Starting phenix.real_space_refine on Thu Feb 5 20:12:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4p_70110/02_2026/9o4p_70110.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4p_70110/02_2026/9o4p_70110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o4p_70110/02_2026/9o4p_70110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4p_70110/02_2026/9o4p_70110.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o4p_70110/02_2026/9o4p_70110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4p_70110/02_2026/9o4p_70110.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians Ca 9 9.91 5 S 112 5.16 5 C 12308 2.51 5 N 3256 2.21 5 O 3892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19577 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "F" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "J" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" 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: "W" 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: "X" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.47, per 1000 atoms: 0.23 Number of scatterers: 19577 At special positions: 0 Unit cell: (126.875, 126.875, 100.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 9 19.99 S 112 16.00 O 3892 8.00 N 3256 7.00 C 12308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.04 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.04 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 336 " distance=2.04 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.04 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.04 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 336 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.04 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.04 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 336 " distance=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA R 3 " - " MAN R 5 " " BMA U 3 " - " MAN U 5 " " BMA X 3 " - " MAN X 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " BETA1-6 " NAG O 1 " - " FUC O 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 6 " " NAG U 1 " - " FUC U 6 " " NAG X 1 " - " FUC X 6 " NAG-ASN " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 146 " " NAG P 1 " - " ASN B 88 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 146 " " NAG S 1 " - " ASN C 88 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 146 " " NAG V 1 " - " ASN D 88 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN D 146 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 887.8 milliseconds 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 52 sheets defined 3.7% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.683A pdb=" N SER A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.683A pdb=" N SER B 110 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.683A pdb=" N SER C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.683A pdb=" N SER D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 412A through 414 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.327A pdb=" N SER A 445 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N SER A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.996A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER A 160 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE A 173 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.661A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 202 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 213 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR A 207 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 4.659A pdb=" N TYR A 252 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 264 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.010A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N CYS A 280 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.416A pdb=" N ASN A 372 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 399 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 392 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.327A pdb=" N SER B 445 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.996A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER B 160 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE B 173 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.661A pdb=" N SER B 179 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 202 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 213 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 207 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AB3, first strand: chain 'B' and resid 223 through 224 removed outlier: 4.659A pdb=" N TYR B 252 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 264 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.010A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N CYS B 280 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 353 through 356 removed outlier: 6.416A pdb=" N ASN B 372 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY B 399 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 392 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.327A pdb=" N SER C 445 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.996A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER C 160 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE C 173 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.661A pdb=" N SER C 179 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 202 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP C 213 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR C 207 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AC1, first strand: chain 'C' and resid 223 through 224 removed outlier: 4.659A pdb=" N TYR C 252 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 264 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.010A pdb=" N CYS C 278 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N CYS C 280 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.416A pdb=" N ASN C 372 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY C 399 " --> pdb=" O ASN C 372 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 392 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.327A pdb=" N SER D 445 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.996A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER D 160 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE D 173 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.661A pdb=" N SER D 179 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 202 