Starting phenix.real_space_refine on Thu Sep 18 10:41:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hio_0226/09_2025/6hio_0226_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hio_0226/09_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_0226/09_2025/6hio_0226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hio_0226/09_2025/6hio_0226.map" model { file = "/net/cci-nas-00/data/ceres_data/6hio_0226/09_2025/6hio_0226_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hio_0226/09_2025/6hio_0226_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} 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: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} 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: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} 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: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} 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: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} 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: 3.97, per 1000 atoms: 0.25 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: 1.33 Conformation dependent library (CDL) restraints added in 797.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 2.76 Time building geometry restraints manager: 1.82 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: 0.01 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.710 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG D 28 TYR 0.030 0.003 TYR A 116 PHE 0.025 0.004 PHE E 153 TRP 0.046 0.004 TRP C 168 HIS 0.009 0.003 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00958 (16515) covalent geometry : angle 1.17224 (22570) SS BOND : bond 0.00276 ( 5) SS BOND : angle 1.31151 ( 10) hydrogen bonds : bond 0.30948 ( 725) hydrogen bonds : angle 9.98914 ( 2175) link_BETA1-4 : bond 0.00774 ( 10) link_BETA1-4 : angle 1.94432 ( 30) link_NAG-ASN : bond 0.00984 ( 15) link_NAG-ASN : angle 2.97610 ( 45) *********************** 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 : 0.640 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: 0.1305 time to fit residues: 30.4085 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 : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 124 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN E 119 HIS E 124 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN E 158 HIS 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 124 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 158 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.052996 restraints weight = 67874.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054565 restraints weight = 35306.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.055591 restraints weight = 22309.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.056251 restraints weight = 15966.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056669 restraints weight = 12647.013| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16545 Z= 0.168 Angle : 0.739 7.819 22655 Z= 0.373 Chirality : 0.047 0.214 2680 Planarity : 0.005 0.039 2750 Dihedral : 9.838 83.700 2645 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.12 % Allowed : 3.01 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.17), residues: 1905 helix: -1.31 (0.16), residues: 755 sheet: -2.45 (0.23), residues: 400 loop : -2.03 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 420 TYR 0.022 0.002 TYR A 67 PHE 0.015 0.002 PHE D 212 TRP 0.021 0.002 TRP C 168 HIS 0.002 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00353 (16515) covalent geometry : angle 0.73146 (22570) SS BOND : bond 0.00244 ( 5) SS BOND : angle 3.07308 ( 10) hydrogen bonds : bond 0.06491 ( 725) hydrogen bonds : angle 