Starting phenix.real_space_refine on Fri Jul 3 14:14:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvm_39608/07_2026/8yvm_39608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvm_39608/07_2026/8yvm_39608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yvm_39608/07_2026/8yvm_39608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvm_39608/07_2026/8yvm_39608_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yvm_39608/07_2026/8yvm_39608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvm_39608/07_2026/8yvm_39608.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.065 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 8992 2.51 5 N 2450 2.21 5 O 3037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14579 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: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "F" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.75, per 1000 atoms: 0.19 Number of scatterers: 14579 At special positions: 0 Unit cell: (92.3812, 113.865, 131.052, 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 3037 8.00 N 2450 7.00 C 8992 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=2.02 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=2.01 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.02 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=2.02 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=2.01 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=2.02 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=2.02 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=2.01 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.07 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=1, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN N 4 " - " MAN N 5 " " MAN R 4 " - " MAN R 5 " " MAN V 4 " - " MAN V 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 6 " - " MAN J 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 J 3 " - " MAN J 6 " " MAN J 6 " - " MAN J 8 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA R 3 " - " MAN R 6 " " MAN R 6 " - " MAN R 8 " " BMA V 3 " - " MAN V 6 " " MAN V 6 " - " MAN V 8 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 G 1 " - " ASN A 146 " " NAG H 1 " - " ASN A 367 " " NAG I 1 " - " ASN A 329 " " NAG J 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 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 548.1 milliseconds 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: 12 helices and 30 sheets defined 3.6% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.578A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.580A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.553A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.577A 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 'C' and resid 329 through 333 removed outlier: 3.540A pdb=" N SER C 333 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.579A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.522A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.779A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.790A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.927A 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: 4.733A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.651A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.787A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR A 252 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 254 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.588A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.655A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.207A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 16.276A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.273A 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: 3.789A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.926A 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: 4.841A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.121A 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: 6.650A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.448A 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: 3.786A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR B 252 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 254 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE B 256 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.589A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.654A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.208A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 16.276A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.274A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.791A pdb=" N GLY C 96 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.927A 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: 4.842A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 4.121A 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: 6.652A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.447A 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: 3.786A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR C 252 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR C 267 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE C 254 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE C 256 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.588A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.285A 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: 7.011A pdb=" N ASP C 402 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N GLU C 375 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ARG C 400 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 11.199A pdb=" N PHE C 377 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 13.244A pdb=" N VAL C 398 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 16.276A pdb=" N VAL C 379 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 16.272A pdb=" N VAL C 396 " --> pdb=" O VAL C 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.788A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.927A 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: 4.840A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 4.120A 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: 6.651A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.447A 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: 3.786A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR D 252 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR D 267 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE D 254 " --> pdb=" O THR D 265 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE D 256 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.587A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER D 311 " --> pdb=" O ASN D 306 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.653A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASP D 402 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N GLU D 375 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N ARG D 400 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N PHE D 377 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 13.208A pdb=" N VAL D 398 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 16.276A pdb=" N VAL D 379 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 16.272A pdb=" N VAL D 396 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 19 through 24 removed outlier: 3.556A pdb=" N THR E 75 " --> pdb=" O SER E 64 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.405A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 97 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.518A pdb=" N SER F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.005A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN F 39 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL F 112 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.005A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN F 39 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 101 through 102 439 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2397 1.31 - 1.44: 4309 1.44 - 1.57: 8058 1.57 - 1.69: 0 1.69 - 1.82: 116 Bond restraints: 14880 Sorted by residual: bond pdb=" N PRO D 468 " pdb=" CD PRO D 468 " ideal model delta sigma weight residual 1.473 1.304 0.169 1.40e-02 5.10e+03 1.45e+02 bond pdb=" CA SER D 440 " pdb=" CB SER D 440 " ideal model delta sigma weight residual 1.535 1.460 0.075 1.32e-02 5.74e+03 3.20e+01 bond pdb=" CA SER F 108 " pdb=" CB SER F 108 " ideal model delta sigma weight residual 1.528 1.445 0.083 1.59e-02 