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP D 213 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR D 207 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AC8, first strand: chain 'D' and resid 223 through 224 removed outlier: 4.659A pdb=" N TYR D 252 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS D 264 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.010A pdb=" N CYS D 278 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N CYS D 280 " --> pdb=" O THR D 288 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 353 through 356 removed outlier: 6.416A pdb=" N ASN D 372 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY D 399 " --> pdb=" O ASN D 372 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 392 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.703A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.560A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.646A pdb=" N VAL E 103 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.703A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.560A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.646A pdb=" N VAL F 103 " --> pdb=" O ARG F 95 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.703A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.560A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.646A pdb=" N VAL G 103 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.703A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.560A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.646A pdb=" N VAL H 103 " --> pdb=" O ARG H 95 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.578A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.745A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.744A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.578A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.745A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.744A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.578A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.745A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.744A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.578A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.745A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.744A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1728 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: 3.76 Time building geometry restraints manager: 2.34 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: 6188 1.34 - 1.46: 5332 1.46 - 1.58: 8400 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 20064 Sorted by residual: bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sigma weight residual 1.410 1.458 -0.048 2.00e-02 2.50e+03 5.83e+00 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 25724 1.74 - 3.49: 1244 3.49 - 5.23: 252 5.23 - 6.97: 48 6.97 - 8.72: 4 Bond angle restraints: 27272 Sorted by residual: angle pdb=" CA HIS A 296 " pdb=" CB HIS A 296 " pdb=" CG HIS A 296 " ideal model delta sigma weight residual 113.80 118.51 -4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" CA HIS D 296 " pdb=" CB HIS D 296 " pdb=" CG HIS D 296 " ideal model delta sigma weight residual 113.80 118.51 -4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" CA HIS B 296 " pdb=" CB HIS B 296 " pdb=" CG HIS B 296 " ideal model delta sigma weight residual 113.80 118.51 -4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" CA HIS C 296 " pdb=" CB HIS C 296 " pdb=" CG HIS C 296 " ideal model delta sigma weight residual 113.80 118.51 -4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" N LEU B 464 " pdb=" CA LEU B 464 " pdb=" C LEU B 464 " ideal model delta sigma weight residual 109.81 118.53 -8.72 2.21e+00 2.05e-01 1.56e+01 ... (remaining 27267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 11480 21.20 - 42.40: 644 42.40 - 63.59: 120 63.59 - 84.79: 56 84.79 - 105.99: 16 Dihedral angle restraints: 12316 sinusoidal: 5292 harmonic: 7024 Sorted by residual: dihedral pdb=" CD ARG D 224 " pdb=" NE ARG D 224 " pdb=" CZ ARG D 224 " pdb=" NH1 ARG D 224 " ideal model delta sinusoidal sigma weight residual 0.00 62.76 -62.76 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CD ARG B 224 " pdb=" NE ARG B 224 " pdb=" CZ ARG B 224 " pdb=" NH1 ARG B 224 " ideal model delta sinusoidal sigma weight residual 0.00 62.76 -62.76 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CD ARG A 224 " pdb=" NE ARG A 224 " pdb=" CZ ARG A 224 " pdb=" NH1 ARG A 224 " ideal model delta sinusoidal sigma weight residual 0.00 62.76 -62.76 1 1.00e+01 1.00e-02 5.21e+01 ... (remaining 12313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2372 0.065 - 0.130: 584 0.130 - 0.195: 68 0.195 - 0.260: 8 0.260 - 0.325: 4 Chirality restraints: 3036 Sorted by residual: chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 3033 not shown) Planarity restraints: 3484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 224 " 0.821 9.50e-02 1.11e+02 3.69e-01 9.21e+01 pdb=" NE ARG B 224 " -0.069 2.00e-02 2.50e+03 pdb=" CZ ARG B 224 " 0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG B 224 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B 224 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 224 " 0.821 9.50e-02 1.11e+02 3.69e-01 9.21e+01 pdb=" NE ARG D 224 " -0.069 2.00e-02 2.50e+03 pdb=" CZ ARG D 224 " 0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG D 224 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 224 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 224 " 0.821 9.50e-02 1.11e+02 3.69e-01 9.21e+01 pdb=" NE ARG A 224 " -0.069 2.00e-02 2.50e+03 pdb=" CZ ARG A 224 " 0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG A 224 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 224 " 0.004 2.00e-02 2.50e+03 ... (remaining 3481 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2692 2.76 - 3.30: 18828 3.30 - 3.83: 34104 3.83 - 4.37: 43340 4.37 - 4.90: 74144 Nonbonded interactions: 173108 Sorted by model distance: nonbonded pdb=" OD1 ASP D 379 " pdb="CA CA D 502 " model vdw 2.226 2.510 nonbonded pdb=" OD1 ASP C 379 " pdb="CA CA C 502 " model vdw 2.226 2.510 nonbonded pdb=" OD1 ASP A 379 " pdb="CA CA A 502 " model vdw 2.226 2.510 nonbonded pdb=" OD1 ASP B 379 " pdb="CA CA B 502 " model vdw 2.226 2.510 nonbonded pdb=" O3 NAG R 2 " pdb=" O2 BMA R 3 " model vdw 2.227 3.040 ... (remaining 173103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 83 through 502) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.420 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.006 