6.39346 ( 2175) link_BETA1-4 : bond 0.00261 ( 10) link_BETA1-4 : angle 1.17971 ( 30) link_NAG-ASN : bond 0.00131 ( 15) link_NAG-ASN : angle 1.84097 ( 45) *********************** 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 148 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8534 (m-40) cc_final: 0.7935 (p0) REVERT: A 210 MET cc_start: 0.8077 (tmm) cc_final: 0.7729 (tmm) REVERT: A 235 MET cc_start: 0.8856 (mmt) cc_final: 0.8316 (mmt) REVERT: A 254 PHE cc_start: 0.9538 (t80) cc_final: 0.9229 (t80) REVERT: A 258 LEU cc_start: 0.9691 (mm) cc_final: 0.9443 (mm) REVERT: A 441 TYR cc_start: 0.8100 (t80) cc_final: 0.7802 (t80) REVERT: E 254 PHE cc_start: 0.9583 (t80) cc_final: 0.9369 (t80) REVERT: E 403 LEU cc_start: 0.9288 (tp) cc_final: 0.9087 (pt) REVERT: E 419 MET cc_start: 0.9368 (ptp) cc_final: 0.9085 (ptm) REVERT: E 441 TYR cc_start: 0.7937 (t80) cc_final: 0.7708 (t80) REVERT: B 205 ASN cc_start: 0.8519 (m-40) cc_final: 0.8242 (p0) REVERT: B 254 PHE cc_start: 0.9559 (t80) cc_final: 0.9108 (t80) REVERT: B 258 LEU cc_start: 0.9729 (mm) cc_final: 0.9394 (mm) REVERT: B 419 MET cc_start: 0.9372 (ptp) cc_final: 0.9044 (ptm) REVERT: B 436 LEU cc_start: 0.9215 (mm) cc_final: 0.9002 (pp) REVERT: B 441 TYR cc_start: 0.7835 (t80) cc_final: 0.7632 (t80) REVERT: C 254 PHE cc_start: 0.9593 (t80) cc_final: 0.9318 (t80) REVERT: C 259 LEU cc_start: 0.9502 (mm) cc_final: 0.9143 (mm) REVERT: C 419 MET cc_start: 0.9175 (ptp) cc_final: 0.8720 (ptm) REVERT: D 210 MET cc_start: 0.8189 (tmm) cc_final: 0.7809 (tmm) REVERT: D 254 PHE cc_start: 0.9562 (t80) cc_final: 0.9132 (t80) REVERT: D 258 LEU cc_start: 0.9766 (mm) cc_final: 0.9561 (mm) REVERT: D 419 MET cc_start: 0.9384 (ptp) cc_final: 0.9027 (ptm) outliers start: 2 outliers final: 2 residues processed: 148 average time/residue: 0.1011 time to fit residues: 24.2200 Evaluate side-chains 109 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 77 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS C 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.053096 restraints weight = 68916.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054598 restraints weight = 37021.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.055572 restraints weight = 23739.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.056178 restraints weight = 17229.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.056618 restraints weight = 13825.901| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16545 Z= 0.158 Angle : 0.639 6.185 22655 Z= 0.322 Chirality : 0.044 0.176 2680 Planarity : 0.004 0.038 2750 Dihedral : 8.271 75.296 2645 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.19), residues: 1905 helix: -0.41 (0.17), residues: 770 sheet: -2.38 (0.23), residues: 385 loop : -1.77 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 420 TYR 0.023 0.002 TYR A 67 PHE 0.030 0.002 PHE E 265 TRP 0.018 0.002 TRP B 168 HIS 0.002 0.001 HIS D 158 Details of bonding type rmsd covalent geometry : bond 0.00333 (16515) covalent geometry : angle 0.63213 (22570) SS BOND : bond 0.00515 ( 5) SS BOND : angle 1.41593 ( 10) hydrogen bonds : bond 0.04793 ( 725) hydrogen bonds : angle 5.48048 ( 2175) link_BETA1-4 : bond 0.00231 ( 10) link_BETA1-4 : angle 1.27124 ( 30) link_NAG-ASN : bond 0.00274 ( 15) link_NAG-ASN : angle 1.86183 ( 45) *********************** 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 120 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.508 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 205 ASN cc_start: 0.8558 (m-40) cc_final: 0.8001 (p0) REVERT: A 235 MET cc_start: 0.8784 (mmt) cc_final: 0.8523 (mmt) REVERT: A 403 LEU cc_start: 0.9466 (tp) cc_final: 0.9245 (pt) REVERT: A 441 TYR cc_start: 0.8036 (t80) cc_final: 0.7748 (t80) REVERT: E 238 ASP cc_start: 0.7998 (t70) cc_final: 0.7609 (t0) REVERT: E 419 MET cc_start: 0.9449 (ptp) cc_final: 0.9114 (ptm) REVERT: B 254 PHE cc_start: 0.9557 (t80) cc_final: 0.9206 (t80) REVERT: B 258 LEU cc_start: 0.9681 (mm) cc_final: 0.9426 (mm) REVERT: B 419 MET cc_start: 0.9426 (ptp) cc_final: 0.9092 (ptm) REVERT: B 441 TYR cc_start: 0.7845 (t80) cc_final: 0.7585 (t80) REVERT: C 210 MET cc_start: 0.9000 (tpp) cc_final: 0.8662 (tpp) REVERT: C 419 MET cc_start: 0.9362 (ptp) cc_final: 0.8966 (ptm) REVERT: C 436 LEU cc_start: 0.9278 (mm) cc_final: 0.9071 (pp) REVERT: D 52 ASP cc_start: 0.8172 (p0) cc_final: 0.7960 (p0) REVERT: D 254 PHE cc_start: 0.9504 (t80) cc_final: 0.9173 (t80) REVERT: D 258 LEU cc_start: 0.9698 (mm) cc_final: 0.9363 (mm) REVERT: D 419 MET cc_start: 0.9528 (ptp) cc_final: 0.9177 (ptm) REVERT: D 436 LEU cc_start: 0.9187 (mm) cc_final: 0.8959 (pp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1027 time to fit residues: 19.7690 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 : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 140 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.068682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.052201 restraints weight = 69206.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.053661 restraints weight = 37505.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.054618 restraints weight = 24274.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.055216 restraints weight = 17699.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.055650 restraints weight = 14228.923| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16545 Z= 0.193 Angle : 0.654 7.417 22655 Z= 0.327 Chirality : 0.045 0.193 2680 Planarity : 0.004 0.033 2750 Dihedral : 7.592 72.836 2645 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.19), residues: 1905 helix: 0.12 (0.18), residues: 775 sheet: -2.51 (0.23), residues: 395 loop : -1.66 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.022 0.002 TYR A 67 PHE 0.016 0.002 PHE E 242 TRP 0.015 0.002 TRP B 156 HIS 0.002 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00418 (16515) covalent geometry : angle 0.64835 (22570) SS BOND : bond 0.00206 ( 5) SS BOND : angle 1.34589 ( 10) hydrogen bonds : bond 0.04248 ( 725) hydrogen bonds : angle 5.24109 ( 2175) link_BETA1-4 : bond 0.00296 ( 10) link_BETA1-4 : angle 1.17656 ( 30) link_NAG-ASN : bond 0.00362 ( 15) link_NAG-ASN : angle 1.86747 ( 45) *********************** 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 119 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8614 (m-40) cc_final: 0.8025 (p0) REVERT: A 403 LEU cc_start: 0.9480 (tp) cc_final: 0.9265 (pt) REVERT: A 419 MET cc_start: 0.9470 (ptp) cc_final: 0.9205 (ptp) REVERT: E 235 MET cc_start: 0.8551 (mmt) cc_final: 0.8293 (mpp) REVERT: E 419 MET cc_start: 0.9457 (ptp) cc_final: 0.9092 (ptm) REVERT: E 441 TYR cc_start: 0.8244 (t80) cc_final: 0.7893 (t80) REVERT: B 254 PHE cc_start: 0.9541 (t80) cc_final: 0.9275 (t80) REVERT: B 258 LEU cc_start: 0.9679 (mm) cc_final: 0.9417 (mm) REVERT: B 419 MET cc_start: 0.9431 (ptp) cc_final: 0.9066 (ptm) REVERT: B 428 ARG cc_start: 0.8753 (mtt-85) cc_final: 0.8551 (tmt170) REVERT: C 210 MET cc_start: 0.8931 (tpp) cc_final: 0.8635 (tpp) REVERT: C 235 MET cc_start: 0.8629 (mmt) cc_final: 0.8008 (mpp) REVERT: C 419 MET cc_start: 0.9394 (ptp) cc_final: 0.9020 (ptm) REVERT: D 52 ASP cc_start: 0.8221 (p0) cc_final: 0.7898 (p0) REVERT: D 235 MET cc_start: 0.8805 (mmt) cc_final: 0.8461 (mpp) REVERT: D 254 PHE cc_start: 0.9487 (t80) cc_final: 0.9174 (t80) REVERT: D 258 LEU cc_start: 0.9679 (mm) cc_final: 0.9383 (mm) REVERT: D 300 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8713 (tm-30) REVERT: D 419 MET