Starting phenix.real_space_refine on Sat Jul 4 10:16:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4p_70110/07_2026/9o4p_70110.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4p_70110/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9o4p_70110/07_2026/9o4p_70110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4p_70110/07_2026/9o4p_70110.map" model { file = "/net/cci-nas-00/data/ceres_data/9o4p_70110/07_2026/9o4p_70110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4p_70110/07_2026/9o4p_70110.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 3.90, per 1000 atoms: 0.20 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: 1.79 Conformation dependent library (CDL) restraints added in 721.6 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: 0.71 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: 4.06 Time building geometry restraints manager: 2.22 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 3.250 nonbonded pdb=" OD1 ASP C 379 " pdb="CA CA C 502 " model vdw 2.226 3.250 nonbonded pdb=" OD1 ASP A 379 " pdb="CA CA A 502 " model vdw 2.226 3.250 nonbonded pdb=" OD1 ASP B 379 " pdb="CA CA B 502 " model vdw 2.226 3.250 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: 11.570 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 17.820 Find NCS groups from input model: 0.470 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 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/Z covalent geometry : bond 0.00568 / 0.24 (20064) covalent geometry : angle 0.87713 / 0.45 (27272) SS BOND : bond 0.00487 / 0.30 ( 40) SS BOND : angle 1.53862 / 1.05 ( 80) hydrogen bonds : bond 0.21124 / 14.64 ( 636) hydrogen bonds : angle 9.56948 / 6.84 ( 1728) link_ALPHA1-3 : bond 0.00725 / 0.34 ( 4) link_ALPHA1-3 : angle 3.31886 / 1.88 ( 12) link_ALPHA1-6 : bond 0.01072 / 0.51 ( 4) link_ALPHA1-6 : angle 2.14220 / 1.20 ( 12) link_BETA1-4 : bond 0.01705 / 1.02 ( 16) link_BETA1-4 : angle 4.86074 / 3.47 ( 48) link_BETA1-6 : bond 0.00705 / 0.33 ( 4) link_BETA1-6 : angle 1.31806 / 0.73 ( 12) link_NAG-ASN : bond 0.00316 / 0.21 ( 12) link_NAG-ASN : angle 2.08244 / 1.25 ( 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 : 0.763 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: 0.5878 time to fit residues: 266.1722 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 : 0.754 ------------------------------------------------------------------------------- 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... 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 = 0.3356 r_free = 0.3356 target = 0.101239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.075205 restraints weight = 31777.228| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.34 r_work: 0.2877 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 20144 Z= 0.181 Angle : 0.686 10.656 27472 Z= 0.352 Chirality : 0.050 0.283 3036 Planarity : 0.005 0.048 3472 Dihedral : 10.960 81.642 3476 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.72 % Allowed : 11.69 % Favored : 86.59 % 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: -0.64 (1.06), residues: 24 sheet: 1.40 (0.16), residues: 984 loop : -0.45 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 61 TYR 0.010 0.002 TYR D 252 PHE 0.022 0.002 PHE A 410 TRP 0.021 0.002 TRP B 456 HIS 0.009 0.002 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (20064) covalent geometry : angle 0.66279 / 0.35 (27272) SS BOND : bond 0.00306 / 0.18 ( 40) SS BOND : angle 1.86525 / 1.29 ( 80) hydrogen bonds : bond 0.04050 / 2.77 ( 636) hydrogen bonds : angle 6.77233 / 4.79 ( 1728) link_ALPHA1-3 : bond 0.01381 / 0.65 ( 4) link_ALPHA1-3 : angle 1.01483 / 0.53 ( 12) link_ALPHA1-6 : bond 0.00875 / 0.41 ( 4) link_ALPHA1-6 : angle 1.27040 / 0.72 ( 12) link_BETA1-4 : bond 0.01894 / 1.15 ( 16) link_BETA1-4 : angle 3.32121 / 2.46 ( 48) link_BETA1-6 : bond 0.00969 / 0.46 ( 4) link_BETA1-6 : angle 1.16280 / 0.66 ( 12) link_NAG-ASN : bond 0.00205 / 0.12 ( 12) link_NAG-ASN : angle 1.75340 / 1.11 ( 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 352 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 316 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8949 (mm-30) REVERT: B 174 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8943 (mm-30) REVERT: C 174 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8951 (mm-30) REVERT: D 174 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8945 (mm-30) REVERT: E 66 ARG cc_start: 0.8752 (mtm110) cc_final: 0.7975 (ttp80) REVERT: F 66 ARG cc_start: 0.8749 (mtm110) cc_final: 0.7966 (ttp80) REVERT: G 66 ARG cc_start: 0.8753 (mtm110) cc_final: 0.7978 (ttp80) REVERT: H 66 ARG cc_start: 0.8759 (mtm110) cc_final: 0.7984 (ttp80) REVERT: I 17 ASP cc_start: 0.8297 (m-30) cc_final: 0.8069 (m-30) REVERT: I 24 ARG cc_start: 0.8492 (ttm110) cc_final: 0.7936 (tpp80) REVERT: J 17 ASP cc_start: 0.8297 (m-30) cc_final: 0.8069 (m-30) REVERT: J 24 ARG cc_start: 0.8514 (ttm110) cc_final: 0.7956 (tpp80) REVERT: K 17 ASP cc_start: 0.8303 (m-30) cc_final: 0.8075 (m-30) REVERT: K 24 ARG cc_start: 0.8514 (ttm110) cc_final: 0.7955 (tpp80) REVERT: L 17 ASP cc_start: 0.8294 (m-30) cc_final: 0.8066 (m-30) REVERT: L 24 ARG cc_start: 0.8505 (ttm110) cc_final: 0.7946 (tpp80) outliers start: 36 outliers final: 12 residues processed: 328 average time/residue: 0.5610 time to fit residues: 209.7814 Evaluate side-chains 312 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 300 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 6.