0.051 20144 Z= 0.243 Angle : 0.908 12.177 27472 Z= 0.455 Chirality : 0.057 0.325 3036 Planarity : 0.020 0.369 3472 Dihedral : 14.911 105.987 7740 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.19 % Allowed : 3.05 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2456 helix: -0.81 (0.92), residues: 24 sheet: 1.44 (0.17), residues: 944 loop : -0.64 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.006 ARG D 224 TYR 0.022 0.003 TYR A 316 PHE 0.026 0.003 PHE C 422 TRP 0.015 0.002 TRP C 456 HIS 0.011 0.003 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00568 (20064) covalent geometry : angle 0.87713 (27272) SS BOND : bond 0.00487 ( 40) SS BOND : angle 1.53862 ( 80) hydrogen bonds : bond 0.21124 ( 636) hydrogen bonds : angle 9.56948 ( 1728) link_ALPHA1-3 : bond 0.00725 ( 4) link_ALPHA1-3 : angle 3.31886 ( 12) link_ALPHA1-6 : bond 0.01072 ( 4) link_ALPHA1-6 : angle 2.14220 ( 12) link_BETA1-4 : bond 0.01705 ( 16) link_BETA1-4 : angle 4.86074 ( 48) link_BETA1-6 : bond 0.00705 ( 4) link_BETA1-6 : angle 1.31806 ( 12) link_NAG-ASN : bond 0.00316 ( 12) link_NAG-ASN : angle 2.08244 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 396 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 ARG cc_start: 0.8544 (mtm110) cc_final: 0.8211 (ttp80) REVERT: F 66 ARG cc_start: 0.8544 (mtm110) cc_final: 0.8208 (ttp80) REVERT: G 66 ARG cc_start: 0.8539 (mtm110) cc_final: 0.8204 (ttp80) REVERT: H 66 ARG cc_start: 0.8543 (mtm110) cc_final: 0.8209 (ttp80) outliers start: 4 outliers final: 0 residues processed: 400 average time/residue: 0.6073 time to fit residues: 273.2023 Evaluate side-chains 320 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 412AHIS B 184 HIS ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN C 184 HIS ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN D 184 HIS ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 ASN I 6 GLN J 6 GLN K 6 GLN L 6 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.077191 restraints weight = 32003.158| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.32 r_work: 0.2856 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20144 Z= 0.181 Angle : 0.683 10.690 27472 Z= 0.351 Chirality : 0.050 0.250 3036 Planarity : 0.005 0.048 3472 Dihedral : 10.923 81.032 3476 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.72 % Allowed : 11.50 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2456 helix: -0.66 (1.06), residues: 24 sheet: 1.38 (0.16), residues: 988 loop : -0.44 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 156 TYR 0.011 0.002 TYR D 252 PHE 0.023 0.002 PHE A 410 TRP 0.021 0.002 TRP A 456 HIS 0.009 0.002 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00415 (20064) covalent geometry : angle 0.65865 (27272) SS BOND : bond 0.00292 ( 40) SS BOND : angle 1.94836 ( 80) hydrogen bonds : bond 0.04029 ( 636) hydrogen bonds : angle 6.74860 ( 1728) link_ALPHA1-3 : bond 0.01397 ( 4) link_ALPHA1-3 : angle 0.97838 ( 12) link_ALPHA1-6 : bond 0.00897 ( 4) link_ALPHA1-6 : angle 1.28461 ( 12) link_BETA1-4 : bond 0.01882 ( 16) link_BETA1-4 : angle 3.30735 ( 48) link_BETA1-6 : bond 0.00965 ( 4) link_BETA1-6 : angle 1.22590 ( 12) link_NAG-ASN : bond 0.00213 ( 12) link_NAG-ASN : angle 1.75045 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8933 (mm-30) REVERT: B 174 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8930 (mm-30) REVERT: C 174 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8933 (mm-30) REVERT: D 174 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8932 (mm-30) REVERT: E 66 ARG cc_start: 0.8775 (mtm110) cc_final: 0.8008 (ttp80) REVERT: F 66 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8000 (ttp80) REVERT: G 66 ARG cc_start: 0.8781 (mtm110) cc_final: 0.8017 (ttp80) REVERT: H 66 ARG cc_start: 0.8784 (mtm110) cc_final: 0.8019 (ttp80) REVERT: I 17 ASP cc_start: 0.8303 (m-30) cc_final: 0.8080 (m-30) REVERT: I 24 ARG cc_start: 0.8470 (ttm110) cc_final: 0.7917 (tpp80) REVERT: J 17 ASP cc_start: 0.8299 (m-30) cc_final: 0.8074 (m-30) REVERT: J 24 ARG cc_start: 0.8490 (ttm110) cc_final: 0.7935 (tpp80) REVERT: K 17 ASP cc_start: 0.8304 (m-30) cc_final: 0.8079 (m-30) REVERT: K 24 ARG cc_start: 0.8494 (ttm110) cc_final: 0.7941 (tpp80) REVERT: L 17 ASP cc_start: 0.8301 (m-30) cc_final: 0.8075 (m-30) REVERT: L 24 ARG cc_start: 0.8488 (ttm110) cc_final: 0.7933 (tpp80) outliers start: 36 outliers final: 12 residues processed: 332 average time/residue: 0.5424 time to fit residues: 204.6139 Evaluate side-chains 316 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 304 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 60 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.0170 chunk 209 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 190 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS B 412AHIS C 296 HIS C 412AHIS D 296 HIS D 412AHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.098578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.072317 restraints weight = 32123.948| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.35 r_work: 0.2821 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20144 Z= 0.169 Angle : 0.630 11.495 27472 Z= 0.318 Chirality : 0.048 0.195 3036 Planarity : 0.005 0.041 3472 Dihedral : 9.792 66.380 3476 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.10 % Allowed : 13.74 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 2456 helix: -0.34 (1.12), residues: 24 sheet: 1.19 (0.16), residues: 992 loop : -0.44 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 103 TYR 0.011 0.001 TYR D 252 PHE 0.018 0.002 PHE B 410 TRP 0.022 0.002 TRP A 456 HIS 0.007 0.002 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00380 (20064) covalent geometry : angle 0.61064 (27272) SS BOND : bond 0.00233 ( 40) SS BOND : angle 1.46549 ( 80) hydrogen bonds : bond 0.03560 ( 636) hydrogen bonds : angle 6.24900 ( 1728) link_ALPHA1-3 : bond 0.01597 ( 4) link_ALPHA1-3 : angle 1.06398 ( 12) link_ALPHA1-6 : bond 0.01033 ( 4) link_ALPHA1-6 : angle 1.45772 ( 12) link_BETA1-4 : bond 0.01641 ( 16) link_BETA1-4 : angle 2.93597 ( 48) link_BETA1-6 : bond 0.00899 ( 4) link_BETA1-6 : angle 1.24655 ( 12) link_NAG-ASN : bond 0.00102 ( 12) link_NAG-ASN : angle 1.59818 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 316 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8873 (mm-30) REVERT: B 174 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8872 (mm-30) REVERT: C 174 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8872 (mm-30) REVERT: D 174 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8875 (mm-30) REVERT: E 64 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: E 66 ARG cc_start: 0.8810 (mtm110) cc_final: 0.8002 (ttp80) REVERT: F 64 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: F 66 ARG cc_start: 0.8813 (mtm110) cc_final: 0.8007 (ttp80) REVERT: G 64 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: G 66 ARG cc_start: 0.8808 (mtm110) cc_final: 0.7999 (ttp80) REVERT: H 64 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: H 66 ARG cc_start: 0.8817 (mtm110) cc_final: 0.8014 (ttp80) REVERT: I 17 ASP cc_start: 0.8398 (m-30) cc_final: 0.8137 (m-30) REVERT: I 24 ARG cc_start: 0.8498 (ttm110) cc_final: 0.7946 (tpp80) REVERT: I 42 LYS cc_start: 0.8751 (tppp) cc_final: 0.8479 (mmmm) REVERT: I 103 ARG cc_start: 0.8028 (ttp-110) cc_final: 0.7824 (ttp80) REVERT: J 17 ASP cc_start: 0.8395 (m-30) cc_final: 0.8133 (m-30) REVERT: J 24 ARG cc_start: 0.8517 (ttm110) cc_final: 0.7964 (tpp80) REVERT: J 42 LYS cc_start: 0.8745 (tppp) cc_final: 0.8474 (mmmm) REVERT: J 103 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7834 (ttp80) REVERT: K 17 ASP cc_start: 0.8387 (m-30) cc_final: 0.8125 (m-30) REVERT: K 24 ARG cc_start: 0.8515 (ttm110) cc_final: 0.7960 (tpp80) REVERT: K 42 LYS cc_start: 0.8746 (tppp) cc_final: 0.8477 (mmmm) REVERT: K 103 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7820 (ttp80) REVERT: L 17 ASP cc_start: 0.8393 (m-30) cc_final: 0.8130 (m-30) REVERT: L 24 ARG cc_start: 0.8509 (ttm110) cc_final: 0.7956 (tpp80) REVERT: L 42 LYS cc_start: 0.8748 (tppp) cc_final: 0.8475 (mmmm) REVERT: L 103 ARG cc_start: 0.8030 (ttp-110) cc_final: 0.7827 (ttp80) outliers start: 44 outliers final: 12 residues processed: 336 average time/residue: 0.5491 time to fit residues: 210.0943 Evaluate side-chains 308 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 292 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** 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 = 0.3255 r_free = 0.3255 target = 0.095324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.068485 restraints weight = 32173.963| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.36 r_work: 0.2741 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20144 Z= 0.272 Angle : 0.675 14.634 27472 Z= 0.336 Chirality : 0.050 0.211 3036 Planarity : 0.005 0.040 3472 Dihedral : 9.402 59.526 3476 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.29 % Allowed : 15.27 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2456 helix: -0.64 (1.01), residues: 24 sheet: 1.03 (0.16), residues: 992 loop : -0.52 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 103 TYR 0.013 0.002 TYR D 252 PHE 0.020 0.002 PHE B 410 TRP 0.024 0.002 TRP A 456 HIS 0.010 0.003 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00637 (20064) covalent geometry : angle 0.65501 (27272) SS BOND : bond 0.00334 ( 40) SS BOND : angle 1.69475 ( 80) hydrogen bonds : bond 0.03690 ( 636) hydrogen bonds : angle 6.22842 ( 1728) link_ALPHA1-3 : bond 0.01450 ( 4) link_ALPHA1-3 : angle 1.11740 ( 12) link_ALPHA1-6 : bond 0.01048 ( 4) link_ALPHA1-6 : angle 1.50192 ( 12) link_BETA1-4 : bond 0.01468 ( 16) link_BETA1-4 : angle 2.94248 ( 48) link_BETA1-6 : bond 0.00873 ( 4) link_BETA1-6 : angle 1.22157 ( 12) link_NAG-ASN : bond 0.00206 ( 12) link_NAG-ASN : angle 1.78210 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 0.585 Fit side-chains REVERT: A 174 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8870 (mm-30) REVERT: B 174 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8871 (mm-30) REVERT: C 174 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8870 (mm-30) REVERT: D 174 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8869 (mm-30) REVERT: E 12 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8039 (mtpt) REVERT: E 46 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: E 64 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: E 66 ARG cc_start: 0.8800 (mtm110) cc_final: 0.7990 (ttp80) REVERT: F 12 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8039 (mtpt) REVERT: F 46 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: F 64 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: F 66 ARG cc_start: 0.8803 (mtm110) cc_final: 0.7994 (ttp80) REVERT: G 12 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8045 (mtpt) REVERT: G 46 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.6988 (tm-30) REVERT: G 64 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: G 66 ARG cc_start: 0.8794 (mtm110) cc_final: 0.7979 (ttp80) REVERT: H 12 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8044 (mtpt) REVERT: H 46 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: H 64 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: H 66 ARG cc_start: 0.8811 (mtm110) cc_final: 0.8011 (ttp80) REVERT: I 17 ASP cc_start: 0.8408 (m-30) cc_final: 0.8130 (m-30) REVERT: I 24 ARG cc_start: 0.8491 (ttm110) cc_final: 0.7911 (tpp80) REVERT: I 42 LYS cc_start: 0.8765 (tppp) cc_final: 0.8496 (mmmm) REVERT: I 45 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8484 (ptpt) REVERT: J 17 ASP cc_start: 0.8396 (m-30) cc_final: 0.8117 (m-30) REVERT: J 24 ARG cc_start: 0.8494 (ttm110) cc_final: 0.7913 (tpp80) REVERT: J 42 LYS cc_start: 0.8769 (tppp) cc_final: 0.8500 (mmmm) REVERT: J 45 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8482 (ptpt) REVERT: K 17 ASP cc_start: 0.8394 (m-30) cc_final: 0.8115 (m-30) REVERT: K 24 ARG cc_start: 0.8491 (ttm110) cc_final: 0.7909 (tpp80) REVERT: K 42 LYS cc_start: 0.8764 (tppp) cc_final: 0.8496 (mmmm) REVERT: K 45 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8487 (ptpt) REVERT: L 17 ASP cc_start: 0.8403 (m-30) cc_final: 0.8124 (m-30) REVERT: L 24 ARG cc_start: 0.8497 (ttm110) cc_final: 0.7914 (tpp80) REVERT: L 42 LYS cc_start: 0.8778 (tppp) cc_final: 0.8507 (mmmm) REVERT: L 45 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8478 (ptpt) outliers start: 48 outliers final: 8 residues processed: 304 average time/residue: 0.5437 time to fit residues: 188.8300 Evaluate side-chains 304 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 206 optimal weight: 8.9990 chunk 225 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS C 296 HIS D 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.068739 restraints weight = 32078.840| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.36 r_work: 0.2744 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20144 Z= 0.210 Angle : 0.638 13.867 27472 Z= 0.316 Chirality : 0.048 0.208 3036 Planarity : 0.004 0.040 3472 Dihedral : 