Starting phenix.real_space_refine on Thu Sep 18 05:41:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyx_60582/09_2025/8zyx_60582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyx_60582/09_2025/8zyx_60582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zyx_60582/09_2025/8zyx_60582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyx_60582/09_2025/8zyx_60582.map" model { file = "/net/cci-nas-00/data/ceres_data/8zyx_60582/09_2025/8zyx_60582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyx_60582/09_2025/8zyx_60582.cif" } resolution = 2.33 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= 0.122 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 4 9.91 5 S 96 5.16 5 C 8959 2.51 5 N 2456 2.21 5 O 2993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14508 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "C" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "D" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "F" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "J" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.75, per 1000 atoms: 0.26 Number of scatterers: 14508 At special positions: 0 Unit cell: (90.736, 108.712, 130.968, 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 4 19.99 S 96 16.00 O 2993 8.00 N 2456 7.00 C 8959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 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 337 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.02 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 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 337 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 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 337 " 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=2.04 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.06 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 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 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN N 4 " - " MAN N 5 " " MAN R 4 " - " MAN R 5 " " MAN V 4 " - " MAN V 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " MAN I 6 " - " MAN I 7 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA N 3 " - " MAN N 6 " " BMA R 3 " - " MAN R 6 " " BMA V 3 " - " MAN V 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " 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 V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A 501 " - " ASN A 86 " " NAG A 502 " - " ASN A 234 " " NAG B 501 " - " ASN B 86 " " NAG B 502 " - " ASN B 234 " " NAG C 501 " - " ASN C 86 " " NAG C 502 " - " ASN C 234 " " NAG D 501 " - " ASN D 86 " " NAG D 502 " - " ASN D 234 " " NAG E 1 " - " ASN A 146 " " NAG G 1 " - " ASN A 367 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 200 " " NAG K 1 " - " ASN B 146 " " NAG L 1 " - " ASN B 367 " " NAG M 1 " - " ASN B 329 " " NAG N 1 " - " ASN B 200 " " NAG O 1 " - " ASN C 146 " " NAG P 1 " - " ASN C 367 " " NAG Q 1 " - " ASN C 329 " " NAG R 1 " - " ASN C 200 " " NAG S 1 " - " ASN D 146 " " NAG T 1 " - " ASN D 367 " " NAG U 1 " - " ASN D 329 " " NAG V 1 " - " ASN D 200 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 479.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 31 sheets defined 3.3% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 104 through 111 removed outlier: 4.471A pdb=" N GLY A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.609A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.572A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.517A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.604A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.538A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.704A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.987A pdb=" N THR F 91 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.972A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 5.373A pdb=" N PHE A 97 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR A 449 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N CYS A 447 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.704A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.644A pdb=" N ALA A 201 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A 216 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 203 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A 205 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.776A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.457A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.500A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.266A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 15.896A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.232A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.198A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.782A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.534A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.772A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.618A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 