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 chunk 209 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412AHIS ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412AHIS ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.071282 restraints weight = 31904.894| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.35 r_work: 0.2802 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20144 Z= 0.204 Angle : 0.665 12.863 27472 Z= 0.335 Chirality : 0.049 0.201 3036 Planarity : 0.005 0.041 3472 Dihedral : 9.724 64.866 3476 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.10 % Allowed : 14.65 % Favored : 83.25 % 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: 0.34 (0.16), residues: 2456 helix: -0.30 (1.14), residues: 24 sheet: 1.18 (0.16), residues: 992 loop : -0.46 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 103 TYR 0.013 0.002 TYR D 252 PHE 0.019 0.002 PHE D 410 TRP 0.026 0.002 TRP D 456 HIS 0.007 0.002 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (20064) covalent geometry : angle 0.64357 / 0.33 (27272) SS BOND : bond 0.00281 / 0.18 ( 40) SS BOND : angle 1.86376 / 1.27 ( 80) hydrogen bonds : bond 0.03789 / 2.61 ( 636) hydrogen bonds : angle 6.29525 / 4.45 ( 1728) link_ALPHA1-3 : bond 0.01506 / 0.71 ( 4) link_ALPHA1-3 : angle 1.02750 / 0.54 ( 12) link_ALPHA1-6 : bond 0.01050 / 0.50 ( 4) link_ALPHA1-6 : angle 1.44401 / 0.83 ( 12) link_BETA1-4 : bond 0.01522 / 0.92 ( 16) link_BETA1-4 : angle 2.91997 / 2.16 ( 48) link_BETA1-6 : bond 0.00899 / 0.42 ( 4) link_BETA1-6 : angle 1.25067 / 0.71 ( 12) link_NAG-ASN : bond 0.00145 / 0.09 ( 12) link_NAG-ASN : angle 1.65855 / 1.05 ( 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 348 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8849 (mm-30) REVERT: B 174 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8844 (mm-30) REVERT: C 174 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8848 (mm-30) REVERT: D 174 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8846 (mm-30) REVERT: E 46 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: E 64 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: E 66 ARG cc_start: 0.8815 (mtm110) cc_final: 0.7995 (ttp80) REVERT: F 46 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: F 64 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: F 66 ARG cc_start: 0.8819 (mtm110) cc_final: 0.8004 (ttp80) REVERT: G 46 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: G 64 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: G 66 ARG cc_start: 0.8813 (mtm110) cc_final: 0.7990 (ttp80) REVERT: H 46 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: H 64 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: H 66 ARG cc_start: 0.8818 (mtm110) cc_final: 0.8006 (ttp80) REVERT: I 17 ASP cc_start: 0.8414 (m-30) cc_final: 0.8152 (m-30) REVERT: I 24 ARG cc_start: 0.8501 (ttm110) cc_final: 0.7929 (tpp80) REVERT: I 42 LYS cc_start: 0.8742 (tppp) cc_final: 0.8458 (mmmm) REVERT: J 17 ASP cc_start: 0.8412 (m-30) cc_final: 0.8149 (m-30) REVERT: J 24 ARG cc_start: 0.8528 (ttm110) cc_final: 0.7950 (tpp80) REVERT: J 42 LYS cc_start: 0.8748 (tppp) cc_final: 0.8467 (mmmm) REVERT: K 17 ASP cc_start: 0.8408 (m-30) cc_final: 0.8145 (m-30) REVERT: K 24 ARG cc_start: 0.8514 (ttm110) cc_final: 0.7938 (tpp80) REVERT: K 42 LYS cc_start: 0.8743 (tppp) cc_final: 0.8462 (mmmm) REVERT: L 17 ASP cc_start: 0.8407 (m-30) cc_final: 0.8143 (m-30) REVERT: L 24 ARG cc_start: 0.8518 (ttm110) cc_final: 0.7944 (tpp80) REVERT: L 42 LYS cc_start: 0.8749 (tppp) cc_final: 0.8465 (mmmm) outliers start: 44 outliers final: 8 residues processed: 324 average time/residue: 0.5638 time to fit residues: 208.5294 Evaluate side-chains 304 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 0.5980 chunk 189 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS C 296 HIS D 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.067070 restraints weight = 31976.149| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.38 r_work: 0.2732 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 20144 Z= 0.291 Angle : 0.694 15.418 27472 Z= 0.345 Chirality : 0.051 0.221 3036 Planarity : 0.005 0.040 3472 Dihedral : 9.287 59.548 3476 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.67 % Allowed : 14.84 % Favored : 82.49 % 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: 0.08 (0.16), residues: 2456 helix: -0.60 (1.00), residues: 24 sheet: 0.96 (0.17), residues: 992 loop : -0.59 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 103 TYR 0.013 0.002 TYR A 273 PHE 0.021 0.002 PHE C 410 TRP 0.026 0.002 TRP C 456 HIS 0.006 0.002 HIS D 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.29 (20064) covalent geometry : angle 0.67345 / 0.34 (27272) SS BOND : bond 0.00440 / 0.27 ( 40) SS BOND : angle 1.73957 / 1.16 ( 80) hydrogen bonds : bond 0.03801 / 2.62 ( 636) hydrogen bonds : angle 6.26032 / 4.43 ( 1728) link_ALPHA1-3 : bond 0.01484 / 0.70 ( 4) link_ALPHA1-3 : angle 1.18870 / 0.62 ( 12) link_ALPHA1-6 : bond 0.01052 / 0.50 ( 4) link_ALPHA1-6 : angle 1.52198 / 0.87 ( 12) link_BETA1-4 : bond 0.01451 / 0.88 ( 16) link_BETA1-4 : angle 2.98960 / 2.21 ( 48) link_BETA1-6 : bond 0.00870 / 0.41 ( 4) link_BETA1-6 : angle 1.23317 / 0.71 ( 12) link_NAG-ASN : bond 0.00261 / 0.16 ( 12) link_NAG-ASN : angle 1.85643 / 