Starting phenix.real_space_refine on Sat Jun 14 12:34:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hio_0226/06_2025/6hio_0226_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hio_0226/06_2025/6hio_0226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hio_0226/06_2025/6hio_0226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hio_0226/06_2025/6hio_0226.map" model { file = "/net/cci-nas-00/data/ceres_data/6hio_0226/06_2025/6hio_0226_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hio_0226/06_2025/6hio_0226_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 45 5.16 5 C 10565 2.51 5 N 2585 2.21 5 O 2890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16085 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 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: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: "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: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "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: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.67, per 1000 atoms: 0.60 Number of scatterers: 16085 At special positions: 0 Unit cell: (96.627, 94.549, 163.123, 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 45 16.00 O 2890 8.00 N 2585 7.00 C 10565 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 E 135 " - pdb=" SG CYS E 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG B 501 " - " ASN B 82 " " NAG C 501 " - " ASN C 82 " " NAG D 902 " - " ASN D 82 " " NAG E 902 " - " ASN E 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN E 164 " " NAG I 1 " - " ASN E 148 " " NAG J 1 " - " ASN B 164 " " NAG K 1 " - " ASN B 148 " " NAG L 1 " - " ASN C 164 " " NAG M 1 " - " ASN C 148 " " NAG N 1 " - " ASN D 164 " " NAG O 1 " - " ASN D 148 " Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 2.1 seconds 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 45.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 Processing helix chain 'A' and resid 53 through 56 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: 3.519A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 240 removed outlier: 5.048A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 4.102A pdb=" N PHE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 248 removed outlier: 3.583A pdb=" N SER A 248 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 249 through 273 removed outlier: 3.867A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.968A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 402 through 414 Processing helix chain 'A' and resid 415 through 460 removed outlier: 3.571A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 53 through 56 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: 3.519A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 240 removed outlier: 5.049A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix removed outlier: 4.102A pdb=" N PHE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 248 removed outlier: 3.583A pdb=" N SER E 248 " --> pdb=" O PRO E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 245 through 248' Processing helix chain 'E' and resid 249 through 273 removed outlier: 3.868A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.968A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA E 292 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 332 Processing helix chain 'E' and resid 402 through 414 Processing helix chain 'E' and resid 415 through 460 removed outlier: 3.571A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 452 " --> pdb=" O TYR E 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 53 through 56 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: 3.518A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 240 removed outlier: 5.049A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix removed outlier: 4.101A pdb=" N PHE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.582A pdb=" N SER B 248 " --> pdb=" O PRO B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 249 through 273 removed outlier: 3.867A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.968A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 415 through 460 removed outlier: 3.571A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 53 through 56 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: 3.519A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 240 removed outlier: 5.050A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 4.101A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 248 removed outlier: 3.583A pdb=" N SER C 248 " --> pdb=" O PRO C 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 248' Processing helix chain 'C' and resid 249 through 273 removed outlier: 3.867A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.969A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 332 Processing helix chain 'C' and resid 402 through 414 Processing helix chain 'C' and resid 415 through 460 removed outlier: 3.571A pdb=" N VAL C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 53 through 56 