311 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.545A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 372 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP B 399 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 378 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.699A pdb=" N GLY C 96 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.711A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 157 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.422A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.683A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.386A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.794A pdb=" N LEU C 372 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP C 399 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS C 378 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN C 393 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.667A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.735A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.538A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 231 through 233 removed outlier: 3.711A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.358A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.491A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU D 372 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP D 399 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS D 378 " --> pdb=" O ASN D 393 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN D 393 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.600A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AD1, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AD2, first strand: chain 'J' and resid 11 through 13 removed outlier: 6.725A pdb=" N LEU J 34 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 11 through 13 Processing sheet with id=AD4, first strand: chain 'J' and resid 19 through 24 447 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2553 1.32 - 1.45: 4390 1.45 - 1.58: 7756 1.58 - 1.71: 0 1.71 - 1.84: 116 Bond restraints: 14815 Sorted by residual: bond pdb=" CA SER A 388 " pdb=" CB SER A 388 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.39e-02 5.18e+03 1.92e+01 bond pdb=" C SER C 228 " pdb=" O SER C 228 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.02e-02 9.61e+03 1.83e+01 bond pdb=" CA SER B 388 " pdb=" CB SER B 388 " ideal model delta sigma weight residual 1.528 1.467 0.060 1.58e-02 4.01e+03 1.46e+01 bond pdb=" CA TYR D 130 " pdb=" C TYR D 130 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" C CYS D 129 " pdb=" O CYS D 129 " ideal model delta sigma weight residual 1.235 1.195 0.039 1.18e-02 7.18e+03 1.11e+01 ... (remaining 14810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 19743 2.96 - 5.92: 312 5.92 - 8.87: 40 8.87 - 11.83: 3 11.83 - 14.79: 3 Bond angle restraints: 20101 Sorted by residual: angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" C PRO B 386 " ideal model delta sigma weight residual 111.41 96.62 14.79 1.50e+00 4.44e-01 9.72e+01 angle pdb=" N PRO A 386 " pdb=" CA PRO A 386 " pdb=" C PRO A 386 " ideal model delta sigma weight residual 111.22 98.44 12.78 1.40e+00 5.10e-01 8.33e+01 angle pdb=" N ARG D 430 " pdb=" CA ARG D 430 " pdb=" C ARG D 430 " ideal model delta sigma weight residual 110.50 120.60 -10.10 1.41e+00 5.03e-01 5.13e+01 angle pdb=" CA ASN C 146 " pdb=" CB ASN C 146 " pdb=" CG ASN C 146 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" C ARG C 283 " pdb=" CA ARG C 283 " pdb=" CB ARG C 283 " ideal model delta sigma weight residual 112.09 120.78 -8.69 1.43e+00 4.89e-01 3.69e+01 ... (remaining 20096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8857 25.94 - 51.88: 514 51.88 - 77.82: 96 77.82 - 103.76: 59 103.76 - 129.70: 45 Dihedral angle restraints: 9571 sinusoidal: 4535 harmonic: 5036 Sorted by residual: dihedral pdb=" CB CYS B 183 " pdb=" SG CYS B 183 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual -86.00 -170.98 84.98 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS C 183 " pdb=" SG CYS C 183 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS D 183 " pdb=" SG CYS D 183 " pdb=" SG CYS D 230 " pdb=" CB CYS D 230 " ideal model delta sinusoidal sigma weight residual -86.00 -165.93 79.93 1 1.00e+01 1.00e-02 7.92e+01 ... (remaining 9568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2256 0.114 - 0.228: 87 0.228 - 0.342: 15 0.342 - 0.456: 2 0.456 - 0.570: 4 Chirality restraints: 2364 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-02 2.50e+03 7.82e+02 chirality pdb=" C1 MAN V 4 " pdb=" O3 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 2.11 0.29 2.00e-02 2.50e+03 2.04e+02 chirality pdb=" C1 