8.808 59.773 3476 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.24 % Allowed : 14.31 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2456 helix: -0.80 (0.96), residues: 24 sheet: 0.87 (0.17), residues: 992 loop : -0.56 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 103 TYR 0.012 0.001 TYR D 252 PHE 0.018 0.002 PHE A 410 TRP 0.019 0.002 TRP A 456 HIS 0.005 0.002 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00483 (20064) covalent geometry : angle 0.61805 (27272) SS BOND : bond 0.00285 ( 40) SS BOND : angle 1.47187 ( 80) hydrogen bonds : bond 0.03354 ( 636) hydrogen bonds : angle 6.05996 ( 1728) link_ALPHA1-3 : bond 0.01536 ( 4) link_ALPHA1-3 : angle 1.26980 ( 12) link_ALPHA1-6 : bond 0.01112 ( 4) link_ALPHA1-6 : angle 1.52307 ( 12) link_BETA1-4 : bond 0.01443 ( 16) link_BETA1-4 : angle 2.93810 ( 48) link_BETA1-6 : bond 0.00857 ( 4) link_BETA1-6 : angle 1.18982 ( 12) link_NAG-ASN : bond 0.00228 ( 12) link_NAG-ASN : angle 1.67148 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 296 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8882 (mm-30) REVERT: B 174 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8883 (mm-30) REVERT: C 174 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8885 (mm-30) REVERT: D 174 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8888 (mm-30) REVERT: E 46 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: E 64 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: E 66 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8006 (ttp80) REVERT: F 46 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: F 64 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: F 66 ARG cc_start: 0.8777 (mtm110) cc_final: 0.8015 (ttp80) REVERT: G 46 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: G 64 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: G 66 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8001 (ttp80) REVERT: H 46 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: H 64 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: H 66 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8022 (ttp80) REVERT: I 17 ASP cc_start: 0.8391 (m-30) cc_final: 0.8097 (m-30) REVERT: I 32 TYR cc_start: 0.8455 (m-80) cc_final: 0.8241 (m-80) REVERT: I 42 LYS cc_start: 0.8773 (tppp) cc_final: 0.8493 (mmmm) REVERT: I 45 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8482 (ptpt) REVERT: I 69 THR cc_start: 0.8870 (m) cc_final: 0.8586 (p) REVERT: I 103 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7881 (ttp80) REVERT: J 17 ASP cc_start: 0.8392 (m-30) cc_final: 0.8099 (m-30) REVERT: J 32 TYR cc_start: 0.8465 (m-80) cc_final: 0.8251 (m-80) REVERT: J 42 LYS cc_start: 0.8784 (tppp) cc_final: 0.8505 (mmmm) REVERT: J 45 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8478 (ptpt) REVERT: J 69 THR cc_start: 0.8869 (m) cc_final: 0.8587 (p) REVERT: J 103 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7883 (ttp80) REVERT: K 17 ASP cc_start: 0.8380 (m-30) cc_final: 0.8085 (m-30) REVERT: K 32 TYR cc_start: 0.8474 (m-80) cc_final: 0.8257 (m-80) REVERT: K 42 LYS cc_start: 0.8775 (tppp) cc_final: 0.8496 (mmmm) REVERT: K 45 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8487 (ptpt) REVERT: K 69 THR cc_start: 0.8873 (m) cc_final: 0.8590 (p) REVERT: K 103 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7865 (ttp80) REVERT: L 17 ASP cc_start: 0.8392 (m-30) cc_final: 0.8098 (m-30) REVERT: L 32 TYR cc_start: 0.8458 (m-80) cc_final: 0.8244 (m-80) REVERT: L 42 LYS cc_start: 0.8781 (tppp) cc_final: 0.8501 (mmmm) REVERT: L 45 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8482 (ptpt) REVERT: L 69 THR cc_start: 0.8875 (m) cc_final: 0.8585 (p) REVERT: L 103 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7875 (ttp80) outliers start: 68 outliers final: 24 residues processed: 328 average time/residue: 0.5425 time to fit residues: 203.5509 Evaluate side-chains 320 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 10 PHE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain L residue 10 PHE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 192 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** 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 = 0.3263 r_free = 0.3263 target = 0.096016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.069373 restraints weight = 31842.114| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.36 r_work: 0.2747 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20144 Z= 0.191 Angle : 0.635 14.111 27472 Z= 0.312 Chirality : 0.048 0.206 3036 Planarity : 0.004 0.040 3472 Dihedral : 8.525 59.587 3476 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.29 % Allowed : 16.22 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2456 helix: -0.83 (0.93), residues: 24 sheet: 0.94 (0.17), residues: 964 loop : -0.70 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 103 TYR 0.012 0.001 TYR D 252 PHE 0.016 0.002 PHE A 410 TRP 0.015 0.001 TRP A 456 HIS 0.010 0.002 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00442 (20064) covalent geometry : angle 0.61372 (27272) SS BOND : bond 0.00381 ( 40) SS BOND : angle 1.75267 ( 80) hydrogen bonds : bond 0.03222 ( 636) hydrogen bonds : angle 6.00330 ( 1728) link_ALPHA1-3 : bond 0.01589 ( 4) link_ALPHA1-3 : angle 1.37057 ( 12) link_ALPHA1-6 : bond 0.01128 ( 4) link_ALPHA1-6 : angle 1.49640 ( 12) link_BETA1-4 : bond 0.01429 ( 16) link_BETA1-4 : angle 2.93324 ( 48) link_BETA1-6 : bond 0.00855 ( 4) link_BETA1-6 : angle 1.19738 ( 12) link_NAG-ASN : bond 0.00195 ( 12) link_NAG-ASN : angle 1.61982 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 0.828 Fit side-chains REVERT: A 174 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8880 (mm-30) REVERT: B 174 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8877 (mm-30) REVERT: C 174 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8879 (mm-30) REVERT: D 174 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8882 (mm-30) REVERT: E 46 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: E 64 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: E 66 ARG cc_start: 0.8764 (mtm110) cc_final: 0.7989 (ttp80) REVERT: F 46 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: F 64 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: F 66 ARG cc_start: 0.8767 (mtm110) cc_final: 0.7998 (ttp80) REVERT: G 46 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: G 64 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: G 66 ARG cc_start: 0.8759 (mtm110) cc_final: 0.7988 (ttp80) REVERT: H 