3.96e+03 2.72e+01 bond pdb=" CA SER C 440 " pdb=" CB SER C 440 " ideal model delta sigma weight residual 1.534 1.465 0.070 1.34e-02 5.57e+03 2.70e+01 bond pdb=" CA SER D 334 " pdb=" CB SER D 334 " ideal model delta sigma weight residual 1.535 1.470 0.065 1.32e-02 5.74e+03 2.39e+01 ... (remaining 14875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 19191 3.21 - 6.42: 911 6.42 - 9.63: 73 9.63 - 12.84: 9 12.84 - 16.05: 2 Bond angle restraints: 20186 Sorted by residual: angle pdb=" C ARG F 98 " pdb=" CA ARG F 98 " pdb=" CB ARG F 98 " ideal model delta sigma weight residual 109.33 93.28 16.05 1.97e+00 2.58e-01 6.64e+01 angle pdb=" N PRO C 468 " pdb=" CA PRO C 468 " pdb=" C PRO C 468 " ideal model delta sigma weight residual 111.14 123.83 -12.69 1.56e+00 4.11e-01 6.62e+01 angle pdb=" C LYS B 431 " pdb=" CA LYS B 431 " pdb=" CB LYS B 431 " ideal model delta sigma weight residual 109.83 117.56 -7.73 9.90e-01 1.02e+00 6.10e+01 angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" C PRO B 386 " ideal model delta sigma weight residual 111.22 100.56 10.66 1.40e+00 5.10e-01 5.80e+01 angle pdb=" CA GLY D 244 " pdb=" C GLY D 244 " pdb=" O GLY D 244 " ideal model delta sigma weight residual 122.16 116.25 5.91 8.20e-01 1.49e+00 5.20e+01 ... (remaining 20181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 9037 21.77 - 43.54: 543 43.54 - 65.32: 57 65.32 - 87.09: 56 87.09 - 108.86: 32 Dihedral angle restraints: 9725 sinusoidal: 4689 harmonic: 5036 Sorted by residual: dihedral pdb=" C ARG F 98 " pdb=" N ARG F 98 " pdb=" CA ARG F 98 " pdb=" CB ARG F 98 " ideal model delta harmonic sigma weight residual -122.60 -100.68 -21.92 0 2.50e+00 1.60e-01 7.69e+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 -152.92 66.92 1 1.00e+01 1.00e-02 5.84e+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 -152.89 66.89 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 9722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.269: 2337 0.269 - 0.539: 56 0.539 - 0.808: 7 0.808 - 1.077: 2 1.077 - 1.346: 1 Chirality restraints: 2403 Sorted by residual: chirality pdb=" C1 MAN N 4 " pdb=" O3 BMA N 3 " pdb=" C2 MAN N 4 " pdb=" O5 MAN N 4 " both_signs ideal model delta sigma weight residual False 2.40 1.05 1.35 2.00e-02 2.50e+03 4.53e+03 chirality pdb=" C1 MAN R 4 " pdb=" O3 BMA R 3 " pdb=" C2 MAN R 4 " pdb=" O5 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.40 1.54 0.86 2.00e-02 2.50e+03 1.87e+03 chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.67 0.73 2.00e-02 2.50e+03 1.35e+03 ... (remaining 2400 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " -0.359 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG B 502 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " 0.545 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " 0.352 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG A 501 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " 0.083 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " 0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG C 502 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.086 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.176 2.00e-02 2.50e+03 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 279 2.62 - 3.19: 12670 3.19 - 3.76: 22180 3.76 - 4.33: 34630 4.33 - 4.90: 57336 Nonbonded interactions: 127095 Sorted by model distance: nonbonded pdb=" OE2 GLU F 6 " pdb=" N GLY F 116 " model vdw 2.050 3.120 nonbonded pdb=" O GLY B 297 " pdb="CA CA B 503 " model vdw 2.145 3.250 nonbonded pdb=" O HIS D 347 " pdb="CA CA D 503 " model vdw 2.146 3.250 nonbonded pdb=" O ASP F 104 " pdb=" OD1 ASP F 104 " model vdw 2.167 3.040 nonbonded pdb=" O ASP E 83 " pdb=" OH TYR E 87 " model vdw 2.200 3.040 ... (remaining 127090 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 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.460 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.011 0.169 14987 Z= 0.635 Angle : 1.481 17.295 20466 Z= 0.898 Chirality : 0.104 1.346 2403 Planarity : 0.024 0.307 2508 Dihedral : 15.795 108.862 6409 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.12 % Favored : 93.54 % Rotamer: Outliers : 0.20 % Allowed : 3.39 % Favored : 96.42 % Cbeta Deviations : 1.31 % 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 are not related in a simple