MAN V 7 " pdb=" O3 MAN V 6 " pdb=" C2 MAN V 7 " pdb=" O5 MAN V 7 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.71e+02 ... (remaining 2361 not shown) Planarity restraints: 2535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " -0.150 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" C7 NAG C 502 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " -0.113 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " 0.193 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " 0.139 2.00e-02 2.50e+03 1.15e-01 1.64e+02 pdb=" C7 NAG O 2 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " -0.179 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.133 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" C7 NAG M 2 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.100 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.174 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.018 2.00e-02 2.50e+03 ... (remaining 2532 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 117 2.55 - 3.14: 11022 3.14 - 3.72: 24194 3.72 - 4.31: 37387 4.31 - 4.90: 59510 Nonbonded interactions: 132230 Sorted by model distance: nonbonded pdb=" O ASP A 293 " pdb="CA CA A 503 " model vdw 1.959 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D 503 " model vdw 1.982 2.510 nonbonded pdb=" O HIS A 347 " pdb="CA CA A 503 " model vdw 2.046 2.510 nonbonded pdb=" O ASP C 293 " pdb="CA CA C 503 " model vdw 2.062 2.510 nonbonded pdb=" O HIS B 347 " pdb="CA CA B 503 " model vdw 2.153 2.510 ... (remaining 132225 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'R' selection = chain 'V' } 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.300 Find NCS groups from input model: 0.370 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 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 0.061 14913 Z= 0.335 Angle : 1.042 18.486 20357 Z= 0.553 Chirality : 0.061 0.570 2364 Planarity : 0.014 0.432 2511 Dihedral : 20.045 129.696 6255 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 0.46 % Allowed : 16.47 % Favored : 83.07 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.20), residues: 1766 helix: -0.75 (0.92), residues: 24 sheet: 0.15 (0.20), residues: 684 loop : -0.51 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 210 TYR 0.014 0.002 TYR B 155 PHE 0.013 0.002 PHE A 354 TRP 0.015 0.002 TRP B 178 HIS 0.011 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00544 (14815) covalent geometry : angle 0.90593 (20101) SS BOND : bond 0.00590 ( 38) SS BOND : angle 1.34971 ( 76) hydrogen bonds : bond 0.20898 ( 437) hydrogen bonds : angle 9.15962 ( 1209) link_ALPHA1-2 : bond 0.02608 ( 4) link_ALPHA1-2 : angle 4.89717 ( 12) link_ALPHA1-3 : bond 0.02219 ( 8) link_ALPHA1-3 : angle 5.10729 ( 24) link_ALPHA1-6 : bond 0.02105 ( 4) link_ALPHA1-6 : angle 1.69229 ( 12) link_BETA1-4 : bond 0.04103 ( 20) link_BETA1-4 : angle 6.10579 ( 60) link_NAG-ASN : bond 0.00921 ( 24) link_NAG-ASN : angle 5.61290 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7837 (p0) REVERT: A 381 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 390 LEU cc_start: 0.8777 (tp) cc_final: 0.8443 (tp) REVERT: C 387 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7615 (mptt) REVERT: C 391 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: C 415 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7981 (tppt) REVERT: C 435 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: D 210 ARG cc_start: 0.8369 (mtt90) cc_final: 0.8124 (mtt90) REVERT: F 3 GLN cc_start: 0.8452 (tt0) cc_final: 0.8072 (tt0) REVERT: F 21 SER cc_start: 0.8752 (m) cc_final: 0.8232 (p) REVERT: F 33 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8187 (mm-30) REVERT: J 104 LEU cc_start: 0.7876 (mp) cc_final: 0.7630 (mp) outliers start: 7 outliers final: 2 residues processed: 186 average time/residue: 0.7027 time to fit residues: 142.5645 Evaluate side-chains 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 385 ASN B 391 GLN C 273 GLN D 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.104360 restraints weight = 14760.861| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.68 r_work: 0.3108 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14913 Z= 0.178 Angle : 0.768 11.766 20357 Z= 0.371 Chirality : 0.050 0.289 2364 Planarity : 0.004 0.075 2511 Dihedral : 16.131 120.846 3170 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.89 % Allowed : 15.89 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.20), residues: 1766 helix: -0.02 (0.85), residues: 28 sheet: 0.50 (0.21), residues: 627 loop : -0.59 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.012 0.002 TYR B 121 PHE 0.013 0.002 PHE B 410 TRP 0.015 0.002 TRP B 178 HIS 0.006 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00377 (14815) covalent geometry : angle 0.70862 (20101) SS BOND : bond 0.00562 ( 38) SS BOND : angle 1.41678 ( 