1.19 ( 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 348 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8864 (mm-30) REVERT: B 174 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8861 (mm-30) REVERT: C 174 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8866 (mm-30) REVERT: D 174 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8866 (mm-30) REVERT: E 46 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: E 64 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: E 66 ARG cc_start: 0.8777 (mtm110) cc_final: 0.8007 (ttp80) REVERT: F 46 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: F 64 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: F 66 ARG cc_start: 0.8783 (mtm110) cc_final: 0.8013 (ttp80) REVERT: G 46 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: G 64 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: G 66 ARG cc_start: 0.8769 (mtm110) cc_final: 0.7993 (ttp80) REVERT: H 46 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: H 64 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: H 66 ARG cc_start: 0.8784 (mtm110) cc_final: 0.8017 (ttp80) REVERT: I 17 ASP cc_start: 0.8403 (m-30) cc_final: 0.8110 (m-30) REVERT: I 42 LYS cc_start: 0.8762 (tppp) cc_final: 0.8474 (mmmm) REVERT: I 45 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8496 (ptpt) REVERT: J 17 ASP cc_start: 0.8399 (m-30) cc_final: 0.8106 (m-30) REVERT: J 42 LYS cc_start: 0.8774 (tppp) cc_final: 0.8491 (mmmm) REVERT: J 45 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8494 (ptpt) REVERT: K 17 ASP cc_start: 0.8391 (m-30) cc_final: 0.8097 (m-30) REVERT: K 42 LYS cc_start: 0.8767 (tppp) cc_final: 0.8482 (mmmm) REVERT: K 45 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8496 (ptpt) REVERT: L 17 ASP cc_start: 0.8398 (m-30) cc_final: 0.8104 (m-30) REVERT: L 42 LYS cc_start: 0.8776 (tppp) cc_final: 0.8487 (mmmm) REVERT: L 45 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8491 (ptpt) outliers start: 56 outliers final: 19 residues processed: 316 average time/residue: 0.5656 time to fit residues: 205.0278 Evaluate side-chains 305 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 206 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 229 optimal weight: 0.2980 chunk 196 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3273 r_free = 0.3273 target = 0.096705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.069893 restraints weight = 31867.959| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.38 r_work: 0.2772 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20144 Z= 0.175 Angle : 0.642 14.409 27472 Z= 0.316 Chirality : 0.048 0.209 3036 Planarity : 0.004 0.041 3472 Dihedral : 8.967 59.995 3476 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.67 % Allowed : 15.41 % Favored : 81.92 % 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 (0.16), residues: 2456 helix: -0.81 (0.93), residues: 24 sheet: 0.94 (0.17), residues: 968 loop : -0.69 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 103 TYR 0.013 0.001 TYR A 252 PHE 0.017 0.001 PHE A 410 TRP 0.016 0.001 TRP C 456 HIS 0.008 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (20064) covalent geometry : angle 0.62057 / 0.31 (27272) SS BOND : bond 0.00289 / 0.20 ( 40) SS BOND : angle 1.65503 / 1.10 ( 80) hydrogen bonds : bond 0.03270 / 2.27 ( 636) hydrogen bonds : angle 6.05431 / 4.28 ( 1728) link_ALPHA1-3 : bond 0.01604 / 0.76 ( 4) link_ALPHA1-3 : angle 1.30332 / 0.69 ( 12) link_ALPHA1-6 : bond 0.01110 / 0.52 ( 4) link_ALPHA1-6 : angle 1.50334 / 0.86 ( 12) link_BETA1-4 : bond 0.01439 / 0.87 ( 16) link_BETA1-4 : angle 2.95034 / 2.19 ( 48) link_BETA1-6 : bond 0.00887 / 0.42 ( 4) link_BETA1-6 : angle 1.19907 / 0.67 ( 12) link_NAG-ASN : bond 0.00204 / 0.12 ( 12) link_NAG-ASN : angle 1.68359 / 1.07 ( 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 339 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 283 time to evaluate : 0.772 Fit side-chains REVERT: A 174 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8874 (mm-30) REVERT: B 174 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8868 (mm-30) REVERT: C 174 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8869 (mm-30) REVERT: D 174 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8872 (mm-30) REVERT: E 12 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.7997 (mtpt) REVERT: E 46 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7673 (tm-30) REVERT: E 64 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: E 66 ARG cc_start: 0.8784 (mtm110) cc_final: 0.8017 (ttp80) REVERT: F 12 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.7999 (mtpt) REVERT: F 46 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7676 (tm-30) REVERT: F 64 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: F 66 ARG cc_start: 0.8795 (mtm110) cc_final: 0.8034 (ttp80) REVERT: G 12 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8002 (mtpt) REVERT: G 46 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7662 (tm-30) REVERT: G 64 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: G 66 ARG cc_start: 0.8786 (mtm110) cc_final: 0.8018 (ttp80) REVERT: H 12 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8002 (mtpt) REVERT: H 46 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7667 (tm-30) REVERT: H 64 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8057 (mt0) REVERT: H 66 ARG cc_start: 