46 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: H 64 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: H 66 ARG cc_start: 0.8764 (mtm110) cc_final: 0.7997 (ttp80) REVERT: I 17 ASP cc_start: 0.8389 (m-30) cc_final: 0.8095 (m-30) REVERT: I 24 ARG cc_start: 0.8458 (ttm110) cc_final: 0.7976 (tpp80) REVERT: I 32 TYR cc_start: 0.8478 (m-80) cc_final: 0.8261 (m-80) REVERT: I 42 LYS cc_start: 0.8786 (tppp) cc_final: 0.8503 (mmmm) REVERT: I 45 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8488 (ptpt) REVERT: I 69 THR cc_start: 0.8852 (m) cc_final: 0.8577 (p) REVERT: J 17 ASP cc_start: 0.8391 (m-30) cc_final: 0.8097 (m-30) REVERT: J 24 ARG cc_start: 0.8444 (ttm110) cc_final: 0.7963 (tpp80) REVERT: J 32 TYR cc_start: 0.8484 (m-80) cc_final: 0.8269 (m-80) REVERT: J 42 LYS cc_start: 0.8797 (tppp) cc_final: 0.8517 (mmmm) REVERT: J 45 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8487 (ptpt) REVERT: J 69 THR cc_start: 0.8859 (m) cc_final: 0.8583 (p) REVERT: K 17 ASP cc_start: 0.8385 (m-30) cc_final: 0.8091 (m-30) REVERT: K 24 ARG cc_start: 0.8450 (ttm110) cc_final: 0.7970 (tpp80) REVERT: K 32 TYR cc_start: 0.8494 (m-80) cc_final: 0.8274 (m-80) REVERT: K 42 LYS cc_start: 0.8788 (tppp) cc_final: 0.8506 (mmmm) REVERT: K 45 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8491 (ptpt) REVERT: K 69 THR cc_start: 0.8854 (m) cc_final: 0.8579 (p) REVERT: L 17 ASP cc_start: 0.8386 (m-30) cc_final: 0.8092 (m-30) REVERT: L 24 ARG cc_start: 0.8446 (ttm110) cc_final: 0.7969 (tpp80) REVERT: L 32 TYR cc_start: 0.8478 (m-80) cc_final: 0.8259 (m-80) REVERT: L 42 LYS cc_start: 0.8795 (tppp) cc_final: 0.8510 (mmmm) REVERT: L 45 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8484 (ptpt) REVERT: L 69 THR cc_start: 0.8859 (m) cc_final: 0.8581 (p) outliers start: 48 outliers final: 12 residues processed: 304 average time/residue: 0.5451 time to fit residues: 188.1598 Evaluate side-chains 292 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS C 296 HIS D 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.070032 restraints weight = 32016.887| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.38 r_work: 0.2771 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20144 Z= 0.166 Angle : 0.616 13.224 27472 Z= 0.302 Chirality : 0.047 0.196 3036 Planarity : 0.004 0.040 3472 Dihedral : 8.012 59.410 3476 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.91 % Allowed : 16.41 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.16), residues: 2456 helix: -0.97 (0.91), residues: 24 sheet: 0.92 (0.17), residues: 972 loop : -0.68 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 364 TYR 0.013 0.001 TYR B 252 PHE 0.015 0.002 PHE D 410 TRP 0.013 0.001 TRP A 456 HIS 0.005 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00379 (20064) covalent geometry : angle 0.59516 (27272) SS BOND : bond 0.00244 ( 40) SS BOND : angle 1.58933 ( 80) hydrogen bonds : bond 0.03065 ( 636) hydrogen bonds : angle 5.90980 ( 1728) link_ALPHA1-3 : bond 0.01660 ( 4) link_ALPHA1-3 : angle 1.50803 ( 12) link_ALPHA1-6 : bond 0.01132 ( 4) link_ALPHA1-6 : angle 1.48923 ( 12) link_BETA1-4 : bond 0.01424 ( 16) link_BETA1-4 : angle 2.92277 ( 48) link_BETA1-6 : bond 0.00843 ( 4) link_BETA1-6 : angle 1.18824 ( 12) link_NAG-ASN : bond 0.00182 ( 12) link_NAG-ASN : angle 1.51766 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 284 time to evaluate : 0.782 Fit side-chains REVERT: A 174 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8857 (mm-30) REVERT: B 174 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8864 (mm-30) REVERT: C 174 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8870 (mm-30) REVERT: D 174 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8864 (mm-30) REVERT: E 12 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.7987 (mtpt) REVERT: E 46 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: E 64 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: E 66 ARG cc_start: 0.8766 (mtm110) cc_final: 0.7991 (ttp80) REVERT: F 12 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.7995 (mtpt) REVERT: F 46 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: F 64 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: F 66 ARG cc_start: 0.8766 (mtm110) cc_final: 0.7993 (ttp80) REVERT: G 12 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.7999 (mtpt) REVERT: G 46 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: G 64 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: G 66 ARG cc_start: 0.8764 (mtm110) cc_final: 0.7995 (ttp80) REVERT: H 12 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.7988 (mtpt) REVERT: H 46 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: H 64 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: H 66 ARG cc_start: 0.8770 (mtm110) cc_final: 0.8006 (ttp80) REVERT: I 17 ASP cc_start: 0.8452 (m-30) cc_final: 0.8166 (m-30) REVERT: I 24 ARG cc_start: 0.8459 (ttm110) cc_final: 0.7992 (tpp80) REVERT: I 42 LYS cc_start: 0.8815 (tppp) cc_final: 0.8541 (mmmm) REVERT: I 69 THR cc_start: 0.8830 (m) cc_final: 0.8564 (p) REVERT: J 17 ASP cc_start: 0.8457 (m-30) cc_final: 0.8171 (m-30) REVERT: J 24 ARG cc_start: 0.8444 (ttm110) cc_final: 0.7979 (tpp80) REVERT: J 42 LYS cc_start: 0.8829 (tppp) cc_final: 0.8557 (mmmm) REVERT: J 69 THR cc_start: 0.8834 (m) cc_final: 0.8569 (p) REVERT: K 17 ASP cc_start: 0.8452 (m-30) cc_final: 0.8165 (m-30) REVERT: K 24 ARG cc_start: 0.8445 (ttm110) cc_final: 0.7981 (tpp80) REVERT: K 42 LYS cc_start: 0.8819 (tppp) cc_final: 0.8544 (mmmm) REVERT: K 69 THR cc_start: 0.8830 (m) cc_final: 0.8568 (p) REVERT: L 17 ASP cc_start: 0.8448 (m-30) cc_final: 0.8160 (m-30) REVERT: L 24 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7978 (tpp80) REVERT: L 42 LYS cc_start: 0.8821 (tppp) cc_final: 0.8546 (mmmm) REVERT: L 69 THR cc_start: 0.8830 (m) cc_final: 0.8567 (p) outliers start: 40 outliers final: 16 residues processed: 300 average time/residue: 0.5744 time to fit residues: 195.4271 Evaluate side-chains 300 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS C 296 HIS D 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.067702 restraints weight = 31973.730| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.37 r_work: 0.2715 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 20144 Z= 0.281 Angle : 0.675 15.238 27472 Z= 0.331 Chirality : 0.050 0.209 3036 Planarity : 0.005 0.042 3472 Dihedral : 7.927 59.531 3476 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.10 % Allowed : 15.84 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2456 