76) hydrogen bonds : bond 0.04993 ( 437) hydrogen bonds : angle 7.34759 ( 1209) link_ALPHA1-2 : bond 0.01097 ( 4) link_ALPHA1-2 : angle 2.93120 ( 12) link_ALPHA1-3 : bond 0.01774 ( 8) link_ALPHA1-3 : angle 4.23358 ( 24) link_ALPHA1-6 : bond 0.00420 ( 4) link_ALPHA1-6 : angle 1.71863 ( 12) link_BETA1-4 : bond 0.00814 ( 20) link_BETA1-4 : angle 2.82215 ( 60) link_NAG-ASN : bond 0.00400 ( 24) link_NAG-ASN : angle 3.13783 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8021 (mt-10) REVERT: A 390 LEU cc_start: 0.8827 (tp) cc_final: 0.8442 (tp) REVERT: C 387 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7110 (mmtm) REVERT: C 415 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8027 (tppt) REVERT: D 128 LYS cc_start: 0.8403 (mtmp) cc_final: 0.8169 (ptpt) REVERT: D 210 ARG cc_start: 0.8454 (mtt90) cc_final: 0.8238 (mtt90) REVERT: D 249 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7587 (mtpp) REVERT: D 313 VAL cc_start: 0.8914 (t) cc_final: 0.8694 (t) REVERT: F 3 GLN cc_start: 0.8460 (tt0) cc_final: 0.8086 (tt0) REVERT: F 21 SER cc_start: 0.8886 (m) cc_final: 0.8369 (p) REVERT: F 33 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: F 46 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8443 (tt0) outliers start: 29 outliers final: 18 residues processed: 193 average time/residue: 0.6694 time to fit residues: 140.8083 Evaluate side-chains 195 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 0.0970 chunk 60 optimal weight: 0.0670 chunk 126 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 391 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN D 147 ASN D 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108734 restraints weight = 14933.382| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.70 r_work: 0.3172 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14913 Z= 0.123 Angle : 0.666 10.086 20357 Z= 0.323 Chirality : 0.047 0.304 2364 Planarity : 0.004 0.043 2511 Dihedral : 13.349 117.185 3157 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.69 % Allowed : 17.25 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.20), residues: 1766 helix: 0.19 (0.95), residues: 28 sheet: 0.57 (0.21), residues: 616 loop : -0.61 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 210 TYR 0.012 0.001 TYR B 121 PHE 0.011 0.001 PHE B 354 TRP 0.013 0.001 TRP B 178 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00247 (14815) covalent geometry : angle 0.62066 (20101) SS BOND : bond 0.00283 ( 38) SS BOND : angle 0.77776 ( 76) hydrogen bonds : bond 0.03958 ( 437) hydrogen bonds : angle 6.85522 ( 1209) link_ALPHA1-2 : bond 0.01249 ( 4) link_ALPHA1-2 : angle 2.64888 ( 12) link_ALPHA1-3 : bond 0.01485 ( 8) link_ALPHA1-3 : angle 3.65929 ( 24) link_ALPHA1-6 : bond 0.00782 ( 4) link_ALPHA1-6 : angle 1.44073 ( 12) link_BETA1-4 : bond 0.00803 ( 20) link_BETA1-4 : angle 2.45536 ( 60) link_NAG-ASN : bond 0.00328 ( 24) link_NAG-ASN : angle 2.47450 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 390 LEU cc_start: 0.8782 (tp) cc_final: 0.8425 (tp) REVERT: C 387 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7015 (mmtm) REVERT: C 415 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8020 (tppt) REVERT: D 210 ARG cc_start: 0.8384 (mtt90) cc_final: 0.8153 (mtt90) REVERT: D 249 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7612 (mtpp) REVERT: D 313 VAL cc_start: 0.8911 (t) cc_final: 0.8689 (t) REVERT: F 3 GLN cc_start: 0.8443 (tt0) cc_final: 0.8085 (tt0) REVERT: F 21 SER cc_start: 0.8882 (m) cc_final: 0.8377 (p) REVERT: F 33 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: F 82 GLN cc_start: 0.8899 (tp40) cc_final: 0.8675 (tp-100) REVERT: J 103 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7347 (tptm) outliers start: 26 outliers final: 13 residues processed: 188 average time/residue: 0.7056 time to fit residues: 143.9927 Evaluate side-chains 186 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 103 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 158 optimal weight: 0.0170 chunk 95 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN C 273 GLN C 465 ASN D 273 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104920 restraints weight = 14781.700| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.67 r_work: 0.3116 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14913 Z= 0.198 Angle : 0.724 9.578 20357 Z= 0.357 Chirality : 0.049 0.288 2364 Planarity : 0.004 0.044 2511 Dihedral : 12.635 115.181 3157 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.99 % Allowed : 16.21 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.19), residues: 1766 helix: -0.24 (0.83), residues: 28 sheet: 0.43 (0.21), residues: 636 loop : -0.60 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.013 0.002 TYR C 155 PHE 0.013 0.002 PHE B 354 TRP 0.014 0.002 TRP B 178 HIS 0.007 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00425 (14815) covalent geometry : angle 0.67643 (20101) SS BOND : bond 0.00363 ( 38) SS BOND : angle 1.10553 ( 76) hydrogen bonds : bond 0.04610 ( 437) hydrogen bonds : angle 7.01715 ( 1209) link_ALPHA1-2 : bond 0.01182 ( 4) link_ALPHA1-2 : angle 2.33871 ( 12) link_ALPHA1-3 : bond 0.01479 ( 8) link_ALPHA1-3 : angle 3.79566 ( 24) link_ALPHA1-6 : bond 0.00570 ( 4) link_ALPHA1-6 : angle 1.73965 ( 12) link_BETA1-4 : bond 0.00740 ( 20) link_BETA1-4 : angle 2.54161 ( 60) link_NAG-ASN : bond 0.00593 ( 24) link_NAG-ASN : angle 2.71892 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ARG cc_start: 0.8054 (mtp85) cc_final: 0.7694 (mtm180) REVERT: A 318 CYS cc_start: 0.7713 (m) cc_final: 0.7483 (m) REVERT: A 381 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 390 LEU cc_start: 0.8798 (tp) cc_final: 0.8429 (tp) REVERT: C 387 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7060 (mmtm) REVERT: C 415 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8042 (tppt) REVERT: D 210 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8275 (mtt90) REVERT: D 249 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7382 (mtpp) REVERT: D 387 LYS cc_start: 0.8280 (mttm) cc_final: 0.7918 (mttp) REVERT: F 3 GLN cc_start: 0.8451 (tt0) cc_final: 0.8094 (tt0) REVERT: F 21 SER cc_start: 0.8892 (m) cc_final: 0.8411 (p) REVERT: F 33 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: J 103 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7438 (tptm) outliers start: 46 outliers final: 24 residues processed: 202 average time/residue: 0.6772 time to fit residues: 149.6243 Evaluate side-chains 198 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 103 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 134 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN C 273 GLN C 465 ASN D 173 GLN D 273 GLN D 306 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105123 restraints weight = 14851.352| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.68 r_work: 0.3121 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14913 Z= 0.178 Angle : 0.696 9.567 20357 Z= 0.344 Chirality : 0.048 0.288 2364 Planarity : 0.004 0.044 2511 Dihedral : 12.324 113.085 3157 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.41 % Allowed : 17.25 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.19), residues: 1766 helix: -0.18 (0.86), residues: 28 sheet: 0.24 (0.20), residues: 658 loop : -0.50 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 210 TYR 0.013 0.002 TYR B 121 PHE 0.013 0.002 PHE A 354 TRP 0.015 0.002 TRP B 178 HIS 0.006 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00380 (14815) covalent geometry : angle 0.65090 (20101) SS BOND : bond 0.00315 ( 38) SS BOND : angle 0.97581 ( 76) hydrogen bonds : bond 0.04355 ( 437) hydrogen bonds : angle 6.92082 ( 1209) link_ALPHA1-2 : bond 0.01152 ( 4) link_ALPHA1-2 : angle 2.43500 ( 12) link_ALPHA1-3 : bond 0.01485 ( 8) link_ALPHA1-3 : angle 3.81049 ( 24) link_ALPHA1-6 : bond 0.00545 ( 4) link_ALPHA1-6 : angle 1.64942 ( 12) link_BETA1-4 : bond 0.00741 ( 20) link_BETA1-4 : angle 2.39867 ( 60) link_NAG-ASN : bond 0.00377 ( 24) link_NAG-ASN : angle 2.59093 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7701 (mtm180) REVERT: A 381 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8050 (mt-10) REVERT: A 390 LEU cc_start: 0.8806 (tp) cc_final: 0.8444 (tp) REVERT: C 387 LYS cc_start: 0.7737 (mtpt) cc_final: 0.7135 (mmtm) REVERT: C 415 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7999 (tppt) REVERT: C 435 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8362 (pm20) REVERT: D 210 ARG cc_start: 0.8536 (mtt90) cc_final: 0.8282 (mtt90) REVERT: D 249 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7370 (mtpp) REVERT: D 387 LYS cc_start: 0.8335 (mttm) cc_final: 0.7974 (mttp) REVERT: F 3 GLN cc_start: 0.8455 (tt0) cc_final: 0.8102 (tt0) REVERT: F 21 SER cc_start: 0.8905 (m) cc_final: 0.8423 (p) REVERT: F 33 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: J 103 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7432 (tptm) outliers start: 37 outliers final: 23 residues processed: 195 average time/residue: 0.7004 time to fit residues: 149.4355 Evaluate side-chains 198 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 103 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 169 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN C 273 GLN C 465 ASN D 173 GLN D 273 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.105310 restraints weight = 14807.934| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.68 r_work: 0.3124 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14913 Z= 0.175 Angle : 0.697 9.560 20357 Z= 0.344 Chirality : 0.048 0.282 2364 Planarity : 0.004 0.044 2511 Dihedral : 12.046 111.311 3157 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.47 % Allowed : 