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: 3.519A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 240 removed outlier: 5.049A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 4.101A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 248 removed outlier: 3.583A pdb=" N SER D 248 " --> pdb=" O PRO D 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 245 through 248' Processing helix chain 'D' and resid 249 through 273 removed outlier: 3.867A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.968A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA D 292 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 Processing helix chain 'D' and resid 402 through 414 Processing helix chain 'D' and resid 415 through 460 removed outlier: 3.572A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR D 451 " --> pdb=" O ALA D 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105 removed outlier: 7.257A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 65 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 195 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 103 through 105 removed outlier: 7.257A pdb=" N VAL E 132 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL E 57 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN E 50 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG E 65 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 89 Processing sheet with id=AA7, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 105 removed outlier: 7.256A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 65 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP B 42 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 89 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.941A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.941A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 195 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 103 through 105 removed outlier: 7.257A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 65 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 42 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 85 through 89 Processing sheet with id=AB6, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 216 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 195 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 105 removed outlier: 7.256A pdb=" N VAL D 132 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG D 65 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP D 42 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 85 through 89 Processing sheet with id=AC1, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.941A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.941A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN D 195 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 2175 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 4.40 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: 4898 1.34 - 1.46: 4092 1.46 - 1.58: 7455 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 16515 Sorted by residual: bond pdb=" CG SRO D 901 " pdb=" CD2 SRO D 901 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CG SRO E 901 " pdb=" CD2 SRO E 901 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CG SRO C 502 " pdb=" CD2 SRO C 502 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CG SRO B 502 " pdb=" CD2 SRO B 502 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CG SRO A 502 " pdb=" CD2 SRO A 502 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.91e+01 ... (remaining 16510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 22367 4.32 - 8.64: 178 8.64 - 12.96: 15 12.96 - 17.28: 5 17.28 - 21.60: 5 Bond angle restraints: 22570 Sorted by residual: angle pdb=" CA LEU B 131 " pdb=" CB LEU B 131 " pdb=" CG LEU B 131 " ideal model delta sigma weight residual 116.30 137.90 -21.60 3.50e+00 8.16e-02 3.81e+01 angle pdb=" CA LEU C 131 " pdb=" CB LEU C 131 " pdb=" CG LEU C 131 " ideal model delta sigma weight residual 116.30 137.90 -21.60 3.50e+00 8.16e-02 3.81e+01 angle pdb=" CA LEU D 131 " pdb=" CB LEU D 131 " pdb=" CG LEU D 131 " ideal model delta sigma weight residual 116.30 137.90 -21.60 3.50e+00 8.16e-02 3.81e+01 angle pdb=" CA LEU A 131 " pdb=" CB LEU A 131 " pdb=" CG LEU A 131 " ideal model delta sigma weight residual 116.30 137.87 -21.57 3.50e+00 8.16e-02 3.80e+01 angle pdb=" CA LEU E 131 " pdb=" CB LEU E 131 " pdb=" CG LEU E 131 " ideal model delta sigma weight residual 116.30 137.81 -21.51 3.50e+00 8.16e-02 3.78e+01 ... (remaining 22565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 9291 15.87 - 31.74: 539 31.74 - 47.60: 160 47.60 - 63.47: 30 63.47 - 79.34: 25 Dihedral angle restraints: 10045 sinusoidal: 4305 harmonic: 5740 Sorted by residual: dihedral pdb=" CA GLN D 66 " pdb=" C GLN D 66 " pdb=" N TYR D 67 " pdb=" CA TYR D 67 " ideal model delta harmonic sigma weight residual 180.00 146.64 33.36 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA GLN A 66 " pdb=" C GLN A 66 " pdb=" N TYR A 67 " pdb=" CA TYR A 67 " ideal model delta harmonic sigma weight