helix: -0.94 (0.90), residues: 24 sheet: 0.92 (0.17), residues: 972 loop : -0.69 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 300 TYR 0.012 0.002 TYR B 252 PHE 0.019 0.002 PHE C 410 TRP 0.017 0.002 TRP C 456 HIS 0.008 0.002 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00656 (20064) covalent geometry : angle 0.65106 (27272) SS BOND : bond 0.00417 ( 40) SS BOND : angle 2.11738 ( 80) hydrogen bonds : bond 0.03444 ( 636) hydrogen bonds : angle 6.07353 ( 1728) link_ALPHA1-3 : bond 0.01568 ( 4) link_ALPHA1-3 : angle 1.56719 ( 12) link_ALPHA1-6 : bond 0.01074 ( 4) link_ALPHA1-6 : angle 1.50914 ( 12) link_BETA1-4 : bond 0.01370 ( 16) link_BETA1-4 : angle 2.97859 ( 48) link_BETA1-6 : bond 0.00808 ( 4) link_BETA1-6 : angle 1.18578 ( 12) link_NAG-ASN : bond 0.00292 ( 12) link_NAG-ASN : angle 1.68697 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 0.718 Fit side-chains REVERT: A 174 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8861 (mm-30) REVERT: B 174 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8864 (mm-30) REVERT: C 174 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8877 (mm-30) REVERT: D 174 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8866 (mm-30) REVERT: E 12 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.7999 (mtpt) REVERT: E 46 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: E 64 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: E 66 ARG cc_start: 0.8738 (mtm110) cc_final: 0.7956 (ttp80) REVERT: F 12 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8002 (mtpt) REVERT: F 46 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: F 64 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: F 66 ARG cc_start: 0.8736 (mtm110) cc_final: 0.7956 (ttp80) REVERT: G 12 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8007 (mtpt) REVERT: G 46 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: G 64 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: G 66 ARG cc_start: 0.8740 (mtm110) cc_final: 0.7963 (ttp80) REVERT: H 12 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.7999 (mtpt) REVERT: H 46 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: H 64 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: H 66 ARG cc_start: 0.8742 (mtm110) cc_final: 0.7972 (ttp80) REVERT: I 17 ASP cc_start: 0.8450 (m-30) cc_final: 0.8152 (m-30) REVERT: I 24 ARG cc_start: 0.8407 (ttm110) cc_final: 0.7916 (tpp80) REVERT: I 42 LYS cc_start: 0.8819 (tppp) cc_final: 0.8539 (mmmm) REVERT: I 69 THR cc_start: 0.8849 (m) cc_final: 0.8566 (p) REVERT: J 17 ASP cc_start: 0.8446 (m-30) cc_final: 0.8147 (m-30) REVERT: J 24 ARG cc_start: 0.8406 (ttm110) cc_final: 0.7917 (tpp80) REVERT: J 42 LYS cc_start: 0.8831 (tppp) cc_final: 0.8552 (mmmm) REVERT: J 69 THR cc_start: 0.8858 (m) cc_final: 0.8577 (p) REVERT: K 17 ASP cc_start: 0.8441 (m-30) cc_final: 0.8142 (m-30) REVERT: K 24 ARG cc_start: 0.8396 (ttm110) cc_final: 0.7909 (tpp80) REVERT: K 42 LYS cc_start: 0.8825 (tppp) cc_final: 0.8543 (mmmm) REVERT: K 69 THR cc_start: 0.8847 (m) cc_final: 0.8569 (p) REVERT: L 17 ASP cc_start: 0.8444 (m-30) cc_final: 0.8146 (m-30) REVERT: L 24 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7903 (tpp80) REVERT: L 42 LYS cc_start: 0.8827 (tppp) cc_final: 0.8544 (mmmm) REVERT: L 69 THR cc_start: 0.8853 (m) cc_final: 0.8570 (p) outliers start: 44 outliers final: 12 residues processed: 302 average time/residue: 0.5400 time to fit residues: 185.5076 Evaluate side-chains 298 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 66 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 30 optimal weight: 0.0370 chunk 120 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS C 296 HIS D 296 HIS I 6 GLN J 6 GLN K 6 GLN L 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.096407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.069735 restraints weight = 31513.920| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.36 r_work: 0.2752 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20144 Z= 0.154 Angle : 0.622 13.832 27472 Z= 0.305 Chirality : 0.047 0.186 3036 Planarity : 0.004 0.039 3472 Dihedral : 7.674 59.527 3476 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.53 % Allowed : 16.41 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2456 helix: -0.99 (0.88), residues: 24 sheet: 0.88 (0.17), residues: 972 loop : -0.63 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.013 0.001 TYR A 252 PHE 0.015 0.002 PHE A 410 TRP 0.018 0.001 TRP A 295 HIS 0.008 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00346 (20064) covalent geometry : angle 0.60038 (27272) SS BOND : bond 0.00228 ( 40) SS BOND : angle 1.63795 ( 80) hydrogen bonds : bond 0.03024 ( 636) hydrogen bonds : angle 5.95750 ( 1728) link_ALPHA1-3 : bond 0.01654 ( 4) link_ALPHA1-3 : angle 1.66523 ( 12) link_ALPHA1-6 : bond 0.01106 ( 4) link_ALPHA1-6 : angle 1.45820 ( 12) link_BETA1-4 : bond 0.01417 ( 16) link_BETA1-4 : angle 2.95564 ( 48) link_BETA1-6 : bond 0.00839 ( 4) link_BETA1-6 : angle 1.19359 ( 12) link_NAG-ASN : bond 0.00196 ( 12) link_NAG-ASN : angle 1.56005 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 0.812 Fit side-chains REVERT: A 174 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8848 (mm-30) REVERT: B 174 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8852 (mm-30) REVERT: C 174 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8858 (mm-30) REVERT: D 174 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8856 (mm-30) REVERT: E 46 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: E 64 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: E 66 ARG cc_start: 0.8742 (mtm110) cc_final: 0.7959 (ttp80) REVERT: F 46 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: F 64 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: F 66 ARG cc_start: 0.8744 (mtm110) cc_final: 0.7966 (ttp80) REVERT: G 46 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: G 64 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: G 66 ARG cc_start: 0.8742 (mtm110) cc_final: 0.7966 (ttp80) REVERT: H 46 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: H 64 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: H 66 ARG cc_start: 0.8750 (mtm110) cc_final: 0.7976 (ttp80) REVERT: I 17 ASP cc_start: 0.8457 (m-30) cc_final: 0.8165 (m-30) REVERT: I 24 ARG cc_start: 0.8397 (ttm110) cc_final: 0.7918 (tpp80) REVERT: I 42 LYS cc_start: 0.8810 (tppp) cc_final: 0.8534 (mmmm) REVERT: I 69 THR cc_start: 0.8819 (m) cc_final: 0.8548 (p) REVERT: J 17 ASP cc_start: 0.8459 (m-30) cc_final: 