17.84 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.19), residues: 1766 helix: -0.29 (0.83), residues: 28 sheet: 0.33 (0.20), residues: 646 loop : -0.52 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 210 TYR 0.012 0.002 TYR B 121 PHE 0.013 0.002 PHE A 354 TRP 0.015 0.002 TRP B 178 HIS 0.006 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00372 (14815) covalent geometry : angle 0.65284 (20101) SS BOND : bond 0.00342 ( 38) SS BOND : angle 1.04800 ( 76) hydrogen bonds : bond 0.04276 ( 437) hydrogen bonds : angle 6.88128 ( 1209) link_ALPHA1-2 : bond 0.01127 ( 4) link_ALPHA1-2 : angle 2.47539 ( 12) link_ALPHA1-3 : bond 0.01464 ( 8) link_ALPHA1-3 : angle 3.81301 ( 24) link_ALPHA1-6 : bond 0.00516 ( 4) link_ALPHA1-6 : angle 1.70789 ( 12) link_BETA1-4 : bond 0.00740 ( 20) link_BETA1-4 : angle 2.35461 ( 60) link_NAG-ASN : bond 0.00501 ( 24) link_NAG-ASN : angle 2.50935 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7702 (mtm180) REVERT: A 381 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 390 LEU cc_start: 0.8815 (tp) cc_final: 0.8451 (tp) REVERT: C 387 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7101 (mmtm) REVERT: C 415 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8010 (tppt) REVERT: C 435 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: D 210 ARG cc_start: 0.8542 (mtt90) cc_final: 0.8281 (mtt90) REVERT: D 249 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7389 (mtpp) REVERT: D 387 LYS cc_start: 0.8328 (mttm) cc_final: 0.7965 (mttp) REVERT: F 3 GLN cc_start: 0.8459 (tt0) cc_final: 0.8121 (tt0) REVERT: F 21 SER cc_start: 0.8916 (m) cc_final: 0.8435 (p) REVERT: F 33 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7996 (mm-30) REVERT: J 103 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7453 (tptm) outliers start: 38 outliers final: 23 residues processed: 201 average time/residue: 0.6514 time to fit residues: 143.7784 Evaluate side-chains 201 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 103 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN C 273 GLN C 465 ASN D 273 GLN F 35 ASN F 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105924 restraints weight = 14788.199| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.68 r_work: 0.3131 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14913 Z= 0.163 Angle : 0.687 9.550 20357 Z= 0.338 Chirality : 0.048 0.283 2364 Planarity : 0.004 0.043 2511 Dihedral : 11.766 109.704 3157 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.67 % Allowed : 18.23 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.19), residues: 1766 helix: -0.19 (0.85), residues: 28 sheet: 0.35 (0.20), residues: 646 loop : -0.51 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 210 TYR 0.013 0.002 TYR B 121 PHE 0.013 0.002 PHE A 354 TRP 0.015 0.001 TRP B 178 HIS 0.005 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00344 (14815) covalent geometry : angle 0.64153 (20101) SS BOND : bond 0.00317 ( 38) SS BOND : angle 1.04257 ( 76) hydrogen bonds : bond 0.04130 ( 437) hydrogen bonds : angle 6.83167 ( 1209) link_ALPHA1-2 : bond 0.01210 ( 4) link_ALPHA1-2 : angle 2.57070 ( 12) link_ALPHA1-3 : bond 0.01471 ( 8) link_ALPHA1-3 : angle 3.81836 ( 24) link_ALPHA1-6 : bond 0.00517 ( 4) link_ALPHA1-6 : angle 1.69049 ( 12) link_BETA1-4 : bond 0.00742 ( 20) link_BETA1-4 : angle 2.28693 ( 60) link_NAG-ASN : bond 0.00368 ( 24) link_NAG-ASN : angle 2.58451 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ARG cc_start: 0.8045 (mtp85) cc_final: 0.7708 (mtm180) REVERT: A 381 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 390 LEU cc_start: 0.8812 (tp) cc_final: 0.8449 (tp) REVERT: A 430 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8159 (mmt90) REVERT: C 387 LYS cc_start: 0.7686 (mtpt) cc_final: 0.7067 (mmtm) REVERT: C 415 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7961 (tppt) REVERT: C 435 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8396 (pm20) REVERT: D 210 ARG cc_start: 0.8530 (mtt90) cc_final: 0.8270 (mtt90) REVERT: D 249 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7401 (mtpp) REVERT: D 387 LYS cc_start: 0.8322 (mttm) cc_final: 0.7965 (mttp) REVERT: F 3 GLN cc_start: 0.8454 (tt0) cc_final: 0.8126 (tt0) REVERT: F 21 SER cc_start: 0.8920 (m) cc_final: 0.8434 (p) REVERT: F 33 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: J 103 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7425 (tptm) outliers start: 41 outliers final: 25 residues processed: 194 average time/residue: 0.6571 time to fit residues: 139.7336 Evaluate side-chains 197 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 103 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 116 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN C 273 GLN C 465 ASN D 173 GLN D 273 GLN D 306 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102248 restraints