cc_start: 0.9509 (ptp) cc_final: 0.9172 (ptm) REVERT: D 436 LEU cc_start: 0.9216 (mm) cc_final: 0.8986 (pp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1057 time to fit residues: 19.9704 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 : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 37 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** ** A 309 HIS ** 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 124 GLN ** 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 = 0.3156 r_free = 0.3156 target = 0.064809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.048173 restraints weight = 71567.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.049507 restraints weight = 39236.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.050397 restraints weight = 25828.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.050977 restraints weight = 19163.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.051333 restraints weight = 15576.030| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 16545 Z= 0.405 Angle : 0.867 10.028 22655 Z= 0.427 Chirality : 0.047 0.160 2680 Planarity : 0.005 0.043 2750 Dihedral : 7.653 70.318 2645 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.19), residues: 1905 helix: 0.23 (0.18), residues: 780 sheet: -2.51 (0.22), residues: 380 loop : -1.78 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.018 0.002 TYR E 126 PHE 0.018 0.003 PHE A 212 TRP 0.039 0.003 TRP E 168 HIS 0.005 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00866 (16515) covalent geometry : angle 0.85779 (22570) SS BOND : bond 0.01340 ( 5) SS BOND : angle 1.93053 ( 10) hydrogen bonds : bond 0.04486 ( 725) hydrogen bonds : angle 5.59322 ( 2175) link_BETA1-4 : bond 0.00913 ( 10) link_BETA1-4 : angle 1.73327 ( 30) link_NAG-ASN : bond 0.01124 ( 15) link_NAG-ASN : angle 2.62200 ( 45) *********************** 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 105 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 MET cc_start: 0.9504 (ptp) cc_final: 0.9277 (ptm) REVERT: E 419 MET cc_start: 0.9495 (ptp) cc_final: 0.9138 (ptm) REVERT: B 210 MET cc_start: 0.9090 (tpp) cc_final: 0.8674 (tpp) REVERT: B 235 MET cc_start: 0.8831 (mpp) cc_final: 0.8511 (mpp) REVERT: B 419 MET cc_start: 0.9465 (ptp) cc_final: 0.9097 (ptm) REVERT: B 436 LEU cc_start: 0.9336 (mm) cc_final: 0.9118 (pp) REVERT: C 210 MET cc_start: 0.9017 (tpp) cc_final: 0.8715 (tpp) REVERT: C 235 MET cc_start: 0.8615 (mmt) cc_final: 0.8078 (mpp) REVERT: C 419 MET cc_start: 0.9487 (ptp) cc_final: 0.9091 (ptm) REVERT: C 441 TYR cc_start: 0.8676 (t80) cc_final: 0.8473 (t80) REVERT: D 210 MET cc_start: 0.9056 (tpp) cc_final: 0.8793 (tpp) REVERT: D 235 MET cc_start: 0.8756 (mmt) cc_final: 0.8407 (mpp) REVERT: D 254 PHE cc_start: 0.9493 (t80) cc_final: 0.9211 (t80) REVERT: D 258 LEU cc_start: 0.9638 (mm) cc_final: 0.9348 (mm) REVERT: D 300 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8758 (tm-30) REVERT: D 419 MET cc_start: 0.9566 (ptp) cc_final: 0.9271 (ptm) REVERT: D 436 LEU cc_start: 0.9237 (mm) cc_final: 0.9021 (pp) REVERT: D 441 TYR cc_start: 0.8752 (t80) cc_final: 0.8460 (t80) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1071 time to fit residues: 17.9234 Evaluate side-chains 86 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 168 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 169 optimal weight: 0.1980 chunk 174 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.6544 ------------------------------------------------------------------------------- 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 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 = 0.3220 r_free = 0.3220 target = 0.067575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.050697 restraints weight = 69177.