0.8167 (m-30) REVERT: J 24 ARG cc_start: 0.8394 (ttm110) cc_final: 0.7913 (tpp80) REVERT: J 42 LYS cc_start: 0.8823 (tppp) cc_final: 0.8547 (mmmm) REVERT: J 69 THR cc_start: 0.8820 (m) cc_final: 0.8553 (p) REVERT: K 17 ASP cc_start: 0.8452 (m-30) cc_final: 0.8158 (m-30) REVERT: K 24 ARG cc_start: 0.8396 (ttm110) cc_final: 0.7921 (tpp80) REVERT: K 42 LYS cc_start: 0.8815 (tppp) cc_final: 0.8537 (mmmm) REVERT: K 69 THR cc_start: 0.8820 (m) cc_final: 0.8557 (p) REVERT: L 17 ASP cc_start: 0.8453 (m-30) cc_final: 0.8162 (m-30) REVERT: L 24 ARG cc_start: 0.8385 (ttm110) cc_final: 0.7912 (tpp80) REVERT: L 42 LYS cc_start: 0.8818 (tppp) cc_final: 0.8540 (mmmm) REVERT: L 69 THR cc_start: 0.8826 (m) cc_final: 0.8554 (p) outliers start: 32 outliers final: 20 residues processed: 304 average time/residue: 0.5732 time to fit residues: 197.6867 Evaluate side-chains 304 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 213 optimal weight: 0.6980 chunk 151 optimal weight: 0.0670 chunk 81 optimal weight: 0.6980 chunk 226 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 46 optimal weight: 0.0010 chunk 233 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS A 313 GLN B 296 HIS C 296 HIS D 296 HIS D 313 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.070887 restraints weight = 31721.118| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.38 r_work: 0.2775 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20144 Z= 0.128 Angle : 0.601 12.799 27472 Z= 0.295 Chirality : 0.046 0.178 3036 Planarity : 0.004 0.038 3472 Dihedral : 7.447 59.272 3476 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.95 % Allowed : 17.37 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2456 helix: -1.06 (0.88), residues: 24 sheet: 0.87 (0.16), residues: 972 loop : -0.58 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 61 TYR 0.013 0.001 TYR C 252 PHE 0.013 0.001 PHE A 410 TRP 0.012 0.001 TRP A 178 HIS 0.011 0.002 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00283 (20064) covalent geometry : angle 0.58040 (27272) SS BOND : bond 0.00217 ( 40) SS BOND : angle 1.47527 ( 80) hydrogen bonds : bond 0.02858 ( 636) hydrogen bonds : angle 5.84307 ( 1728) link_ALPHA1-3 : bond 0.01581 ( 4) link_ALPHA1-3 : angle 1.64362 ( 12) link_ALPHA1-6 : bond 0.01134 ( 4) link_ALPHA1-6 : angle 1.43084 ( 12) link_BETA1-4 : bond 0.01435 ( 16) link_BETA1-4 : angle 2.91769 ( 48) link_BETA1-6 : bond 0.00846 ( 4) link_BETA1-6 : angle 1.19601 ( 12) link_NAG-ASN : bond 0.00156 ( 12) link_NAG-ASN : angle 1.43167 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 0.725 Fit side-chains REVERT: A 174 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8861 (mm-30) REVERT: B 174 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8857 (mm-30) REVERT: C 174 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8871 (mm-30) REVERT: D 174 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8866 (mm-30) REVERT: E 46 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: E 64 GLN cc_start: 0.8715 (tt0) cc_final: 0.8137 (mt0) REVERT: E 66 ARG cc_start: 0.8739 (mtm110) cc_final: 0.7962 (ttp80) REVERT: F 46 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: F 64 GLN cc_start: 0.8711 (tt0) cc_final: 0.8131 (mt0) REVERT: F 66 ARG cc_start: 0.8747 (mtm110) cc_final: 0.7974 (ttp80) REVERT: G 46 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: G 64 GLN cc_start: 0.8716 (tt0) cc_final: 0.8137 (mt0) REVERT: G 66 ARG cc_start: 0.8744 (mtm110) cc_final: 0.7976 (ttp80) REVERT: H 46 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: H 64 GLN cc_start: 0.8715 (tt0) cc_final: 0.8136 (mt0) REVERT: H 66 ARG cc_start: 0.8746 (mtm110) cc_final: 0.7976 (ttp80) REVERT: I 17 ASP cc_start: 0.8448 (m-30) cc_final: 0.8160 (m-30) REVERT: I 24 ARG cc_start: 0.8402 (ttm110) cc_final: 0.7983 (tpp80) REVERT: I 42 LYS cc_start: 0.8807 (tppp) cc_final: 0.8533 (mmmm) REVERT: I 69 THR cc_start: 0.8799 (m) cc_final: 0.8545 (p) REVERT: J 17 ASP cc_start: 0.8449 (m-30) cc_final: 0.8161 (m-30) REVERT: J 24 ARG cc_start: 0.8398 (ttm110) cc_final: 0.7978 (tpp80) REVERT: J 42 LYS cc_start: 0.8821 (tppp) cc_final: 0.8550 (mmmm) REVERT: J 69 THR cc_start: 0.8807 (m) cc_final: 0.8552 (p) REVERT: K 17 ASP cc_start: 0.8437 (m-30) cc_final: 0.8147 (m-30) REVERT: K 24 ARG cc_start: 0.8397 (ttm110) cc_final: 0.7981 (tpp80) REVERT: K 42 LYS cc_start: 0.8815 (tppp) cc_final: 0.8540 (mmmm) REVERT: K 69 THR cc_start: 0.8797 (m) cc_final: 0.8551 (p) REVERT: L 17 ASP cc_start: 0.8447 (m-30) cc_final: 0.8160 (m-30) REVERT: L 24 ARG cc_start: 0.8388 (ttm110) cc_final: 0.7974 (tpp80) REVERT: L 42 LYS cc_start: 0.8814 (tppp) cc_final: 0.8539 (mmmm) REVERT: L 69 THR cc_start: 0.8805 (m) cc_final: 0.8551 (p) outliers start: 20 outliers final: 8 residues processed: 304 average time/residue: 0.5268 time to fit residues: 182.8311 Evaluate side-chains 288 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 276 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 216 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS A 313 GLN B 296 HIS B 313 GLN C 296 HIS C 313 GLN D 296 HIS D 313 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.068892 restraints weight = 31935.013| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.36 r_work: 0.2723 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20144 Z= 0.208 Angle : 0.636 14.079 27472 Z= 0.311 Chirality : 0.048 0.190 3036 Planarity : 0.004 0.040 3472 Dihedral : 7.413 58.948 3476 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.34 % Allowed : 16.98 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2456 helix: -0.93 (0.90), residues: 24 sheet: 0.87 (0.17), residues: 972 loop : -0.62 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 61 TYR 0.012 0.001 TYR C 252 PHE 0.016 0.002 PHE C 410 TRP 0.014 0.001 TRP C 456 HIS 0.008 0.002 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00484 (20064) covalent geometry : angle 0.61460 (27272) SS BOND : bond 0.00283 ( 40) SS BOND : angle 1.75274 ( 80) hydrogen bonds : bond 0.03148 ( 636) hydrogen bonds : angle 5.91699 ( 1728) link_ALPHA1-3 : bond 0.01590 ( 4) link_ALPHA1-3 : angle 1.65324 ( 12) link_ALPHA1-6 : bond 0.01102 ( 4) link_ALPHA1-6 : angle 1.44945 ( 12) link_BETA1-4 : bond 0.01384 ( 16) link_BETA1-4 : angle 2.93092 ( 48) link_BETA1-6 : bond 0.00772 ( 4) link_BETA1-6 : angle 1.19282 ( 12) link_NAG-ASN : bond 0.00220 ( 12) link_NAG-ASN : angle 1.55843 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6896.55 seconds wall clock time: 118 minutes 23.96 seconds (7103.96 seconds total)