weight = 14671.157| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.65 r_work: 0.3073 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 14913 Z= 0.307 Angle : 0.830 9.815 20357 Z= 0.412 Chirality : 0.053 0.278 2364 Planarity : 0.005 0.053 2511 Dihedral : 12.160 109.819 3157 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.86 % Allowed : 18.10 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.19), residues: 1766 helix: -0.85 (0.84), residues: 24 sheet: 0.17 (0.20), residues: 670 loop : -0.53 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 428 TYR 0.017 0.003 TYR C 155 PHE 0.014 0.003 PHE B 410 TRP 0.017 0.002 TRP B 178 HIS 0.009 0.002 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00675 (14815) covalent geometry : angle 0.78034 (20101) SS BOND : bond 0.00502 ( 38) SS BOND : angle 1.42451 ( 76) hydrogen bonds : bond 0.05311 ( 437) hydrogen bonds : angle 7.24111 ( 1209) link_ALPHA1-2 : bond 0.01175 ( 4) link_ALPHA1-2 : angle 2.53157 ( 12) link_ALPHA1-3 : bond 0.01484 ( 8) link_ALPHA1-3 : angle 4.20433 ( 24) link_ALPHA1-6 : bond 0.00466 ( 4) link_ALPHA1-6 : angle 2.13345 ( 12) link_BETA1-4 : bond 0.00717 ( 20) link_BETA1-4 : angle 2.62241 ( 60) link_NAG-ASN : bond 0.00680 ( 24) link_NAG-ASN : angle 3.03833 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7739 (mtm180) REVERT: A 318 CYS cc_start: 0.7731 (m) cc_final: 0.7498 (m) REVERT: A 381 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 390 LEU cc_start: 0.8831 (tp) cc_final: 0.8532 (tp) REVERT: A 430 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8173 (mmt90) REVERT: C 387 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7253 (mptt) REVERT: C 415 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8061 (tppt) REVERT: C 435 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8423 (pm20) REVERT: D 210 ARG cc_start: 0.8610 (mtt90) cc_final: 0.8346 (mtt90) REVERT: D 249 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7687 (mtpp) REVERT: D 387 LYS cc_start: 0.8385 (mttm) cc_final: 0.7972 (mttp) REVERT: D 430 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8029 (mmt180) REVERT: D 435 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: F 3 GLN cc_start: 0.8516 (tt0) cc_final: 0.8174 (tt0) REVERT: F 21 SER cc_start: 0.8945 (m) cc_final: 0.8451 (p) REVERT: F 33 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8312 (mm-30) outliers start: 44 outliers final: 24 residues processed: 200 average time/residue: 0.6103 time to fit residues: 133.9094 Evaluate side-chains 205 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 142 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 139 optimal weight: 0.0770 chunk 151 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN C 273 GLN C 465 ASN D 273 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106942 restraints weight = 14775.999| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.68 r_work: 0.3147 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14913 Z= 0.139 Angle : 0.691 9.923 20357 Z= 0.339 Chirality : 0.047 0.283 2364 Planarity : 0.004 0.042 2511 Dihedral : 11.409 108.411 3157 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.69 % Allowed : 19.66 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.19), residues: 1766 helix: -0.08 (0.88), residues: 28 sheet: 0.23 (0.20), residues: 666 loop : -0.45 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 224 TYR 0.015 0.002 TYR B 121 PHE 0.013 0.002 PHE A 354 TRP 0.017 0.001 TRP B 178 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00287 (14815) covalent geometry : angle 0.64711 (20101) SS BOND : bond 0.00260 ( 38) SS BOND : angle 1.12035 ( 76) hydrogen bonds : bond 0.03910 ( 437) hydrogen bonds : angle 6.78717 ( 1209) link_ALPHA1-2 : bond 0.01495 ( 4) link_ALPHA1-2 : angle 2.48985 ( 12) link_ALPHA1-3 : bond 0.01492 ( 8) link_ALPHA1-3 : angle 3.86502 ( 24) link_ALPHA1-6 : bond 0.00590 ( 4) link_ALPHA1-6 : angle 1.62607 ( 12) link_BETA1-4 : bond 0.00764 ( 20) link_BETA1-4 : angle 2.17733 ( 60) link_NAG-ASN : bond 0.00524 ( 24) link_NAG-ASN : angle 2.51041 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8024 (mt-10) REVERT: A 390 LEU cc_start: 0.8808 (tp) cc_final: 0.8464 (tp) REVERT: A 430 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8013 (mmt90) REVERT: C 387 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7067 (mmtm) REVERT: C 415 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7960 (tppt) REVERT: C 435 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8360 (pm20) REVERT: D 210 ARG cc_start: 0.8476 (mtt90) cc_final: 0.8242 (mtt90) REVERT: D 249 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7395 (mtpp) REVERT: D 387 LYS cc_start: 0.8337 (mttm) cc_final: 0.7978 (mttp) REVERT: D 430 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7876 (mmt180) REVERT: F 3 GLN cc_start: 0.8487 (tt0) cc_final: 