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.052186 restraints weight = 36523.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.053135 restraints weight = 23397.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.053786 restraints weight = 17046.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.054183 restraints weight = 13619.444| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16545 Z= 0.146 Angle : 0.647 6.959 22655 Z= 0.318 Chirality : 0.044 0.207 2680 Planarity : 0.004 0.038 2750 Dihedral : 7.026 67.422 2645 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.19), residues: 1905 helix: 0.68 (0.19), residues: 775 sheet: -2.42 (0.22), residues: 390 loop : -1.57 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 219 TYR 0.015 0.002 TYR A 67 PHE 0.020 0.001 PHE E 254 TRP 0.019 0.002 TRP C 156 HIS 0.002 0.000 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00311 (16515) covalent geometry : angle 0.64110 (22570) SS BOND : bond 0.00628 ( 5) SS BOND : angle 1.21352 ( 10) hydrogen bonds : bond 0.03797 ( 725) hydrogen bonds : angle 5.12126 ( 2175) link_BETA1-4 : bond 0.00170 ( 10) link_BETA1-4 : angle 1.00207 ( 30) link_NAG-ASN : bond 0.00138 ( 15) link_NAG-ASN : angle 1.81828 ( 45) *********************** 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 109 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 MET cc_start: 0.9181 (mmm) cc_final: 0.8980 (mmm) REVERT: E 235 MET cc_start: 0.8792 (mpp) cc_final: 0.8485 (mpp) REVERT: E 259 LEU cc_start: 0.9456 (mm) cc_final: 0.9243 (mm) REVERT: E 419 MET cc_start: 0.9452 (ptp) cc_final: 0.9083 (ptm) REVERT: B 210 MET cc_start: 0.9118 (tpp) cc_final: 0.8757 (tpp) REVERT: B 235 MET cc_start: 0.8769 (mpp) cc_final: 0.8411 (mpp) REVERT: B 258 LEU cc_start: 0.9626 (mm) cc_final: 0.9405 (mm) REVERT: B 419 MET cc_start: 0.9420 (ptp) cc_final: 0.9051 (ptm) REVERT: C 210 MET cc_start: 0.9043 (tpp) cc_final: 0.8709 (tpp) REVERT: C 235 MET cc_start: 0.8717 (mmt) cc_final: 0.8101 (mpp) REVERT: C 419 MET cc_start: 0.9462 (ptp) cc_final: 0.9085 (ptm) REVERT: D 52 ASP cc_start: 0.8166 (p0) cc_final: 0.7850 (p0) REVERT: D 210 MET cc_start: 0.9024 (tpp) cc_final: 0.8823 (tpp) REVERT: D 258 LEU cc_start: 0.9591 (mm) cc_final: 0.9285 (mm) REVERT: D 419 MET cc_start: 0.9492 (ptp) cc_final: 0.9194 (ptm) REVERT: D 436 LEU cc_start: 0.9222 (mm) cc_final: 0.9011 (pp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1211 time to fit residues: 21.0444 Evaluate side-chains 81 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 112 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.067588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.051105 restraints weight = 68654.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.052540 restraints weight = 36886.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.053456 restraints weight = 23807.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.054105 restraints weight = 17393.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.054491 restraints weight = 13942.170| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16545 Z= 0.167 Angle : 0.643 7.200 22655 Z= 0.317 Chirality : 0.044 0.156 2680 Planarity : 0.004 0.038 2750 Dihedral : 6.639 62.601 2645 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.20), residues: 1905 helix: 1.07 (0.19), residues: 770 sheet: -2.47 (0.22), residues: 400 loop : -1.37 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 420 TYR 0.020 0.001 TYR B 441 PHE 0.017 0.002 PHE B 242 TRP 0.016 0.002 TRP C 156 HIS 0.002 0.001 HIS D 158 Details of bonding type rmsd covalent geometry : bond 0.00362 (16515) covalent geometry : angle 0.63660 (22570) SS BOND : bond 0.00199 ( 5) SS BOND : angle 1.20645 ( 10) hydrogen bonds : bond 0.03586 ( 725) hydrogen bonds : angle 5.00274 ( 2175) link_BETA1-4 : bond 0.00162 ( 10) link_BETA1-4 : angle 1.14064 ( 30) link_NAG-ASN : bond 0.00311 ( 15) link_NAG-ASN : angle 1.84771 ( 45) *********************** 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 103 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 MET cc_start: 0.9448 (ptp) cc_final: 0.9170 (ptp) REVERT: E 235 MET cc_start: 0.8778 (mpp) cc_final: 0.8499 (mpp) REVERT: E 259 LEU cc_start: 0.9471 (mm) cc_final: 0.9263 (mm) REVERT: E 419 MET cc_start: 0.9462 (ptp) cc_final: 0.9097 (ptm) REVERT: B 210 MET cc_start: 0.9136 (tpp) cc_final: 0.8790 (tpp) REVERT: B 235 MET cc_start: 0.8712 (mpp) cc_final: 0.8440 (mpp) REVERT: B 419 MET cc_start: 0.9426 (ptp) cc_final: 0.9090 (ptm) REVERT: C 210 MET cc_start: 0.9014 (tpp) cc_final: 0.8698 (tpp) REVERT: C 235 MET cc_start: 0.8736 (mmt) cc_final: 0.8094 (mpp) REVERT: C 419 MET cc_start: 0.9455 (ptp) cc_final: 0.9084 (ptm) REVERT: D 52 ASP cc_start: 0.8168 (p0) cc_final: 0.7889 (p0) REVERT: D 210 MET cc_start: 0.8999 (tpp) cc_final: 0.8774 (tpp) REVERT: D 254 PHE cc_start: 0.9452 (t80) cc_final: 0.9215 (t80) REVERT: D 258 LEU cc_start: 0.9661 (mm) cc_final: 0.9455 (mm) REVERT: D 419 MET cc_start: 0.9487 (ptp) cc_final: 0.9202 (ptm) REVERT: D 436 LEU cc_start: 0.9209 (mm) cc_final: 0.9003 (pp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1172 time to fit residues: 19.7057 Evaluate side-chains 89 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 149 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 124 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.067241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.050518 restraints weight = 69468.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.051942 restraints weight = 37486.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.052884 restraints weight = 24256.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.053481 restraints weight = 17842.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.053871 restraints weight = 14396.775| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16545 Z= 0.196 Angle : 0.664 7.268 22655 Z= 0.325 Chirality : 0.044 0.197 2680 Planarity : 0.004 0.039 2750 Dihedral : 6.539 60.601 2645 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.20), residues: 1905 helix: 0.89 (0.19), residues: 775 sheet: -2.52 (0.23), residues: 390 loop : -1.42 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 315 TYR 0.014 0.002 TYR B 441 PHE 0.023 0.002 PHE E 254 TRP 0.016 0.002 TRP B 156 HIS 0.002 0.001 HIS D 158 Details of bonding type rmsd covalent geometry : bond 0.00428 (16515) covalent geometry : angle 0.65783 (22570) SS BOND : bond 0.00239 ( 5) SS BOND : angle 1.19639 ( 10) hydrogen bonds : bond 0.03506 ( 725) hydrogen bonds : angle 4.98099 ( 2175) link_BETA1-4 : bond 0.00196 ( 10) link_BETA1-4 : angle 1.20776 ( 30) link_NAG-ASN : bond 0.00394 ( 15) link_NAG-ASN : angle 1.85806 ( 45) *********************** 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 104 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 MET cc_start: 0.9488 (ptp) cc_final: 0.9235 (ptp) REVERT: E 235 MET cc_start: 0.8700 (mpp) cc_final: 0.8436 (mpp) REVERT: E 419 MET cc_start: 0.9491 (ptp) cc_final: 0.9142 (ptm) REVERT: B 210 MET cc_start: 0.9145 (tpp) cc_final: 0.8792 (tpp) REVERT: B 235 MET cc_start: 0.8736 (mpp) cc_final: 0.8405 (mpp) REVERT: B 419 MET cc_start: 0.9440 (ptp) cc_final: 0.9116 (ptm) REVERT: B 436 LEU cc_start: 0.9226 (mm) cc_final: 0.9025 (pp) REVERT: C 210 MET cc_start: 0.8918 (tpp) cc_final: 0.8612 (tpp) REVERT: C 235 MET cc_start: 0.8735 (mmt) cc_final: 0.8124 (mpp) REVERT: C 419 MET cc_start: 0.9465 (ptp) cc_final: 0.9108 (ptm) REVERT: D 52 ASP cc_start: 