way. whole: -1.93 (0.18), residues: 1766 helix: -1.79 (0.71), residues: 24 sheet: -0.12 (0.19), residues: 677 loop : -2.18 (0.16), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 292 TYR 0.032 0.003 TYR F 107 PHE 0.016 0.002 PHE F 29 TRP 0.026 0.002 TRP A 115 HIS 0.012 0.002 HIS C 264 Details of bonding type rmsd/Z covalent geometry : bond 0.01083 / 0.63 (14880) covalent geometry : angle 1.40563 / 0.89 (20186) SS BOND : bond 0.01013 / 0.70 ( 38) SS BOND : angle 2.21808 / 1.61 ( 76) hydrogen bonds : bond 0.12947 / 8.29 ( 426) hydrogen bonds : angle 7.79071 / 5.50 ( 1185) Misc. bond : bond 0.13816 / 7.27 ( 1) link_ALPHA1-2 : bond 0.00673 / 0.34 ( 4) link_ALPHA1-2 : angle 3.71695 / 1.96 ( 12) link_ALPHA1-3 : bond 0.01743 / 0.94 ( 8) link_ALPHA1-3 : angle 3.86081 / 2.10 ( 24) link_ALPHA1-6 : bond 0.00479 / 0.22 ( 8) link_ALPHA1-6 : angle 1.63677 / 0.91 ( 24) link_BETA1-4 : bond 0.00591 / 0.35 ( 24) link_BETA1-4 : angle 3.91960 / 2.68 ( 72) link_NAG-ASN : bond 0.01552 / 0.90 ( 24) link_NAG-ASN : angle 6.36401 / 4.32 ( 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 351 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 348 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 LYS cc_start: 0.7603 (tptt) cc_final: 0.7325 (tptm) REVERT: C 121 TYR cc_start: 0.8673 (p90) cc_final: 0.8469 (p90) REVERT: C 268 LEU cc_start: 0.7695 (tp) cc_final: 0.7442 (tp) REVERT: C 467 MET cc_start: 0.6781 (mtp) cc_final: 0.6505 (mtp) REVERT: D 295 TRP cc_start: 0.7070 (OUTLIER) cc_final: 0.6726 (t-100) REVERT: E 46 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7414 (ttm170) REVERT: F 69 THR cc_start: 0.7648 (p) cc_final: 0.7428 (t) outliers start: 3 outliers final: 2 residues processed: 351 average time/residue: 0.1379 time to fit residues: 67.7658 Evaluate side-chains 215 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 212 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain F residue 29 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 310 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN B 391 GLN C 336 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 347 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111023 restraints weight = 19401.608| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.44 r_work: 0.3342 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 14987 Z= 0.160 Angle : 0.776 9.663 20466 Z= 0.374 Chirality : 0.048 0.282 2403 Planarity : 0.005 0.081 2508 Dihedral : 12.159 77.562 3310 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.56 % Allowed : 11.47 % Favored : 86.97 % 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 are not related in a simple way. whole: -1.58 (0.18), residues: 1766 helix: -1.22 (0.88), residues: 24 sheet: -0.07 (0.20), residues: 651 loop : -1.76 (0.16), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 400 TYR 0.014 0.002 TYR C 284 PHE 0.013 0.002 PHE B 354 TRP 0.022 0.002 TRP C 178 HIS 0.006 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (14880) covalent geometry : angle 0.72911 / 0.36 (20186) SS BOND : bond 0.00319 / 0.22 ( 38) SS BOND : angle 1.04220 / 0.73 ( 76) hydrogen bonds : bond 0.03704 / 2.44 ( 426) hydrogen bonds : angle 6.55575 / 4.56 ( 1185) Misc. bond : bond 0.00152 / 0.08 ( 1) link_ALPHA1-2 : bond 0.00626 / 0.32 ( 4) link_ALPHA1-2 : angle 2.25638 / 1.24 ( 12) link_ALPHA1-3 : bond 0.01174 / 0.65 ( 8) link_ALPHA1-3 : angle 2.41805 / 1.45 ( 24) link_ALPHA1-6 : bond 0.00646 / 0.36 ( 8) link_ALPHA1-6 : angle 1.37961 / 0.76 ( 24) link_BETA1-4 : bond 0.00783 / 0.41 ( 24) link_BETA1-4 : angle 2.56214 / 1.80 ( 72) link_NAG-ASN : bond 0.00617 / 0.36 ( 24) link_NAG-ASN : angle 3.34538 / 2.21 ( 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 251 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.7562 (tttt) cc_final: 0.7315 (ttpp) REVERT: C 318 CYS cc_start: 0.6710 (m) cc_final: 0.6421 (m) REVERT: C 356 ASP cc_start: 0.6230 (t0) cc_final: 0.5956 (t0) REVERT: D 339 ASP cc_start: 0.8369 (m-30) cc_final: 0.8080 (p0) REVERT: D 375 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: D 402 ASP cc_start: 0.8064 (m-30) cc_final: 0.7859 (m-30) outliers start: 24 outliers final: 16 residues processed: 240 average time/residue: 0.1274 time to fit residues: 45.0858 Evaluate side-chains 206 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 