0.8152 (tt0) REVERT: F 21 SER cc_start: 0.8959 (m) cc_final: 0.8478 (p) REVERT: F 33 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7984 (mm-30) REVERT: J 103 LYS cc_start: 0.7563 (ttpt) cc_final: 0.7222 (tptm) outliers start: 26 outliers final: 15 residues processed: 185 average time/residue: 0.6684 time to fit residues: 135.4122 Evaluate side-chains 185 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 0.0470 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 109 optimal weight: 0.0070 chunk 168 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN C 273 GLN C 465 ASN D 273 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108764 restraints weight = 14679.701| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.67 r_work: 0.3168 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14913 Z= 0.129 Angle : 0.672 10.412 20357 Z= 0.328 Chirality : 0.047 0.278 2364 Planarity : 0.003 0.042 2511 Dihedral : 10.913 105.987 3157 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.56 % Allowed : 19.92 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.19), residues: 1766 helix: -0.04 (0.90), residues: 28 sheet: 0.34 (0.20), residues: 650 loop : -0.50 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 150 TYR 0.013 0.001 TYR B 121 PHE 0.013 0.002 PHE A 354 TRP 0.015 0.001 TRP B 178 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00268 (14815) covalent geometry : angle 0.62582 (20101) SS BOND : bond 0.00269 ( 38) SS BOND : angle 1.06843 ( 76) hydrogen bonds : bond 0.03665 ( 437) hydrogen bonds : angle 6.63860 ( 1209) link_ALPHA1-2 : bond 0.01564 ( 4) link_ALPHA1-2 : angle 2.37084 ( 12) link_ALPHA1-3 : bond 0.01490 ( 8) link_ALPHA1-3 : angle 3.89657 ( 24) link_ALPHA1-6 : bond 0.00577 ( 4) link_ALPHA1-6 : angle 1.68835 ( 12) link_BETA1-4 : bond 0.00759 ( 20) link_BETA1-4 : angle 2.12160 ( 60) link_NAG-ASN : bond 0.00266 ( 24) link_NAG-ASN : angle 2.65536 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8036 (mt-10) REVERT: A 390 LEU cc_start: 0.8829 (tp) cc_final: 0.8485 (tp) REVERT: C 234 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7820 (m-40) REVERT: C 387 LYS cc_start: 0.7588 (mtpt) cc_final: 0.6977 (mmtm) REVERT: C 415 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.7951 (tppt) REVERT: C 435 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: D 210 ARG cc_start: 0.8414 (mtt90) cc_final: 0.8178 (mtt90) REVERT: D 249 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7391 (mtpp) REVERT: D 313 VAL cc_start: 0.8943 (t) cc_final: 0.8514 (p) REVERT: D 387 LYS cc_start: 0.8308 (mttm) cc_final: 0.7946 (mttp) REVERT: D 430 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7835 (mmt180) REVERT: F 3 GLN cc_start: 0.8492 (tt0) cc_final: 0.8185 (tt0) REVERT: F 21 SER cc_start: 0.8950 (m) cc_final: 0.8477 (p) REVERT: F 33 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: J 103 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7213 (tptm) outliers start: 24 outliers final: 14 residues processed: 183 average time/residue: 0.6759 time to fit residues: 135.1365 Evaluate side-chains 189 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 135 optimal weight: 6.9990 chunk 126 optimal weight: 0.0050 chunk 168 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 152 optimal weight: 0.0770 overall best weight: 0.7554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 391 GLN C 273 GLN C 465 ASN D 273 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108565 restraints weight = 14698.217| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.69 r_work: 0.3169 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14913 Z= 0.133 Angle : 0.664 9.693 20357 Z= 0.324 Chirality : 0.047 0.279 2364 Planarity : 0.003 0.042 2511 Dihedral : 10.432 102.434 3157 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.63 % Allowed : 19.99 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.20), residues: 1766 helix: 0.03 (0.92), residues: 28 sheet: 0.28 (0.20), residues: 655 loop : -0.44 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 150 TYR 0.013 0.002 TYR B 121 PHE 0.014 0.002 PHE A 354 TRP 0.014 0.001 TRP B 178 HIS 0.004 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00276 (14815) covalent geometry : angle 0.61799 (20101) SS BOND : bond 0.00279 ( 38) SS BOND : angle 1.02149 ( 76) hydrogen bonds : bond 0.03663 ( 437) hydrogen bonds : angle 6.57593 ( 1209) link_ALPHA1-2 : bond 0.01533 ( 4) link_ALPHA1-2 : angle 2.39161 ( 12) link_ALPHA1-3 : bond 0.01484 ( 8) link_ALPHA1-3 : angle 4.08899 ( 24) link_ALPHA1-6 : bond 0.00574 ( 4) link_ALPHA1-6 : angle 1.80990 ( 12) link_BETA1-4 : bond 0.00744 ( 20) link_BETA1-4 : angle 2.06940 ( 60) link_NAG-ASN : bond 0.00284 ( 24) link_NAG-ASN : angle 2.51221 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6017.75 seconds wall clock time: 103 minutes 32.58 seconds (6212.58 seconds total)