0.8787 (mtm110) cc_final: 0.8026 (ttp80) REVERT: I 17 ASP cc_start: 0.8419 (m-30) cc_final: 0.8129 (m-30) REVERT: I 24 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7945 (tpp80) REVERT: I 32 TYR cc_start: 0.8470 (m-80) cc_final: 0.8254 (m-80) REVERT: I 42 LYS cc_start: 0.8790 (tppp) cc_final: 0.8503 (mmmm) REVERT: I 45 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8501 (ptpt) REVERT: I 69 THR cc_start: 0.8875 (m) cc_final: 0.8577 (p) REVERT: J 17 ASP cc_start: 0.8417 (m-30) cc_final: 0.8127 (m-30) REVERT: J 24 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7946 (tpp80) REVERT: J 32 TYR cc_start: 0.8486 (m-80) cc_final: 0.8270 (m-80) REVERT: J 42 LYS cc_start: 0.8803 (tppp) cc_final: 0.8519 (mmmm) REVERT: J 45 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8495 (ptpt) REVERT: J 69 THR cc_start: 0.8883 (m) cc_final: 0.8585 (p) REVERT: K 17 ASP cc_start: 0.8406 (m-30) cc_final: 0.8115 (m-30) REVERT: K 24 ARG cc_start: 0.8434 (ttm110) cc_final: 0.7939 (tpp80) REVERT: K 32 TYR cc_start: 0.8493 (m-80) cc_final: 0.8275 (m-80) REVERT: K 42 LYS cc_start: 0.8794 (tppp) cc_final: 0.8507 (mmmm) REVERT: K 45 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8505 (ptpt) REVERT: K 69 THR cc_start: 0.8880 (m) cc_final: 0.8587 (p) REVERT: L 17 ASP cc_start: 0.8412 (m-30) cc_final: 0.8121 (m-30) REVERT: L 24 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7950 (tpp80) REVERT: L 32 TYR cc_start: 0.8470 (m-80) cc_final: 0.8253 (m-80) REVERT: L 42 LYS cc_start: 0.8799 (tppp) cc_final: 0.8509 (mmmm) REVERT: L 45 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8496 (ptpt) REVERT: L 69 THR cc_start: 0.8881 (m) cc_final: 0.8576 (p) outliers start: 56 outliers final: 20 residues processed: 315 average time/residue: 0.5503 time to fit residues: 198.6211 Evaluate side-chains 312 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 12 LYS Chi-restraints excluded: chain E residue 51 ILE 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 51 ILE 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 51 ILE 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 51 ILE 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 45 LYS Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain L residue 10 PHE 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: 0.8980 chunk 148 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 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: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3287 r_free = 0.3287 target = 0.097598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.070814 restraints weight = 31439.138| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.37 r_work: 0.2774 rms_B_bonded: 2.35 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: 0.8918 moved from start: 0.2795 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= 0.160 Angle : 0.614 13.124 27472 Z= 0.302 Chirality : 0.047 0.202 3036 Planarity : 0.004 0.041 3472 Dihedral : 8.365 59.504 3476 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.62 % Allowed : 15.46 % Favored : 81.92 % 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 (0.17), residues: 2456 helix: -1.00 (0.90), residues: 24 sheet: 0.91 (0.17), residues: 976 loop : -0.66 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 364 TYR 0.013 0.001 TYR D 252 PHE 0.015 0.001 PHE A 410 TRP 0.013 0.001 TRP D 456 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (20064) covalent geometry : angle 0.59415 / 0.30 (27272) SS BOND : bond 0.00238 / 0.16 ( 40) SS BOND : angle 1.43402 / 0.95 ( 80) hydrogen bonds : bond 0.03071 / 2.12 ( 636) hydrogen bonds : angle 5.90751 / 4.17 ( 1728) link_ALPHA1-3 : bond 0.01703 / 0.80 ( 4) link_ALPHA1-3 : angle 1.40797 / 0.75 ( 12) link_ALPHA1-6 : bond 0.01160 / 0.55 ( 4) link_ALPHA1-6 : angle 1.47818 / 0.85 ( 12) link_BETA1-4 : bond 0.01452 / 0.88 ( 16) link_BETA1-4 : angle 2.92419 / 2.17 ( 48) link_BETA1-6 : bond 0.00856 / 0.40 ( 4) link_BETA1-6 : angle 1.19884 / 0.67 ( 12) link_NAG-ASN : bond 0.00181 / 0.11 ( 12) link_NAG-ASN : angle 1.51650 / 0.96 ( 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 348 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 293 time to evaluate : 0.536 Fit side-chains REVERT: A 174 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8869 (mm-30) REVERT: B 174 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8868 (mm-30) REVERT: C 174 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8875 (mm-30) REVERT: D 174 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8871 (mm-30) REVERT: E 12 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.7990 (mtpt) REVERT: E 46 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: E 64 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8077 (mt0) REVERT: E 66 ARG cc_start: 0.8786 (mtm110) cc_final: 0.8002 (ttp80) REVERT: F 12 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8001 (mtpt) REVERT: F 46 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: F 64 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: F 66 ARG cc_start: 0.8789 (mtm110) cc_final: 0.8010 (ttp80) REVERT: G 12 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.7999 (mtpt) REVERT: G 46 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: G 64 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: G 66 ARG cc_start: 0.8782 (mtm110) cc_final: 0.8001 (ttp80) REVERT: H 12 