29 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106483 restraints weight = 19884.812| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.45 r_work: 0.3263 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14987 Z= 0.204 Angle : 0.731 9.670 20466 Z= 0.358 Chirality : 0.049 0.258 2403 Planarity : 0.004 0.055 2508 Dihedral : 10.117 68.939 3306 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.54 % Allowed : 15.57 % Favored : 81.89 % 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 are not related in a simple way. whole: -1.57 (0.19), residues: 1766 helix: -0.73 (1.00), residues: 24 sheet: -0.22 (0.20), residues: 664 loop : -1.65 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 327 TYR 0.021 0.002 TYR B 121 PHE 0.016 0.002 PHE B 354 TRP 0.022 0.002 TRP C 178 HIS 0.006 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (14880) covalent geometry : angle 0.69117 / 0.35 (20186) SS BOND : bond 0.00346 / 0.22 ( 38) SS BOND : angle 0.95436 / 0.67 ( 76) hydrogen bonds : bond 0.03736 / 2.42 ( 426) hydrogen bonds : angle 6.49679 / 4.54 ( 1185) Misc. bond : bond 0.00749 / 0.39 ( 1) link_ALPHA1-2 : bond 0.00270 / 0.14 ( 4) link_ALPHA1-2 : angle 2.46252 / 1.33 ( 12) link_ALPHA1-3 : bond 0.00953 / 0.55 ( 8) link_ALPHA1-3 : angle 2.42365 / 1.45 ( 24) link_ALPHA1-6 : bond 0.00567 / 0.32 ( 8) link_ALPHA1-6 : angle 1.43815 / 0.79 ( 24) link_BETA1-4 : bond 0.00653 / 0.34 ( 24) link_BETA1-4 : angle 2.34491 / 1.65 ( 72) link_NAG-ASN : bond 0.00294 / 0.15 ( 24) link_NAG-ASN : angle 2.77563 / 1.84 ( 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 236 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ASP cc_start: 0.7002 (t70) cc_final: 0.6749 (p0) REVERT: A 432 GLU cc_start: 0.7374 (mp0) cc_final: 0.6856 (mp0) REVERT: C 121 TYR cc_start: 0.8849 (p90) cc_final: 0.8646 (p90) REVERT: C 318 CYS cc_start: 0.6569 (m) cc_final: 0.6182 (m) REVERT: C 338 LEU cc_start: 0.7942 (mt) cc_final: 0.7420 (pt) REVERT: D 339 ASP cc_start: 0.8273 (m-30) cc_final: 0.8073 (p0) REVERT: F 82 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7183 (tm-30) outliers start: 39 outliers final: 27 residues processed: 215 average time/residue: 0.1216 time to fit residues: 39.4129 Evaluate side-chains 204 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 310 HIS D 347 HIS D 441 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108152 restraints weight = 19652.177| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.45 r_work: 0.3293 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14987 Z= 0.143 Angle : 0.646 9.575 20466 Z= 0.319 Chirality : 0.046 0.242 2403 Planarity : 0.004 0.070 2508 Dihedral : 8.848 59.597 3306 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.61 % Allowed : 16.81 % Favored : 80.59 % 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 are not related in a simple way. whole: -1.31 (0.19), residues: 1766 helix: -0.77 (0.99), residues: 24 sheet: -0.02 (0.20), residues: 676 loop : -1.50 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 400 TYR 0.015 0.001 TYR A 121 PHE 0.012 0.002 PHE A 354 TRP 0.020 0.001 TRP C 178 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14880) covalent geometry : angle 0.61267 / 0.31 (20186) SS BOND : bond 0.00250 / 0.16 ( 38) SS BOND : angle 0.72436 / 0.51 ( 76) hydrogen bonds : bond 0.03316 / 2.18 ( 426) hydrogen bonds : angle 6.34550 / 4.42 ( 1185) Misc. bond : bond 0.00374 / 0.20 ( 1) link_ALPHA1-2 : bond 0.00404 / 0.21 ( 4) link_ALPHA1-2 : angle 2.21914 / 1.20 ( 12) link_ALPHA1-3 : bond 0.00979 / 0.55 ( 8) link_ALPHA1-3 : angle 2.16057 / 1.32 ( 24) link_ALPHA1-6 : bond 0.00650 / 0.36 ( 8) link_ALPHA1-6 : angle 1.38007 / 0.76 ( 24) link_BETA1-4 : bond 0.00642 / 0.34 ( 24) link_BETA1-4 : angle 2.00619 / 1.43 ( 72) link_NAG-ASN : bond 0.00218 / 0.11 ( 24) link_NAG-ASN : angle 2.44219 / 1.68 ( 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 234 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLU cc_start: 0.7365 (mp0) cc_final: 0.6887 (mp0) REVERT: C 121 TYR cc_start: 0.8852 (p90) cc_final: 0.8579 (p90) REVERT: C 257 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7537 (mt) REVERT: C 338 LEU cc_start: 0.8008 (mt) cc_final: 0.7462 (pt) REVERT: C 381 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8013 (mm-30) REVERT: D 338 LEU cc_start: 