0.8282 (p0) cc_final: 0.7979 (p0) REVERT: D 210 MET cc_start: 0.9031 (tpp) cc_final: 0.8786 (tpp) REVERT: D 223 TYR cc_start: 0.9049 (m-10) cc_final: 0.8645 (m-80) REVERT: D 235 MET cc_start: 0.8759 (mmt) cc_final: 0.8411 (mpp) REVERT: D 258 LEU cc_start: 0.9647 (mm) cc_final: 0.9398 (mm) REVERT: D 419 MET cc_start: 0.9504 (ptp) cc_final: 0.9217 (ptm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1130 time to fit residues: 19.3538 Evaluate side-chains 85 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 93 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.066328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.049644 restraints weight = 70124.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.051062 restraints weight = 38150.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.051997 restraints weight = 24792.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.052592 restraints weight = 18135.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.052960 restraints weight = 14645.436| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16545 Z= 0.255 Angle : 0.712 8.141 22655 Z= 0.350 Chirality : 0.045 0.224 2680 Planarity : 0.004 0.040 2750 Dihedral : 6.626 59.635 2645 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.12 % Allowed : 0.93 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.19), residues: 1905 helix: 0.87 (0.19), residues: 775 sheet: -2.48 (0.23), residues: 380 loop : -1.56 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 218 TYR 0.021 0.002 TYR B 441 PHE 0.018 0.002 PHE B 242 TRP 0.018 0.002 TRP C 156 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00552 (16515) covalent geometry : angle 0.70559 (22570) SS BOND : bond 0.00389 ( 5) SS BOND : angle 1.30173 ( 10) hydrogen bonds : bond 0.03596 ( 725) hydrogen bonds : angle 5.07927 ( 2175) link_BETA1-4 : bond 0.00375 ( 10) link_BETA1-4 : angle 1.36692 ( 30) link_NAG-ASN : bond 0.00620 ( 15) link_NAG-ASN : angle 2.03153 ( 45) *********************** 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 106 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8094 (p0) cc_final: 0.7874 (p0) REVERT: A 419 MET cc_start: 0.9454 (ptp) cc_final: 0.9160 (ptp) REVERT: E 235 MET cc_start: 0.8642 (mpp) cc_final: 0.8422 (mpp) REVERT: E 419 MET cc_start: 0.9489 (ptp) cc_final: 0.9151 (ptm) REVERT: B 210 MET cc_start: 0.9172 (tpp) cc_final: 0.8819 (tpp) REVERT: B 235 MET cc_start: 0.8647 (mpp) cc_final: 0.8375 (mpp) REVERT: B 419 MET cc_start: 0.9446 (ptp) cc_final: 0.9102 (ptm) REVERT: B 436 LEU cc_start: 0.9242 (mm) cc_final: 0.9024 (pp) REVERT: C 210 MET cc_start: 0.8916 (tpp) cc_final: 0.8565 (tpp) REVERT: C 235 MET cc_start: 0.8724 (mmt) cc_final: 0.8334 (mmt) REVERT: C 419 MET cc_start: 0.9475 (ptp) cc_final: 0.9119 (ptm) REVERT: D 52 ASP cc_start: 0.8252 (p0) cc_final: 0.7952 (p0) REVERT: D 210 MET cc_start: 0.9049 (tpp) cc_final: 0.8801 (tpp) REVERT: D 254 PHE cc_start: 0.9461 (t80) cc_final: 0.9172 (t80) REVERT: D 258 LEU cc_start: 0.9660 (mm) cc_final: 0.9418 (mm) REVERT: D 419 MET cc_start: 0.9500 (ptp) cc_final: 0.9217 (ptm) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1143 time to fit residues: 19.7228 Evaluate side-chains 83 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 186 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.068142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.051371 restraints weight = 68462.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.052896 restraints weight = 36090.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.053851 restraints weight = 22939.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.054497 restraints weight = 16643.