residual 180.00 146.65 33.35 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA GLN C 66 " pdb=" C GLN C 66 " pdb=" N TYR C 67 " pdb=" CA TYR C 67 " ideal model delta harmonic sigma weight residual 180.00 146.65 33.35 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 10042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1755 0.053 - 0.106: 714 0.106 - 0.160: 151 0.160 - 0.213: 45 0.213 - 0.266: 15 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CG LEU A 131 " pdb=" CB LEU A 131 " pdb=" CD1 LEU A 131 " pdb=" CD2 LEU A 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU E 131 " pdb=" CB LEU E 131 " pdb=" CD1 LEU E 131 " pdb=" CD2 LEU E 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU C 131 " pdb=" CB LEU C 131 " pdb=" CD1 LEU C 131 " pdb=" CD2 LEU C 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2677 not shown) Planarity restraints: 2765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " -0.016 2.00e-02 2.50e+03 1.81e-02 8.23e+00 pdb=" CG TRP C 168 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " -0.016 2.00e-02 2.50e+03 1.80e-02 8.12e+00 pdb=" CG TRP D 168 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " -0.016 2.00e-02 2.50e+03 1.80e-02 8.10e+00 pdb=" CG TRP B 168 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " 0.002 2.00e-02 2.50e+03 ... (remaining 2762 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1414 2.73 - 3.27: 16077 3.27 - 3.81: 27559 3.81 - 4.36: 31212 4.36 - 4.90: 51884 Nonbonded interactions: 128146 Sorted by model distance: nonbonded pdb=" OD2 ASP C 238 " pdb=" CD1 LEU C 294 " model vdw 2.185 3.460 nonbonded pdb=" OD2 ASP A 238 " pdb=" CD1 LEU A 294 " model vdw 2.185 3.460 nonbonded pdb=" OD2 ASP B 238 " pdb=" CD1 LEU B 294 " model vdw 2.186 3.460 nonbonded pdb=" OD2 ASP E 238 " pdb=" CD1 LEU E 294 " model vdw 2.186 3.460 nonbonded pdb=" OD2 ASP D 238 " pdb=" CD1 LEU D 294 " model vdw 2.186 3.460 ... (remaining 128141 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 460) selection = (chain 'B' and resid 9 through 460) selection = (chain 'C' and resid 9 through 460) selection = (chain 'D' and resid 9 through 460) selection = (chain 'E' and resid 9 through 460) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.430 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.010 0.088 16545 Z= 0.450 Angle : 1.180 21.599 22655 Z= 0.575 Chirality : 0.062 0.266 2680 Planarity : 0.006 0.058 2750 Dihedral : 12.199 79.339 6290 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.29 % Allowed : 10.14 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.16), residues: 1905 helix: -2.64 (0.14), residues: 640 sheet: -2.24 (0.25), residues: 340 loop : -2.49 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP C 168 HIS 0.009 0.003 HIS B 309 PHE 0.025 0.004 PHE E 153 TYR 0.030 0.003 TYR A 116 ARG 0.005 0.001 ARG D 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00984 ( 15) link_NAG-ASN : angle 2.97610 ( 45) link_BETA1-4 : bond 0.00774 ( 10) link_BETA1-4 : angle 1.94432 ( 30) hydrogen bonds : bond 0.30948 ( 725) hydrogen bonds : angle 9.98914 ( 2175) SS BOND : bond 0.00276 ( 5) SS BOND : angle 1.31151 ( 10) covalent geometry : bond 0.00958 (16515) covalent geometry : angle 1.17224 (22570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7853 (p0) cc_final: 0.7643 (p0) REVERT: A 254 PHE cc_start: 0.9440 (t80) cc_final: 0.9229 (t80) REVERT: A 441 TYR cc_start: 0.8368 (t80) cc_final: 0.8040 (t80) REVERT: E 210 MET cc_start: 0.7966 (tmm) cc_final: 0.7764 (tmm) REVERT: E 254 PHE cc_start: 0.9462 (t80) cc_final: 0.9140 (t80) REVERT: E 259 LEU cc_start: 0.9583 (mm) cc_final: 0.9340 (mm) REVERT: E 441 TYR cc_start: 0.8453 (t80) cc_final: 0.8111 (t80) REVERT: B 254 PHE cc_start: 0.9518 (t80) cc_final: 0.9279 (t80) REVERT: B 259 LEU cc_start: 0.9560 (mm) cc_final: 0.9354 (mm) REVERT: B 441 TYR cc_start: 0.8453 (t80) cc_final: 0.8076 (t80) REVERT: C 254 PHE cc_start: 0.9519 (t80) cc_final: 0.9163 (t80) REVERT: C 259 LEU cc_start: 0.9591 (mm) cc_final: 0.9312 (mm) REVERT: D 52 ASP cc_start: 0.7942 (p0) cc_final: 0.7715 (p0) REVERT: D 254 PHE cc_start: 0.9479 (t80) cc_final: 0.9252 (t80) REVERT: D 259 LEU cc_start: 0.9611 (mm) cc_final: 0.9339 (mm) outliers start: 5 outliers final: 5 residues processed: 154 average time/residue: 0.2779 time to fit residues: 64.6638 Evaluate side-chains 103 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 7.9990 chunk 144 optimal weight: 0.3980 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0270 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 119 HIS A 124 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN E 101 ASN E 119 HIS E 124 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN B 119 HIS B 124 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 158 HIS B 311 GLN C 119 HIS C 124 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 158 HIS D 119 HIS ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.053255 restraints weight = 68029.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.054832 restraints weight = 35451.