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.7986 (mtpt) REVERT: H 46 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: H 64 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: H 66 ARG cc_start: 0.8782 (mtm110) cc_final: 0.8004 (ttp80) REVERT: I 17 ASP cc_start: 0.8472 (m-30) cc_final: 0.8181 (m-30) REVERT: I 24 ARG cc_start: 0.8448 (ttm110) cc_final: 0.7966 (tpp80) REVERT: I 42 LYS cc_start: 0.8811 (tppp) cc_final: 0.8523 (mmmm) REVERT: I 69 THR cc_start: 0.8828 (m) cc_final: 0.8563 (p) REVERT: J 17 ASP cc_start: 0.8472 (m-30) cc_final: 0.8182 (m-30) REVERT: J 24 ARG cc_start: 0.8434 (ttm110) cc_final: 0.7953 (tpp80) REVERT: J 42 LYS cc_start: 0.8827 (tppp) cc_final: 0.8544 (mmmm) REVERT: J 69 THR cc_start: 0.8833 (m) cc_final: 0.8570 (p) REVERT: K 17 ASP cc_start: 0.8454 (m-30) cc_final: 0.8163 (m-30) REVERT: K 24 ARG cc_start: 0.8431 (ttm110) cc_final: 0.7956 (tpp80) REVERT: K 42 LYS cc_start: 0.8817 (tppp) cc_final: 0.8529 (mmmm) REVERT: K 69 THR cc_start: 0.8835 (m) cc_final: 0.8575 (p) REVERT: L 17 ASP cc_start: 0.8459 (m-30) cc_final: 0.8166 (m-30) REVERT: L 24 ARG cc_start: 0.8439 (ttm110) cc_final: 0.7961 (tpp80) REVERT: L 42 LYS cc_start: 0.8812 (tppp) cc_final: 0.8521 (mmmm) REVERT: L 69 THR cc_start: 0.8838 (m) cc_final: 0.8572 (p) outliers start: 55 outliers final: 12 residues processed: 320 average time/residue: 0.5193 time to fit residues: 190.2462 Evaluate side-chains 300 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 106 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 412AHIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.069929 restraints weight = 31717.361| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.39 r_work: 0.2758 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20144 Z= 0.199 Angle : 0.632 13.946 27472 Z= 0.310 Chirality : 0.048 0.199 3036 Planarity : 0.004 0.039 3472 Dihedral : 8.145 59.407 3476 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.96 % Allowed : 15.79 % Favored : 82.25 % 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: 0.00 (0.17), residues: 2456 helix: -0.93 (0.90), residues: 24 sheet: 0.95 (0.17), residues: 972 loop : -0.66 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 300 TYR 0.012 0.001 TYR C 252 PHE 0.016 0.002 PHE C 410 TRP 0.013 0.001 TRP D 456 HIS 0.013 0.002 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (20064) covalent geometry : angle 0.61087 / 0.30 (27272) SS BOND : bond 0.00273 / 0.18 ( 40) SS BOND : angle 1.73519 / 1.15 ( 80) hydrogen bonds : bond 0.03144 / 2.18 ( 636) hydrogen bonds : angle 5.94584 / 4.21 ( 1728) link_ALPHA1-3 : bond 0.01660 / 0.78 ( 4) link_ALPHA1-3 : angle 1.49163 / 0.79 ( 12) link_ALPHA1-6 : bond 0.01114 / 0.53 ( 4) link_ALPHA1-6 : angle 1.49896 / 0.86 ( 12) link_BETA1-4 : bond 0.01404 / 0.85 ( 16) link_BETA1-4 : angle 2.93069 / 2.18 ( 48) link_BETA1-6 : bond 0.00825 / 0.39 ( 4) link_BETA1-6 : angle 1.19195 / 0.67 ( 12) link_NAG-ASN : bond 0.00198 / 0.12 ( 12) link_NAG-ASN : angle 1.56816 / 0.99 ( 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 325 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 0.743 Fit side-chains REVERT: A 174 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8872 (mm-30) REVERT: B 174 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8873 (mm-30) REVERT: C 174 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8880 (mm-30) REVERT: D 174 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8870 (mm-30) REVERT: E 12 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.7996 (mtpt) REVERT: E 46 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: E 64 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: E 66 ARG cc_start: 0.8757 (mtm110) cc_final: 0.7967 (ttp80) REVERT: F 12 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8000 (mtpt) REVERT: F 46 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: F 64 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: F 66 ARG cc_start: 0.8758 (mtm110) cc_final: 0.7971 (ttp80) REVERT: G 12 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8006 (mtpt) REVERT: G 46 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: G 64 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: G 66 ARG cc_start: 0.8753 (mtm110) cc_final: 0.7969 (ttp80) REVERT: H 12 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: H 46 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: H 64 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: H 66 ARG cc_start: 0.8762 (mtm110) cc_final: 0.7983 (ttp80) REVERT: I 17 ASP cc_start: 0.8486 (m-30) cc_final: 0.8193 (m-30) REVERT: I 24 ARG cc_start: 0.8428 (ttm110) cc_final: 0.7930 (tpp80) REVERT: I 42 LYS cc_start: 0.8808 (tppp) cc_final: 0.8520 (mmmm) REVERT: I 69 THR cc_start: 0.8822 (m) cc_final: 0.8554 (p) REVERT: J 17 ASP cc_start: 0.8485 (m-30) cc_final: 0.8192 (m-30) REVERT: J 24 ARG cc_start: 0.8429 (ttm110) cc_final: 0.7931 (tpp80) REVERT: J 42 LYS cc_start: 0.8824 (tppp) cc_final: 0.8541 (mmmm) REVERT: J 69 THR cc_start: 0.8828 (m) cc_final: 0.8561 (p) REVERT: K 17 ASP cc_start: 0.8473 (m-30) cc_final: 0.8180 (m-30) REVERT: K 24 ARG cc_start: 0.8417 (ttm110) cc_final: 0.7924 (tpp80) REVERT: K 42 LYS cc_start: 0.8816 (tppp) cc_final: 0.8531 (mmmm) REVERT: K 69 THR cc_start: 0.8822 (m) cc_final: 0.8558 (p) REVERT: L 17 ASP cc_start: 0.8476 (m-30) cc_final: 0.8182 (m-30) REVERT: L 24 ARG cc_start: 0.8422 (ttm110) cc_final: 0.7928 (tpp80) REVERT: L 42 LYS cc_start: 0.8817 (tppp) cc_final: 0.8529 (mmmm) REVERT: L 69 THR cc_start: 0.8831 (m) cc_final: 0.8558 (p) outliers start: 41 outliers final: 12 residues processed: 305 average time/residue: 0.5456 time to fit residues: 189.6008 Evaluate side-chains 296 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 0 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 224 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 51 optimal weight: 0.1980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3273 r_free = 0.3273 target = 0.096806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.070010 restraints weight = 31507.518| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.37 r_work: 0.2769 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20144 Z= 0.186 Angle : 0.625 13.559 27472 Z= 0.307 Chirality : 0.048 0.187 3036 Planarity : 0.004 0.038 3472 Dihedral : 7.743 59.471 3476 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.91 % Allowed : 16.17 % Favored : 81.92 % 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: 0.00 (0.17), residues: 2456 helix: -0.96 (0.90), residues: 24 sheet: 0.91 (0.17), residues: 972 loop : -0.63 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 61 TYR 0.012 0.001 TYR D 252 PHE 0.016 0.002 PHE C 410 TRP 0.012 0.001 TRP A 456 HIS 0.006 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (20064) covalent geometry : angle 0.60418 / 0.30 (27272) SS BOND : bond 0.00304 / 0.20 ( 40) SS BOND : angle 1.62762 / 1.09 ( 80) hydrogen bonds : bond 0.03099 / 2.15 ( 636) hydrogen bonds : angle 5.94357 / 4.21 ( 1728) link_ALPHA1-3 : bond 0.01628 / 0.77 ( 4) link_ALPHA1-3 : angle 1.64447 / 0.88 ( 12) link_ALPHA1-6 : bond 0.01119 / 0.53 ( 4) link_ALPHA1-6 : angle 1.47515 / 0.84 ( 12) link_BETA1-4 : bond 0.01398 / 0.85 ( 16) link_BETA1-4 : angle 2.94368 / 2.19 ( 48) link_BETA1-6 : bond 0.00818 / 0.39 ( 4) link_BETA1-6 : angle 1.18439 / 0.67 ( 12) link_NAG-ASN : bond 0.00193 / 0.12 ( 12) link_NAG-ASN : angle 1.54719 / 0.98 ( 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 328 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 0.787 Fit side-chains REVERT: A 174 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8858 (mm-30) REVERT: B 174 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8854 (mm-30) REVERT: C 174 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8889 (mm-30) REVERT: D 174 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8870 (mm-30) REVERT: E 12 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.7972 (mtpt) REVERT: E 46 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: E 64 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: E 66 ARG cc_start: 0.8725 (mtm110) cc_final: 0.7923 (ttp80) REVERT: F 12 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.7970 (mtpt) REVERT: F 46 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: F 64 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: F 66 ARG cc_start: 0.8728 (mtm110) cc_final: 0.7931 (ttp80) REVERT: G 12 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7974 (mtpt) REVERT: G 46 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: G 64 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: G 66 ARG cc_start: 0.8718 (mtm110) cc_final: 0.7921 (ttp80) REVERT: H 12 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.7962 (mtpt) REVERT: H 46 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: H 64 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8114 (mt0) REVERT: H 66 ARG cc_start: 0.8725 (mtm110) cc_final: 0.7934 (ttp80) REVERT: I 17 ASP cc_start: 0.8443 (m-30) cc_final: 0.8158 (m-30) REVERT: I 24 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7891 (tpp80) REVERT: I 42 LYS cc_start: 0.8803 (tppp) cc_final: 0.8521 (mmmm) REVERT: I 69 THR cc_start: 0.8810 (m) cc_final: 0.8540 (p) REVERT: J 17 ASP cc_start: 0.8441 (m-30) cc_final: 0.8158 (m-30) REVERT: J 24 ARG cc_start: 0.8396 (ttm110) cc_final: 0.7900 (tpp80) REVERT: J 42 LYS cc_start: 0.8812 (tppp) cc_final: 0.8534 (mmmm) REVERT: J 69 THR cc_start: 0.8811 (m) cc_final: 0.8543 (p) REVERT: K 17 ASP cc_start: 0.8424 (m-30) cc_final: 0.8137 (m-30) REVERT: K 24 ARG cc_start: 0.8388 (ttm110) cc_final: 0.7896 (tpp80) REVERT: K 42 LYS cc_start: 0.8803 (tppp) cc_final: 0.8522 (mmmm) REVERT: K 69 THR cc_start: 0.8814 (m) cc_final: 0.8548 (p) REVERT: L 17 ASP cc_start: 0.8432 (m-30) cc_final: 0.8148 (m-30) REVERT: L 24 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7893 (tpp80) REVERT: L 42 LYS cc_start: 0.8810 (tppp) cc_final: 0.8527 (mmmm) REVERT: L 69 THR cc_start: 0.8816 (m) cc_final: 0.8543 (p) outliers start: 40 outliers final: 16 residues processed: 304 average time/residue: 0.5509 time to fit residues: 191.2852 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 : 0.761 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain I residue 10 PHE Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 10 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 66 optimal weight: 0.0070 chunk 101 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 120 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 188 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN J 6 GLN K 6 GLN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.071961 restraints weight = 30773.614| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.36 r_work: 0.2803 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20144 