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054899 restraints weight = 13280.799| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16545 Z= 0.134 Angle : 0.645 7.990 22655 Z= 0.313 Chirality : 0.045 0.225 2680 Planarity : 0.004 0.039 2750 Dihedral : 6.452 62.096 2645 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.20), residues: 1905 helix: 1.09 (0.19), residues: 800 sheet: -2.33 (0.23), residues: 380 loop : -1.36 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 218 TYR 0.029 0.001 TYR B 441 PHE 0.022 0.001 PHE C 254 TRP 0.015 0.001 TRP C 156 HIS 0.002 0.000 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00297 (16515) covalent geometry : angle 0.63995 (22570) SS BOND : bond 0.00102 ( 5) SS BOND : angle 0.86908 ( 10) hydrogen bonds : bond 0.03282 ( 725) hydrogen bonds : angle 4.81322 ( 2175) link_BETA1-4 : bond 0.00199 ( 10) link_BETA1-4 : angle 1.02551 ( 30) link_NAG-ASN : bond 0.00108 ( 15) link_NAG-ASN : angle 1.69323 ( 45) ********************** 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: 1 poor density : 112 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ASN cc_start: 0.8998 (m-40) cc_final: 0.8559 (m110) REVERT: A 419 MET cc_start: 0.9479 (ptp) cc_final: 0.9233 (ptp) REVERT: E 235 MET cc_start: 0.8611 (mpp) cc_final: 0.8375 (mpp) REVERT: E 419 MET cc_start: 0.9475 (ptp) cc_final: 0.9139 (ptm) REVERT: B 210 MET cc_start: 0.9157 (tpp) cc_final: 0.8788 (tpp) REVERT: B 235 MET cc_start: 0.8632 (mpp) cc_final: 0.8373 (mpp) REVERT: B 419 MET cc_start: 0.9427 (ptp) cc_final: 0.9104 (ptm) REVERT: C 210 MET cc_start: 0.8930 (tpp) cc_final: 0.8567 (tpp) REVERT: C 235 MET cc_start: 0.8698 (mmt) cc_final: 0.8426 (mmt) REVERT: C 419 MET cc_start: 0.9451 (ptp) cc_final: 0.9115 (ptm) REVERT: C 436 LEU cc_start: 0.9292 (mm) cc_final: 0.9064 (pp) REVERT: D 52 ASP cc_start: 0.8231 (p0) cc_final: 0.7901 (p0) REVERT: D 210 MET cc_start: 0.9078 (tpp) cc_final: 0.8802 (tpp) REVERT: D 223 TYR cc_start: 0.9085 (m-10) cc_final: 0.8657 (m-80) REVERT: D 254 PHE cc_start: 0.9443 (t80) cc_final: 0.9190 (t80) REVERT: D 258 LEU cc_start: 0.9662 (mm) cc_final: 0.9385 (mm) REVERT: D 419 MET cc_start: 0.9478 (ptp) cc_final: 0.9200 (ptm) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.0902 time to fit residues: 16.7561 Evaluate side-chains 84 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 115 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.068994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.052399 restraints weight = 68552.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.053923 restraints weight = 36492.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054876 restraints weight = 23325.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055505 restraints weight = 16997.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.055901 restraints weight = 13604.810| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16545 Z= 0.116 Angle : 0.634 7.742 22655 Z= 0.306 Chirality : 0.044 0.197 2680 Planarity : 0.004 0.039 2750 Dihedral : 6.215 61.837 2645 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.20), residues: 1905 helix: 1.14 (0.19), residues: 800 sheet: -2.23 (0.23), residues: 380 loop : -1.23 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 251 TYR 0.037 0.002 TYR E 441 PHE 0.020 0.001 PHE E 242 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00258 (16515) covalent geometry : angle 0.62975 (22570) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.86801 ( 10) hydrogen bonds : bond 0.03182 ( 725) hydrogen bonds : angle 4.66502 ( 2175) link_BETA1-4 : bond 0.00198 ( 10) link_BETA1-4 : angle 1.02060 ( 30) link_NAG-ASN : bond 0.00070 ( 15) link_NAG-ASN : angle 1.62029 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1991.27 seconds wall clock time: 35 minutes 33.36 seconds (2133.36 seconds total)