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.055840 restraints weight = 22308.691| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16545 Z= 0.158 Angle : 0.736 7.439 22655 Z= 0.372 Chirality : 0.047 0.233 2680 Planarity : 0.005 0.039 2750 Dihedral : 9.910 84.116 2645 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.17), residues: 1905 helix: -1.38 (0.16), residues: 760 sheet: -2.43 (0.23), residues: 400 loop : -2.08 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 168 HIS 0.002 0.001 HIS B 309 PHE 0.014 0.002 PHE D 212 TYR 0.022 0.002 TYR B 67 ARG 0.005 0.001 ARG A 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 15) link_NAG-ASN : angle 1.87138 ( 45) link_BETA1-4 : bond 0.00280 ( 10) link_BETA1-4 : angle 1.14619 ( 30) hydrogen bonds : bond 0.06569 ( 725) hydrogen bonds : angle 6.48441 ( 2175) SS BOND : bond 0.00313 ( 5) SS BOND : angle 2.83211 ( 10) covalent geometry : bond 0.00326 (16515) covalent geometry : angle 0.72890 (22570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 1.882 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: A 52 ASP cc_start: 0.8108 (p0) cc_final: 0.7859 (p0) REVERT: A 205 ASN cc_start: 0.8536 (m-40) cc_final: 0.7904 (p0) REVERT: A 210 MET cc_start: 0.8092 (tmm) cc_final: 0.7752 (tmm) REVERT: A 235 MET cc_start: 0.8853 (mmt) cc_final: 0.8319 (mmt) REVERT: A 254 PHE cc_start: 0.9487 (t80) cc_final: 0.9120 (t80) REVERT: A 258 LEU cc_start: 0.9691 (mm) cc_final: 0.9485 (mm) REVERT: A 441 TYR cc_start: 0.8157 (t80) cc_final: 0.7849 (t80) REVERT: E 254 PHE cc_start: 0.9597 (t80) cc_final: 0.9381 (t80) REVERT: E 259 LEU cc_start: 0.9460 (mm) cc_final: 0.9254 (mm) REVERT: E 419 MET cc_start: 0.9361 (ptp) cc_final: 0.9068 (ptm) REVERT: B 205 ASN cc_start: 0.8535 (m-40) cc_final: 0.8213 (p0) REVERT: B 254 PHE cc_start: 0.9570 (t80) cc_final: 0.9119 (t80) REVERT: B 258 LEU cc_start: 0.9735 (mm) cc_final: 0.9398 (mm) REVERT: B 419 MET cc_start: 0.9381 (ptp) cc_final: 0.9080 (ptm) REVERT: B 436 LEU cc_start: 0.9232 (mm) cc_final: 0.9023 (pp) REVERT: B 441 TYR cc_start: 0.7872 (t80) cc_final: 0.7669 (t80) REVERT: C 254 PHE cc_start: 0.9599 (t80) cc_final: 0.9317 (t80) REVERT: C 259 LEU cc_start: 0.9521 (mm) cc_final: 0.9119 (mm) REVERT: C 419 MET cc_start: 0.9188 (ptp) cc_final: 0.8744 (ptm) REVERT: D 210 MET cc_start: 0.8188 (tmm) cc_final: 0.7807 (tmm) REVERT: D 254 PHE cc_start: 0.9588 (t80) cc_final: 0.9152 (t80) REVERT: D 258 LEU cc_start: 0.9767 (mm) cc_final: 0.9550 (mm) REVERT: D 419 MET cc_start: 0.9389 (ptp) cc_final: 0.9026 (ptm) outliers start: 2 outliers final: 1 residues processed: 149 average time/residue: 0.2686 time to fit residues: 64.7926 Evaluate side-chains 107 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 55 optimal weight: 0.1980 chunk 66 optimal weight: 6.9990 chunk 182 optimal weight: 0.0040 chunk 135 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 153 optimal weight: 0.0070 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.8414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS E 158 HIS C 101 ASN D 124 GLN D 158 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.069538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.052988 restraints weight = 68545.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.054472 restraints weight = 36798.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.055421 restraints weight = 23706.160| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16545 Z= 0.162 Angle : 0.642 6.658 22655 Z= 0.324 Chirality : 0.044 0.179 2680 Planarity : 0.004 0.032 2750 Dihedral : 8.423 76.192 2645 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.18), residues: 1905 helix: -0.49 (0.17), residues: 770 sheet: -2.35 (0.23), residues: 385 loop : -1.83 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 168 HIS 0.002 0.001 HIS D 158 PHE 0.023 0.002 PHE E 265 TYR 0.023 0.002 TYR A 67 ARG 0.005 0.000 ARG B 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 15) link_NAG-ASN : angle 1.85474 ( 45) link_BETA1-4 : bond 0.00246 ( 10) link_BETA1-4 : angle 1.30810 ( 30) hydrogen bonds : bond 0.04837 ( 725) hydrogen bonds : angle 5.55839 ( 2175) SS BOND : bond 0.01199 ( 5) SS BOND : angle 1.37037 ( 10) covalent geometry : bond 0.00345 (16515) covalent geometry : angle 0.63538 (22570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8132 (p0) cc_final: 0.7867 (p0) REVERT: A 205 ASN cc_start: 0.8577 (m-40) cc_final: 0.7971 (p0) REVERT: A 235 MET cc_start: 0.8715 (mmt) cc_final: 0.8507 (mmt) REVERT: A 238 ASP cc_start: 0.8080 (t70) cc_final: 0.7879 (t0) REVERT: A 441 TYR cc_start: 0.8069 (t80) cc_final: 0.7768 (t80) REVERT: E 238 ASP cc_start: 0.8019 (t70) cc_final: 0.7791 (t0) REVERT: E 419 MET cc_start: 0.9448 (ptp) cc_final: 0.9132 (ptm) REVERT: E 441 TYR cc_start: 0.8364 (t80) cc_final: 0.7946 (t80) REVERT: B 254 PHE cc_start: 0.9560 (t80) cc_final: 0.9183 (t80) REVERT: B 258 LEU cc_start: 0.9689 (mm) cc_final: 0.9447 (mm) REVERT: B 419 MET cc_start: 0.9437 (ptp) cc_final: 0.9098 (ptm) REVERT: B 441 TYR cc_start: 0.7865 (t80) cc_final: 0.7616 (t80) REVERT: C 210 MET cc_start: 0.9019 (tpp) cc_final: 0.8683 (tpp) REVERT: C 419 MET cc_start: 0.9333 (ptp) cc_final: 0.8912 (ptm) REVERT: C 436 LEU cc_start: 0.9293 (mm) cc_final: 0.9082 (pp) REVERT: D 52 ASP cc_start: 0.8325 (p0) cc_final: 0.8087 (p0) REVERT: D 254 PHE cc_start: 0.9514 (t80) cc_final: 0.9168 (t80) REVERT: D 258 LEU cc_start: 0.9695 (mm) cc_final: 0.9371 (mm) REVERT: D 419 MET cc_start: 0.9534 (ptp) cc_final: 0.9192 (ptm) REVERT: D 436 LEU cc_start: 0.9192 (mm) cc_final: 0.8956 (pp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.3555 time to fit residues: 66.2274 Evaluate side-chains 94 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 179 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.068039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.051554 restraints weight = 69025.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.053006 restraints weight = 37464.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.053945 restraints weight = 24228.838| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16545 Z= 0.222 Angle : 0.686 8.557 22655 Z= 0.342 Chirality : 0.045 0.216 2680 Planarity : 0.004 0.036 2750 Dihedral : 7.658 72.429 2645 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1905 helix: 0.12 (0.18), residues: 775 sheet: -2.56 (0.22), residues: 395 loop : -1.73 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 156 HIS 0.003 0.001 HIS E 18 PHE 0.017 0.002 PHE A 254 TYR 0.023 0.002 TYR A 67 ARG 0.002 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 15) link_NAG-ASN : angle 1.98706 ( 45) link_BETA1-4 : bond 0.00235 ( 10) link_BETA1-4 : angle 1.31477 ( 30) hydrogen bonds : bond 0.04308 ( 725) hydrogen bonds : angle 5.31542 ( 2175) SS BOND : bond 0.00239 ( 5) SS BOND : angle 1.41513 ( 10) covalent geometry : bond 0.00478 (16515) covalent geometry : angle 0.67936 (22570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8124 (p0) cc_final: 0.7895 (p0) REVERT: A 205 ASN cc_start: 0.8684 (m-40) cc_final: 0.8043 (p0) REVERT: A 403 LEU cc_start: 0.9492 (tp) cc_final: 0.9272 (pt) REVERT: E 235 MET cc_start: 0.8514 (mmt) cc_final: 0.8245 (mpp) REVERT: E 238 ASP cc_start: 0.8216 (t70) cc_final: 0.7989 (t0) REVERT: E 419 MET cc_start: 0.9470 (ptp) cc_final: 0.9129 (ptm) REVERT: E 441 TYR cc_start: 0.8397 (t80) cc_final: 0.8040 (t80) REVERT: B 254 PHE cc_start: 0.9548 (t80) cc_final: 0.9271 (t80) REVERT: B 258 LEU cc_start: 0.9686 (mm) cc_final: 0.9420 (mm) REVERT: B 419 MET cc_start: 0.9446 (ptp) cc_final: 0.9088 (ptm) REVERT: C 210 MET cc_start: 0.8924 (tpp) cc_final: 0.8627 (tpp) REVERT: C 419 MET cc_start: 0.9429 (ptp) cc_final: 0.9080 (ptm) REVERT: C 436 LEU cc_start: 0.9313 (mm) cc_final: 0.9111 (pp) REVERT: D 235 MET cc_start: 0.8795 (mmt) cc_final: 0.8566 (mmt) REVERT: D 254 PHE cc_start: 0.9495 (t80) cc_final: 0.9174 (t80) REVERT: D 258 LEU cc_start: 0.9684 (mm) cc_final: 0.9398 (mm) REVERT: D 300 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8752 (tm-30) REVERT: D 419 MET cc_start: 0.9538 (ptp) cc_final: 0.9220 (ptm) REVERT: D 436 LEU cc_start: 0.9234 (mm) cc_final: 0.9006 (pp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2307 time to fit residues: 43.4474 Evaluate side-chains 96 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 78 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 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 = 0.3265 r_free = 0.3265 target = 0.069399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.052831 restraints weight = 68924.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.054309 restraints weight = 37205.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055282 restraints weight = 23985.540| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16545 Z= 0.129 Angle : 0.615 6.410 22655 Z= 0.306 Chirality : 0.044 0.169 2680 Planarity : 0.004 0.030 2750 Dihedral : 7.005 70.784 2645 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.19), residues: 1905 helix: 0.49 (0.18), residues: 775 sheet: -2.50 (0.22), residues: 400 loop : -1.54 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 168 HIS 0.001 0.000 HIS E 18 PHE 0.010 0.001 PHE B 254 TYR 0.022 0.002 TYR E 67 ARG 0.002 0.000 ARG C 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 15) link_NAG-ASN : angle 1.71744 ( 45) link_BETA1-4 : bond 0.00222 ( 10) link_BETA1-4 : angle 0.99093 ( 30) hydrogen bonds : bond 0.03919 ( 725) hydrogen bonds : angle 5.00765 ( 2175) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.92944 ( 10) covalent geometry : bond 0.00278 (16515) covalent geometry : angle 0.60964 (22570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8087 (p0) cc_final: 0.7830 (p0) REVERT: A 205 ASN cc_start: 0.8629 (m-40) cc_final: 0.8126 (p0) REVERT: A 403 LEU cc_start: 0.9500 (tp) cc_final: 0.9287 (pt) REVERT: A 419 MET cc_start: 0.9484 (ptp) cc_final: 0.9199 (ptp) REVERT: E 210 MET cc_start: 0.9183 (tpp) cc_final: 0.8958 (mmm) REVERT: E 235 MET cc_start: 0.8503 (mmt) cc_final: 0.8223 (mpp) REVERT: E 419 MET cc_start: 0.9465 (ptp) cc_final: 0.9114 (ptm) REVERT: E 441 TYR cc_start: 0.8346 (t80) cc_final: 0.7970 (t80) REVERT: B 235 MET cc_start: 0.8840 (mpp) cc_final: 0.8452 (mpp) REVERT: B 254 PHE cc_start: 0.9488 (t80) cc_final: 0.9279 (t80) REVERT: B 258 LEU cc_start: 0.9571 (mm) cc_final: 0.9347 (mm) REVERT: B 419 MET cc_start: 0.9423 (ptp) cc_final: 0.9107 (ptm) REVERT: B 428 ARG cc_start: 0.8783 (mtt-85) cc_final: 0.8534 (tmt170) REVERT: C 210 MET cc_start: 0.8981 (tpp) cc_final: 0.8645 (tpp) REVERT: C 419 MET cc_start: 0.9453 (ptp) cc_final: 0.9006 (ppp) REVERT: C 436 LEU cc_start: 0.9307 (mm) cc_final: 0.9093 (pp) REVERT: D 52 ASP cc_start: 0.8264 (p0) cc_final: 0.7935 (p0) REVERT: D 210 MET cc_start: 0.9046 (tpp) cc_final: 0.8790 (tpp) REVERT: D 254 PHE cc_start: 0.9465 (t80) cc_final: 0.9149 (t80) REVERT: D 258 LEU cc_start: 0.9604 (mm) cc_final: 0.9293 (mm) REVERT: D 300 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8727 (tm-30) REVERT: D 419 MET cc_start: 0.9512 (ptp) cc_final: 0.9196 (ptm) REVERT: D 436 LEU cc_start: 0.9223 (mm) cc_final: 0.8984 (pp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2613 time to fit residues: 49.1954 Evaluate side-chains 98 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 118 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 0.3980 chunk 169 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 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 = 0.3242 r_free = 0.3242 target = 0.068459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.051792 restraints weight = 68368.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.053241 restraints weight = 37088.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.054183 restraints weight = 24098.096| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16545 Z= 0.172 Angle : 0.636 6.951 22655 Z= 0.314 Chirality : 0.043 0.162 2680 Planarity : 0.004 0.033 2750 Dihedral : 6.622 65.852 2645 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 1905 helix: 0.66 (0.19), residues: 775 sheet: -2.40 (0.23), residues: 380 loop : -1.46 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 168 HIS 0.002 0.001 HIS E 18 PHE 0.021 0.002 PHE E 254 TYR 0.010 0.001 TYR D 61 ARG 0.002 0.000 ARG C 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 15) link_NAG-ASN : angle 1.81371 ( 45) link_BETA1-4 : bond 0.00186 ( 10) link_BETA1-4 : angle 1.17879 ( 30) hydrogen bonds : bond 0.03790 ( 725) hydrogen bonds : angle 4.92745 ( 2175) SS BOND : bond 0.00578 ( 5) SS BOND : angle 1.22619 ( 10) covalent geometry : bond 0.00372 (16515) covalent geometry : angle 0.62969 (22570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8126 (p0) cc_final: 0.7898 (p0) REVERT: A 205 ASN cc_start: 0.8672 (m-40) cc_final: 0.8124 (p0) REVERT: A 403 LEU cc_start: 0.9500 (tp) cc_final: 0.9284 (pt) REVERT: A 419 MET cc_start: 0.9484 (ptp) cc_final: 0.9194 (ptp) REVERT: E 235 MET cc_start: 0.8459 (mmt) cc_final: 0.8172 (mpp) REVERT: E 419 MET cc_start: 0.9466 (ptp) cc_final: 0.9125 (ptm) REVERT: B 101 ASN cc_start: 0.9111 (m-40) cc_final: 0.8692 (m110) REVERT: B 235 MET cc_start: 0.8771 (mpp) cc_final: 0.8465 (mpp) REVERT: B 258 LEU cc_start: 0.9584 (mm) cc_final: 0.9329 (mm) REVERT: B 419 MET cc_start: 0.9428 (ptp) cc_final: 0.9121 (ptm) REVERT: C 210 MET cc_start: 0.8999 (tpp) cc_final: 0.8642 (tpp) REVERT: C 419 MET cc_start: 0.9461 (ptp) cc_final: 0.9098 (ptm) REVERT: D 52 ASP cc_start: 0.8307 (p0) cc_final: 0.8003 (p0) REVERT: D 254 PHE cc_start: 0.9475 (t80) cc_final: 0.9195 (t80) REVERT: D 258 LEU cc_start: 0.9585 (mm) cc_final: 0.9272 (mm) REVERT: D 419 MET cc_start: 0.9490 (ptp) cc_final: 0.9207 (ptm) REVERT: D 436 LEU cc_start: 0.9230 (mm) cc_final: 0.9003 (pp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2914 time to fit residues: 56.0319 Evaluate side-chains 87 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 165 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN C 124 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.067886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.051190 restraints weight = 69366.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.052612 restraints weight = 37406.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.053548 restraints weight = 24284.210| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16545 Z= 0.195 Angle : 0.659 7.501 22655 Z= 0.324 Chirality : 0.044 0.159 2680 Planarity : 0.004 0.036 2750 Dihedral : 6.469 61.403 2645 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1905 helix: 0.91 (0.19), residues: 775 sheet: -2.45 (0.23), residues: 390 loop : -1.22 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 168 HIS 0.003 0.001 HIS E 18 PHE 0.022 0.002 PHE B 242 TYR 0.024 0.001 TYR B 441 ARG 0.002 0.000 ARG C 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 15) link_NAG-ASN : angle 1.79712 ( 45) link_BETA1-4 : bond 0.00190 ( 10) link_BETA1-4 : angle 1.19750 ( 30) hydrogen bonds : bond 0.03620 ( 725) hydrogen bonds : angle 4.91551 ( 2175) SS BOND : bond 0.00271 ( 5) SS BOND : angle 1.27207 ( 10) covalent geometry : bond 0.00422 (16515) covalent geometry : angle 0.65289 (22570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8152 (p0) cc_final: 0.7923 (p0) REVERT: A 205 ASN cc_start: 0.8653 (m-40) cc_final: 0.8124 (p0) REVERT: A 419 MET cc_start: 0.9482 (ptp) cc_final: 0.9188 (ptp) REVERT: E 235 MET cc_start: 0.8498 (mmt) cc_final: 0.8220 (mpp) REVERT: E 419 MET cc_start: 0.9465 (ptp) cc_final: 0.9122 (ptm) REVERT: B 101 ASN cc_start: 0.9084 (m-40) cc_final: 0.8564 (m110) REVERT: B 235 MET cc_start: 0.8791 (mpp) cc_final: 0.8470 (mpp) REVERT: B 419 MET cc_start: 0.9427 (ptp) cc_final: 0.9114 (ptm) REVERT: C 210 MET cc_start: 0.9014 (tpp) cc_final: 0.8658 (tpp) REVERT: C 419 MET cc_start: 0.9472 (ptp) cc_final: 0.9107 (ptm) REVERT: D 52 ASP cc_start: 0.8303 (p0) cc_final: 0.7968 (p0) REVERT: D 235 MET cc_start: 0.8762 (mmt) cc_final: 0.8429 (mpp) REVERT: D 254 PHE cc_start: 0.9491 (t80) cc_final: 0.9255 (t80) REVERT: D 258 LEU cc_start: 0.9646 (mm) cc_final: 0.9444 (mm) REVERT: D 419 MET cc_start: 0.9494 (ptp) cc_final: 0.9212 (ptm) REVERT: D 436 LEU cc_start: 0.9247 (mm) cc_final: 0.9028 (pp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3077 time to fit residues: 55.3177 Evaluate side-chains 97 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 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 = 0.3238 r_free = 0.3238 target = 0.068326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.051628 restraints weight = 68197.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.053076 restraints weight = 36929.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.054022 restraints weight = 23872.124| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16545 Z= 0.160 Angle : 0.635 7.190 22655 Z= 0.311 Chirality : 0.044 0.178 2680 Planarity : 0.004 0.037 2750 Dihedral : 6.358 60.698 2645 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1905 helix: 0.95 (0.19), residues: 775 sheet: -2.62 (0.22), residues: 415 loop : -1.19 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 156 HIS 0.002 0.001 HIS D 158 PHE 0.025 0.002 PHE C 254 TYR 0.011 0.001 TYR C 67 ARG 0.002 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 15) link_NAG-ASN : angle 1.72834 ( 45) link_BETA1-4 : bond 0.00142 ( 10) link_BETA1-4 : angle 1.13318 ( 30) hydrogen bonds : bond 0.03445 ( 725) hydrogen bonds : angle 4.81756 ( 2175) SS BOND : bond 0.00210 ( 5) SS BOND : angle 1.09481 ( 10) covalent geometry : bond 0.00349 (16515) covalent geometry : angle 0.62957 (22570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8143 (p0) cc_final: 0.7921 (p0) REVERT: A 205 ASN cc_start: 0.8659 (m-40) cc_final: 0.8126 (p0) REVERT: A 419 MET cc_start: 0.9491 (ptp) cc_final: 0.9192 (ptp) REVERT: E 235 MET cc_start: 0.8569 (mmt) cc_final: 0.8262 (mpp) REVERT: E 419 MET cc_start: 0.9455 (ptp) cc_final: 0.9120 (ptm) REVERT: B 101 ASN cc_start: 0.8984 (m-40) cc_final: 0.8450 (m110) REVERT: B 235 MET cc_start: 0.8771 (mpp) cc_final: 0.8481 (mpp) REVERT: B 419 MET cc_start: 0.9433 (ptp) cc_final: 0.9141 (ptm) REVERT: C 210 MET cc_start: 0.9007 (tpp) cc_final: 0.8642 (tpp) REVERT: C 419 MET cc_start: 0.9451 (ptp) cc_final: 0.9073 (ptm) REVERT: D 52 ASP cc_start: 0.8306 (p0) cc_final: 0.7959 (p0) REVERT: D 223 TYR cc_start: 0.8996 (m-10) cc_final: 0.8583 (m-80) REVERT: D 254 PHE cc_start: 0.9480 (t80) cc_final: 0.9234 (t80) REVERT: D 258 LEU cc_start: 0.9645 (mm) cc_final: 0.9407 (mm) REVERT: D 419 MET cc_start: 0.9469 (ptp) cc_final: 0.9165 (ptm) REVERT: D 436 LEU cc_start: 0.9240 (mm) cc_final: 0.9017 (pp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2885 time to fit residues: 53.1220 Evaluate side-chains 95 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 130 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 = 0.3247 r_free = 0.3247 target = 0.068732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.051972 restraints weight = 68362.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.053440 restraints weight = 36669.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.054379 restraints weight = 23760.139| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16545 Z= 0.144 Angle : 0.634 7.416 22655 Z= 0.309 Chirality : 0.044 0.211 2680 Planarity : 0.004 0.037 2750 Dihedral : 6.259 60.754 2645 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.06 % Allowed : 0.46 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1905 helix: 1.25 (0.19), residues: 775 sheet: -2.48 (0.22), residues: 405 loop : -1.15 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 156 HIS 0.002 0.000 HIS D 158 PHE 0.027 0.001 PHE B 242 TYR 0.017 0.001 TYR B 223 ARG 0.001 0.000 ARG A 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 15) link_NAG-ASN : angle 1.68452 ( 45) link_BETA1-4 : bond 0.00125 ( 10) link_BETA1-4 : angle 1.10070 ( 30) hydrogen bonds : bond 0.03336 ( 725) hydrogen bonds : angle 4.74560 ( 2175) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.92071 ( 10) covalent geometry : bond 0.00318 (16515) covalent geometry : angle 0.62941 (22570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8140 (p0) cc_final: 0.7917 (p0) REVERT: A 205 ASN cc_start: 0.8651 (m-40) cc_final: 0.8129 (p0) REVERT: A 419 MET cc_start: 0.9493 (ptp) cc_final: 0.9208 (ptp) REVERT: E 235 MET cc_start: 0.8587 (mmt) cc_final: 0.8286 (mpp) REVERT: E 419 MET cc_start: 0.9463 (ptp) cc_final: 0.9139 (ptm) REVERT: B 101 ASN cc_start: 0.8953 (m-40) cc_final: 0.8431 (m110) REVERT: B 235 MET cc_start: 0.8735 (mpp) cc_final: 0.8431 (mpp) REVERT: B 258 LEU cc_start: 0.9625 (mm) cc_final: 0.9418 (mm) REVERT: B 419 MET cc_start: 0.9432 (ptp) cc_final: 0.9146 (ptm) REVERT: B 436 LEU cc_start: 0.9247 (mm) cc_final: 0.9044 (pp) REVERT: C 210 MET cc_start: 0.9018 (tpp) cc_final: 0.8644 (tpp) REVERT: C 419 MET cc_start: 0.9440 (ptp) cc_final: 0.8999 (ppp) REVERT: D 223 TYR cc_start: 0.9008 (m-10) cc_final: 0.8593 (m-80) REVERT: D 235 MET cc_start: 0.8705 (mmt) cc_final: 0.8451 (mpp) REVERT: D 254 PHE cc_start: 0.9447 (t80) cc_final: 0.9174 (t80) REVERT: D 258 LEU cc_start: 0.9647 (mm) cc_final: 0.9369 (mm) REVERT: D 419 MET cc_start: 0.9452 (ptp) cc_final: 0.9157 (ptm) REVERT: D 436 LEU cc_start: 0.9220 (mm) cc_final: 0.9008 (pp) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.2353 time to fit residues: 43.2474 Evaluate side-chains 97 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 124 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.068482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.051768 restraints weight = 68977.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.053233 restraints weight = 36959.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.054178 restraints weight = 23878.782| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16545 Z= 0.163 Angle : 0.645 8.189 22655 Z= 0.313 Chirality : 0.044 0.179 2680 Planarity : 0.004 0.037 2750 Dihedral : 6.200 59.899 2645 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.12 % Allowed : 0.29 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1905 helix: 1.27 (0.19), residues: 775 sheet: -2.49 (0.22), residues: 405 loop : -1.14 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 156 HIS 0.002 0.001 HIS C 158 PHE 0.026 0.002 PHE B 242 TYR 0.014 0.001 TYR E 223 ARG 0.001 0.000 ARG E 218 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 15) link_NAG-ASN : angle 1.73362 ( 45) link_BETA1-4 : bond 0.00146 ( 10) link_BETA1-4 : angle 1.18658 ( 30) hydrogen bonds : bond 0.03292 ( 725) hydrogen bonds : angle 4.72061 ( 2175) SS BOND : bond 0.00210 ( 5) SS BOND : angle 1.06804 ( 10) covalent geometry : bond 0.00357 (16515) covalent geometry : angle 0.63984 (22570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8195 (p0) cc_final: 0.7962 (p0) REVERT: A 210 MET cc_start: 0.9123 (tpp) cc_final: 0.8834 (tpp) REVERT: A 419 MET cc_start: 0.9488 (ptp) cc_final: 0.9207 (ptp) REVERT: E 235 MET cc_start: 0.8545 (mmt) cc_final: 0.8276 (mpp) REVERT: E 419 MET cc_start: 0.9474 (ptp) cc_final: 0.9159 (ptm) REVERT: B 101 ASN cc_start: 0.8924 (m-40) cc_final: 0.8430 (m110) REVERT: B 235 MET cc_start: 0.8732 (mpp) cc_final: 0.8439 (mpp) REVERT: B 419 MET cc_start: 0.9434 (ptp) cc_final: 0.9160 (ptm) REVERT: B 436 LEU cc_start: 0.9249 (mm) cc_final: 0.9046 (pp) REVERT: C 210 MET cc_start: 0.8939 (tpp) cc_final: 0.8619 (tpp) REVERT: C 419 MET cc_start: 0.9446 (ptp) cc_final: 0.9081 (ptm) REVERT: D 223 TYR cc_start: 0.9057 (m-10) cc_final: 0.8633 (m-80) REVERT: D 254 PHE cc_start: 0.9493 (t80) cc_final: 0.9170 (t80) REVERT: D 258 LEU cc_start: 0.9670 (mm) cc_final: 0.9399 (mm) REVERT: D 419 MET cc_start: 0.9454 (ptp) cc_final: 0.9159 (ptm) REVERT: D 436 LEU cc_start: 0.9225 (mm) cc_final: 0.9009 (pp) outliers start: 2 outliers final: 0 residues processed: 111 average time/residue: 0.2332 time to fit residues: 42.4370 Evaluate side-chains 93 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 37 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.068151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.051450 restraints weight = 69006.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.052912 restraints weight = 36901.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.053844 restraints weight = 23820.638| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16545 Z= 0.174 Angle : 0.650 7.983 22655 Z= 0.316 Chirality : 0.044 0.164 2680 Planarity : 0.004 0.038 2750 Dihedral : 6.178 59.686 2645 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.06 % Allowed : 0.29 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1905 helix: 1.38 (0.19), residues: 775 sheet: -2.50 (0.22), residues: 405 loop : -1.13 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 156 HIS 0.002 0.001 HIS D 158 PHE 0.025 0.002 PHE E 254 TYR 0.011 0.001 TYR B 223 ARG 0.002 0.000 ARG E 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 15) link_NAG-ASN : angle 1.74825 ( 45) link_BETA1-4 : bond 0.00166 ( 10) link_BETA1-4 : angle 1.21577 ( 30) hydrogen bonds : bond 0.03265 ( 725) hydrogen bonds : angle 4.70373 ( 2175) SS BOND : bond 0.00252 ( 5) SS BOND : angle 1.15960 ( 10) covalent geometry : bond 0.00382 (16515) covalent geometry : angle 0.64430 (22570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4418.60 seconds wall clock time: 82 minutes 51.18 seconds (4971.18 seconds total)