Z= 0.118 Angle : 0.593 12.296 27472 Z= 0.292 Chirality : 0.046 0.180 3036 Planarity : 0.004 0.038 3472 Dihedral : 7.453 59.263 3476 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.00 % Allowed : 16.89 % Favored : 82.11 % 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: 0.00 (0.17), residues: 2456 helix: -1.00 (0.91), residues: 24 sheet: 0.90 (0.17), residues: 972 loop : -0.61 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 61 TYR 0.013 0.001 TYR D 252 PHE 0.012 0.001 PHE C 410 TRP 0.011 0.001 TRP D 178 HIS 0.017 0.002 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (20064) covalent geometry : angle 0.57378 / 0.29 (27272) SS BOND : bond 0.00183 / 0.11 ( 40) SS BOND : angle 1.34986 / 0.91 ( 80) hydrogen bonds : bond 0.02783 / 1.93 ( 636) hydrogen bonds : angle 5.78947 / 4.09 ( 1728) link_ALPHA1-3 : bond 0.01661 / 0.78 ( 4) link_ALPHA1-3 : angle 1.69957 / 0.92 ( 12) link_ALPHA1-6 : bond 0.01156 / 0.55 ( 4) link_ALPHA1-6 : angle 1.42293 / 0.81 ( 12) link_BETA1-4 : bond 0.01436 / 0.87 ( 16) link_BETA1-4 : angle 2.90196 / 2.16 ( 48) link_BETA1-6 : bond 0.00845 / 0.40 ( 4) link_BETA1-6 : angle 1.19504 / 0.66 ( 12) link_NAG-ASN : bond 0.00139 / 0.08 ( 12) link_NAG-ASN : angle 1.39752 / 0.88 ( 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 312 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 291 time to evaluate : 0.776 Fit side-chains REVERT: A 174 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8876 (mm-30) REVERT: B 174 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8876 (mm-30) REVERT: C 174 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8879 (mm-30) REVERT: D 174 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8868 (mm-30) REVERT: E 12 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.7982 (mtpt) REVERT: E 46 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: E 64 GLN cc_start: 0.8710 (tt0) cc_final: 0.8132 (mt0) REVERT: E 66 ARG cc_start: 0.8735 (mtm110) cc_final: 0.7938 (ttp80) REVERT: F 12 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.7993 (mtpt) REVERT: F 46 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: F 64 GLN cc_start: 0.8696 (tt0) cc_final: 0.8113 (mt0) REVERT: F 66 ARG cc_start: 0.8735 (mtm110) cc_final: 0.7942 (ttp80) REVERT: G 12 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.7998 (mtpt) REVERT: G 46 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: G 64 GLN cc_start: 0.8700 (tt0) cc_final: 0.8117 (mt0) REVERT: G 66 ARG cc_start: 0.8726 (mtm110) cc_final: 0.7934 (ttp80) REVERT: H 12 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.7987 (mtpt) REVERT: H 46 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: H 64 GLN cc_start: 0.8698 (tt0) cc_final: 0.8115 (mt0) REVERT: H 66 ARG cc_start: 0.8727 (mtm110) cc_final: 0.7932 (ttp80) REVERT: I 17 ASP cc_start: 0.8450 (m-30) cc_final: 0.8162 (m-30) REVERT: I 24 ARG cc_start: 0.8400 (ttm110) cc_final: 0.7946 (tpp80) REVERT: I 42 LYS cc_start: 0.8810 (tppp) cc_final: 0.8536 (mmmm) REVERT: I 69 THR cc_start: 0.8805 (m) cc_final: 0.8547 (p) REVERT: J 17 ASP cc_start: 0.8448 (m-30) cc_final: 0.8159 (m-30) REVERT: J 24 ARG cc_start: 0.8408 (ttm110) cc_final: 0.7951 (tpp80) REVERT: J 42 LYS cc_start: 0.8813 (tppp) cc_final: 0.8544 (mmmm) REVERT: J 69 THR cc_start: 0.8811 (m) cc_final: 0.8555 (p) REVERT: K 17 ASP cc_start: 0.8432 (m-30) cc_final: 0.8141 (m-30) REVERT: K 24 ARG cc_start: 0.8403 (ttm110) cc_final: 0.7952 (tpp80) REVERT: K 42 LYS cc_start: 0.8810 (tppp) cc_final: 0.8535 (mmmm) REVERT: K 69 THR cc_start: 0.8808 (m) cc_final: 0.8563 (p) REVERT: L 17 ASP cc_start: 0.8435 (m-30) cc_final: 0.8145 (m-30) REVERT: L 24 ARG cc_start: 0.8412 (ttm110) cc_final: 0.7958 (tpp80) REVERT: L 42 LYS cc_start: 0.8811 (tppp) cc_final: 0.8535 (mmmm) REVERT: L 69 THR cc_start: 0.8808 (m) cc_final: 0.8551 (p) outliers start: 21 outliers final: 13 residues processed: 300 average time/residue: 0.5200 time to fit residues: 178.9571 Evaluate side-chains 293 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 272 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 296 HIS 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 12 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 10 PHE Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 10 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 213 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3274 r_free = 0.3274 target = 0.096120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.069027 restraints weight = 31342.239| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.38 r_work: 0.2765 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20144 Z= 0.205 Angle : 0.630 13.648 27472 Z= 0.309 Chirality : 0.048 0.187 3036 Planarity : 0.004 0.039 3472 Dihedral : 7.416 58.936 3476 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.95 % Allowed : 16.79 % Favored : 82.25 % 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: -0.92 (0.90), residues: 24 sheet: 0.92 (0.17), residues: 972 loop : -0.62 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 61 TYR 0.012 0.001 TYR B 252 PHE 0.016 0.002 PHE C 410 TRP 0.013 0.001 TRP B 456 HIS 0.009 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (20064) covalent geometry : angle 0.60863 / 0.30 (27272) SS BOND : bond 0.00271 / 0.18 ( 40) SS BOND : angle 1.69448 / 1.13 ( 80) hydrogen bonds : bond 0.03086 / 2.14 ( 636) hydrogen