: 0.8243 (t0) REVERT: A 111 ASN cc_start: 0.9110 (p0) cc_final: 0.8856 (p0) REVERT: A 418 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 421 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8597 (tm-30) REVERT: C 149 CYS cc_start: 0.7929 (m) cc_final: 0.7507 (m) REVERT: C 326 LEU cc_start: 0.8843 (mt) cc_final: 0.8486 (tt) REVERT: C 411 HIS cc_start: 0.8759 (t70) cc_final: 0.8543 (t-170) REVERT: D 404 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8898 (tm-30) REVERT: D 419 MET cc_start: 0.9189 (tpp) cc_final: 0.8971 (mmm) REVERT: E 235 MET cc_start: 0.8897 (mmm) cc_final: 0.8571 (mmp) REVERT: E 326 LEU cc_start: 0.8701 (mt) cc_final: 0.8344 (tt) REVERT: E 421 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8536 (tm-30) outliers start: 52 outliers final: 44 residues processed: 193 average time/residue: 0.1140 time to fit residues: 34.6608 Evaluate side-chains 182 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 144 optimal weight: 0.0020 chunk 124 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.067830 restraints weight = 32267.685| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.28 r_work: 0.2702 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17345 Z= 0.116 Angle : 0.674 17.243 23740 Z= 0.299 Chirality : 0.048 0.391 2815 Planarity : 0.003 0.029 2850 Dihedral : 7.091 59.995 3090 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.75 % Allowed : 15.11 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1950 helix: 1.60 (0.20), residues: 740 sheet: -1.61 (0.22), residues: 445 loop : -1.15 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 120 TYR 0.011 0.001 TYR A 448 PHE 0.011 0.001 PHE E 233 TRP 0.035 0.001 TRP A 320 HIS 0.001 0.000 HIS D 460 Details of bonding type rmsd covalent geometry : bond 0.00242 (17315) covalent geometry : angle 0.61913 (23670) SS BOND : bond 0.00258 ( 5) SS BOND : angle 0.70317 ( 10) hydrogen bonds : bond 0.03542 ( 580) hydrogen bonds : angle 3.78168 ( 1695) Misc. bond : bond 0.00034 ( 5) link_BETA1-4 : bond 0.02291 ( 15) link_BETA1-4 : angle 6.09277 ( 45) link_NAG-ASN : bond 0.00016 ( 5) link_NAG-ASN : angle 1.36855 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8576 (t0) cc_final: 0.8255 (t0) REVERT: A 111 ASN cc_start: 0.9111 (p0) cc_final: 0.8843 (p0) REVERT: A 235 MET cc_start: 0.8766 (mmm) cc_final: 0.8511 (mmp) REVERT: A 418 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 419 MET cc_start: 0.9238 (tpp) cc_final: 0.8968 (mmm) REVERT: A 421 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8590 (tm-30) REVERT: C 326 LEU cc_start: 0.8842 (mt) cc_final: 0.8485 (tt) REVERT: C 411 HIS cc_start: 0.8733 (t70) cc_final: 0.8531 (t-170) REVERT: D 105 ASP cc_start: 0.8712 (t0) cc_final: 0.8445 (t0) REVERT: E 326 LEU cc_start: 0.8690 (mt) cc_final: 0.8334 (tt) REVERT: E 421 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8536 (tm-30) outliers start: 50 outliers final: 43 residues processed: 188 average time/residue: 0.1171 time to fit residues: 34.0673 Evaluate side-chains 176 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 103 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.067621 restraints weight = 32340.968| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.25 r_work: 0.2683 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17345 Z= 0.139 Angle : 0.687 17.452 23740 Z= 0.308 Chirality : 0.048 0.394 2815 Planarity : 0.003 0.028 2850 Dihedral : 7.049 59.480 3090 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.91 % Allowed : 14.89 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1950 helix: 1.69 (0.20), residues: 740 sheet: -1.57 (0.22), residues: 445 loop : -1.12 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 400 TYR 0.012 0.001 TYR A 448 PHE 0.007 0.001 PHE B 265 TRP 0.050 0.002 TRP B 320 HIS 0.002 0.000 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00311 (17315) covalent geometry : angle 0.63259 (23670) SS BOND : bond 0.00284 ( 5) SS BOND : angle 0.79544 ( 10) hydrogen bonds : bond 0.03606 ( 580) hydrogen bonds : angle 3.79776 ( 1695) Misc. bond : bond 0.00021 ( 5) link_BETA1-4 : bond 0.02240 ( 15) link_BETA1-4 : angle 6.14318 ( 45) link_NAG-ASN : bond 0.00145 ( 5) link_NAG-ASN : angle 1.38209 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8579 (t0) cc_final: 0.8243 (t0) REVERT: A 111 ASN cc_start: 0.9120 (p0) cc_final: 0.8857 (p0) REVERT: A 235 MET cc_start: 0.8772 (mmm) cc_final: 0.8536 (mmp) REVERT: A 418 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 419 MET cc_start: 0.9248 (tpp) cc_final: 0.8973 (mmm) REVERT: A 421 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8603 (tm-30) REVERT: C 149 CYS cc_start: 0.7906 (m) cc_final: 0.7554 (m) REVERT: C 326 LEU cc_start: 0.8862 (mt) cc_final: 0.8506 (tt) REVERT: D 105 ASP cc_start: 0.8723 (t0) cc_final: 0.8443 (t0) REVERT: D 404 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8509 (pp30) REVERT: E 326 LEU cc_start: 0.8688 (mt) cc_final: 0.8321 (tt) REVERT: E 421 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8535 (tm-30) outliers start: 53 outliers final: 49 residues processed: 189 average time/residue: 0.1100 time to fit residues: 32.7916 Evaluate side-chains 188 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 160 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 192 optimal weight: 0.0170 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.0098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 411 HIS ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.067966 restraints weight = 32418.032| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.25 r_work: 0.2694 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17345 Z= 0.123 Angle : 0.678 17.319 23740 Z= 0.303 Chirality : 0.048 0.392 2815 Planarity : 0.003 0.039 2850 Dihedral : 6.919 59.896 3090 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.75 % Allowed : 15.05 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1950 helix: 1.80 (0.20), residues: 740 sheet: -1.54 (0.22), residues: 445 loop : -1.08 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 120 TYR 0.011 0.001 TYR A 448 PHE 0.007 0.001 PHE B 265 TRP 0.051 0.002 TRP B 320 HIS 0.002 0.000 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00264 (17315) covalent geometry : angle 0.62340 (23670) SS BOND : bond 0.00263 ( 5) SS BOND : angle 0.80455 ( 10) hydrogen bonds : bond 0.03470 ( 580) hydrogen bonds : angle 3.72898 ( 1695) Misc. bond : bond 0.00022 ( 5) link_BETA1-4 : bond 0.02277 ( 15) link_BETA1-4 : angle 6.09666 ( 45) link_NAG-ASN : bond 0.00041 ( 5) link_NAG-ASN : angle 1.34980 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3318.75 seconds wall clock time: 57 minutes 37.36 seconds (3457.36 seconds total)