bonds : angle 5.85224 / 4.15 ( 1728) link_ALPHA1-3 : bond 0.01573 / 0.74 ( 4) link_ALPHA1-3 : angle 1.65475 / 0.88 ( 12) link_ALPHA1-6 : bond 0.01117 / 0.53 ( 4) link_ALPHA1-6 : angle 1.45069 / 0.83 ( 12) link_BETA1-4 : bond 0.01356 / 0.82 ( 16) link_BETA1-4 : angle 2.90229 / 2.16 ( 48) link_BETA1-6 : bond 0.00779 / 0.37 ( 4) link_BETA1-6 : angle 1.17301 / 0.66 ( 12) link_NAG-ASN : bond 0.00198 / 0.12 ( 12) link_NAG-ASN : angle 1.50167 / 0.95 ( 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 296 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 276 time to evaluate : 0.762 Fit side-chains REVERT: A 174 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8852 (mm-30) REVERT: B 174 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8859 (mm-30) REVERT: C 174 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8861 (mm-30) REVERT: D 174 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8851 (mm-30) REVERT: E 12 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.7968 (mtpt) REVERT: E 46 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: E 64 GLN cc_start: 0.8698 (tt0) cc_final: 0.8110 (mt0) REVERT: E 66 ARG cc_start: 0.8697 (mtm110) cc_final: 0.7881 (ttp80) REVERT: F 12 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.7963 (mtpt) REVERT: F 46 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: F 64 GLN cc_start: 0.8694 (tt0) cc_final: 0.8105 (mt0) REVERT: F 66 ARG cc_start: 0.8696 (mtm110) cc_final: 0.7886 (ttp80) REVERT: G 12 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.7971 (mtpt) REVERT: G 46 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: G 64 GLN cc_start: 0.8691 (tt0) cc_final: 0.8100 (mt0) REVERT: G 66 ARG cc_start: 0.8688 (mtm110) cc_final: 0.7878 (ttp80) REVERT: H 12 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.7966 (mtpt) REVERT: H 46 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: H 64 GLN cc_start: 0.8699 (tt0) cc_final: 0.8111 (mt0) REVERT: H 66 ARG cc_start: 0.8693 (mtm110) cc_final: 0.7885 (ttp80) REVERT: I 17 ASP cc_start: 0.8422 (m-30) cc_final: 0.8136 (m-30) REVERT: I 24 ARG cc_start: 0.8373 (ttm110) cc_final: 0.7887 (tpp80) REVERT: I 42 LYS cc_start: 0.8782 (tppp) cc_final: 0.8509 (mmmm) REVERT: I 69 THR cc_start: 0.8763 (m) cc_final: 0.8492 (p) REVERT: J 17 ASP cc_start: 0.8424 (m-30) cc_final: 0.8137 (m-30) REVERT: J 24 ARG cc_start: 0.8376 (ttm110) cc_final: 0.7891 (tpp80) REVERT: J 42 LYS cc_start: 0.8791 (tppp) cc_final: 0.8521 (mmmm) REVERT: J 69 THR cc_start: 0.8767 (m) cc_final: 0.8493 (p) REVERT: K 17 ASP cc_start: 0.8411 (m-30) cc_final: 0.8124 (m-30) REVERT: K 24 ARG cc_start: 0.8372 (ttm110) cc_final: 0.7890 (tpp80) REVERT: K 42 LYS cc_start: 0.8784 (tppp) cc_final: 0.8510 (mmmm) REVERT: K 69 THR cc_start: 0.8765 (m) cc_final: 0.8502 (p) REVERT: L 17 ASP cc_start: 0.8413 (m-30) cc_final: 0.8127 (m-30) REVERT: L 24 ARG cc_start: 0.8374 (ttm110) cc_final: 0.7892 (tpp80) REVERT: L 42 LYS cc_start: 0.8788 (tppp) cc_final: 0.8514 (mmmm) REVERT: L 69 THR cc_start: 0.8771 (m) cc_final: 0.8500 (p) outliers start: 20 outliers final: 11 residues processed: 288 average time/residue: 0.5706 time to fit residues: 188.0501 Evaluate side-chains 291 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 272 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 336 CYS 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 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 336 CYS Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 12 LYS 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: 1.9990 chunk 76 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 14 optimal weight: 0.2980 chunk 168 optimal weight: 0.1980 chunk 211 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS A 313 GLN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS D 296 HIS D 313 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.070899 restraints weight = 31484.278| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.40 r_work: 0.2800 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20144 Z= 0.130 Angle : 0.599 12.553 27472 Z= 0.295 Chirality : 0.046 0.170 3036 Planarity : 0.004 0.038 3472 Dihedral : 7.276 58.826 3476 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.34 % Allowed : 16.60 % 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: -0.01 (0.17), residues: 2456 helix: -1.03 (0.90), residues: 24 sheet: 0.84 (0.16), residues: 972 loop : -0.58 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 61 TYR 0.013 0.001 TYR B 252 PHE 0.013 0.001 PHE D 410 TRP 0.012 0.001 TRP B 178 HIS 0.024 0.002 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (20064) covalent geometry : angle 0.57943 / 0.29 (27272) SS BOND : bond 0.00185 / 0.12 ( 40) SS BOND : angle 1.37225 / 0.93 ( 80) hydrogen bonds : bond 0.02811 / 1.95 ( 636) hydrogen bonds : angle 5.76692 / 4.08 ( 1728) link_ALPHA1-3 : bond 0.01684 / 0.80 ( 4) link_ALPHA1-3 : angle 1.69223 / 0.91 ( 12) link_ALPHA1-6 : bond 0.01112 / 0.53 ( 4) link_ALPHA1-6 : angle 1.42452 / 0.81 ( 12) link_BETA1-4 : bond 0.01418 / 0.85 ( 16) link_BETA1-4 : angle 2.88099 / 2.14 ( 48) link_BETA1-6 : bond 0.00888 / 0.42 ( 4) link_BETA1-6 : angle 1.20574 / 0.67 ( 12) link_NAG-ASN : bond 0.00145 / 0.09 ( 12) link_NAG-ASN : angle 1.42193 / 0.90 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6953.51 seconds wall clock time: 119 minutes 38.66 seconds (7178.66 seconds total)