0.8435 (mt) cc_final: 0.8222 (mt) REVERT: D 339 ASP cc_start: 0.8227 (m-30) cc_final: 0.8027 (p0) REVERT: D 375 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7954 (pt0) outliers start: 40 outliers final: 29 residues processed: 214 average time/residue: 0.1222 time to fit residues: 39.6197 Evaluate side-chains 210 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 57 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 0.0010 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN D 274 HIS D 347 HIS ** D 441 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 = 0.3752 r_free = 0.3752 target = 0.133239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106623 restraints weight = 19822.042| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.45 r_work: 0.3271 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14987 Z= 0.171 Angle : 0.649 9.603 20466 Z= 0.321 Chirality : 0.046 0.231 2403 Planarity : 0.004 0.037 2508 Dihedral : 8.337 57.826 3304 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.00 % Allowed : 17.33 % Favored : 79.67 % 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 are not related in a simple way. whole: -1.33 (0.19), residues: 1766 helix: -0.94 (0.98), residues: 24 sheet: -0.05 (0.20), residues: 652 loop : -1.47 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 400 TYR 0.016 0.002 TYR A 121 PHE 0.014 0.002 PHE C 132 TRP 0.018 0.001 TRP C 178 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (14880) covalent geometry : angle 0.61643 / 0.31 (20186) SS BOND : bond 0.00283 / 0.18 ( 38) SS BOND : angle 0.71999 / 0.51 ( 76) hydrogen bonds : bond 0.03379 / 2.20 ( 426) hydrogen bonds : angle 6.36947 / 4.45 ( 1185) Misc. bond : bond 0.00180 / 0.09 ( 1) link_ALPHA1-2 : bond 0.00328 / 0.17 ( 4) link_ALPHA1-2 : angle 2.29940 / 1.24 ( 12) link_ALPHA1-3 : bond 0.00931 / 0.52 ( 8) link_ALPHA1-3 : angle 2.24508 / 1.35 ( 24) link_ALPHA1-6 : bond 0.00628 / 0.35 ( 8) link_ALPHA1-6 : angle 1.39877 / 0.77 ( 24) link_BETA1-4 : bond 0.00571 / 0.30 ( 24) link_BETA1-4 : angle 1.94100 / 1.37 ( 72) link_NAG-ASN : bond 0.00221 / 0.11 ( 24) link_NAG-ASN : angle 2.36530 / 1.59 ( 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 227 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLU cc_start: 0.7350 (mp0) cc_final: 0.6920 (mp0) REVERT: C 257 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7472 (mt) REVERT: D 375 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7991 (pt0) outliers start: 46 outliers final: 39 residues processed: 204 average time/residue: 0.1223 time to fit residues: 37.4982 Evaluate side-chains 213 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 151 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 294 ASN B 441 ASN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 347 HIS ** D 441 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 = 0.3745 r_free = 0.3745 target = 0.132676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106173 restraints weight = 19765.984| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.44 r_work: 0.3270 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14987 Z= 0.173 Angle : 0.649 9.863 20466 Z= 0.320 Chirality : 0.047 0.328 2403 Planarity : 0.004 0.039 2508 Dihedral : 8.130 57.838 3304 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.65 % Allowed : 17.79 % Favored : 78.57 % 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 are not related in a simple way. whole: -1.23 (0.19), residues: 1766 helix: -0.99 (0.97), residues: 24 sheet: 0.06 (0.21), residues: 624 loop : -1.39 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 150 TYR 0.018 0.002 TYR C 121 PHE 0.014 0.002 PHE B 410 TRP 0.019 0.001 TRP C 178 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (14880) covalent geometry : angle 0.61440 / 0.31 (20186) SS BOND : bond 0.00270 / 0.17 ( 38) SS BOND : angle 0.73513 / 0.53 ( 76) hydrogen bonds : bond 0.03373 / 2.20 ( 426) hydrogen bonds : angle 6.35383 / 4.44 ( 1185) Misc. bond : bond 0.00099 / 0.05 ( 1) link_ALPHA1-2 : bond 0.00291 / 0.15 ( 4) link_ALPHA1-2 : angle 2.33100 / 1.26 ( 12) link_ALPHA1-3 : bond 0.00988 / 0.57 ( 8) link_ALPHA1-3 : angle 2.24438 / 1.35 ( 24) link_ALPHA1-6 : bond 0.00623 / 0.34 ( 8) link_ALPHA1-6 : angle 1.39905 / 0.77 ( 24) link_BETA1-4 : bond 0.00568 / 0.30 ( 24) link_BETA1-4 : angle 1.85362 / 1.30 ( 72) link_NAG-ASN : bond 0.00208 / 0.10 ( 24) link_NAG-ASN : angle 2.57453 / 1.80 ( 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 237 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 GLU cc_start: 0.7312 (mp0) cc_final: 0.6893 (mp0) REVERT: B 257 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7774 (mt) REVERT: C 121 TYR cc_start: 0.8847 (p90) cc_final: 0.8595 (p90) REVERT: C 257 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7492 (mt) REVERT: D 375 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: E 38 GLN cc_start: 0.8555 (tt0) cc_final: 0.8075 (tt0) outliers start: 56 outliers final: 45 residues processed: 213 average time/residue: 0.1196 time to fit residues: 38.7041 Evaluate side-chains 218 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS D 358 ASN D 391 GLN ** D 441 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 = 0.3749 r_free = 0.3749 target = 0.133025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106424 restraints weight = 19710.597| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.44 r_work: 0.3274 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14987 Z= 0.158 Angle : 0.637 10.298 20466 Z= 0.316 Chirality : 0.046 0.264 2403 Planarity : 0.004 0.039 2508 Dihedral : 7.869 57.707 3304 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.52 % Allowed : 18.63 % Favored : 77.85 % 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 are not related in a simple way. whole: -1.18 (0.19), residues: 1766 helix: -0.95 (0.97), residues: 24 sheet: 0.07 (0.21), residues: 626 loop : -1.34 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.016 0.001 TYR C 121 PHE 0.013 0.002 PHE B 410 TRP 0.019 0.001 TRP C 178 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (14880) covalent geometry : angle 0.60516 / 0.31 (20186) SS BOND : bond 0.00310 / 0.20 ( 38) SS BOND : angle 0.92645 / 0.71 ( 76) hydrogen bonds : bond 0.03283 / 2.14 ( 426) hydrogen bonds : angle 6.28536 / 4.39 ( 1185) Misc. bond : bond 0.00074 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00287 / 0.15 ( 4) link_ALPHA1-2 : angle 2.28689 / 1.23 ( 12) link_ALPHA1-3 : bond 0.00960 / 0.55 ( 8) link_ALPHA1-3 : angle 2.14636 / 1.29 ( 24) link_ALPHA1-6 : bond 0.00640 / 0.35 ( 8) link_ALPHA1-6 : angle 1.39225 / 0.77 ( 24) link_BETA1-4 : bond 0.00567 / 0.30 ( 24) link_BETA1-4 : angle 1.75693 / 1.23 ( 72) link_NAG-ASN : bond 0.00187 / 0.09 ( 24) link_NAG-ASN : angle 2.35149 / 1.61 ( 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 236 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLU cc_start: 0.7259 (mp0) cc_final: 0.6807 (mp0) REVERT: C 121 TYR cc_start: 0.8878 (p90) cc_final: 0.8596 (p90) REVERT: C 128 LYS cc_start: 0.7624 (ptmt) cc_final: 0.7298 (pttt) REVERT: C 257 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7425 (mt) REVERT: C 338 LEU cc_start: 0.7921 (mt) cc_final: 0.7490 (pt) REVERT: D 375 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: E 5 THR cc_start: 0.8293 (m) cc_final: 0.7824 (p) REVERT: E 38 GLN cc_start: 0.8557 (tt0) cc_final: 0.7725 (tt0) REVERT: E 46 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7664 (ttm170) REVERT: E 105 GLU cc_start: 0.7570 (mp0) cc_final: 0.5867 (pp20) outliers start: 54 outliers final: 44 residues processed: 212 average time/residue: 0.1243 time to fit residues: 39.3827 Evaluate side-chains 218 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106376 restraints weight = 19791.545| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.44 r_work: 0.3275 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14987 Z= 0.157 Angle : 0.638 10.220 20466 Z= 0.315 Chirality : 0.047 0.387 2403 Planarity : 0.004 0.039 2508 Dihedral : 7.740 57.858 3304 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.71 % Allowed : 18.57 % Favored : 77.72 % 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 are not related in a simple way. whole: -1.14 (0.19), residues: 1766 helix: -1.01 (0.95), residues: 24 sheet: 0.08 (0.21), residues: 626 loop : -1.31 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.019 0.001 TYR A 121 PHE 0.014 0.002 PHE D 410 TRP 0.018 0.001 TRP C 178 HIS 0.011 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (14880) covalent geometry : angle 0.60406 / 0.31 (20186) SS BOND : bond 0.00280 / 0.18 ( 38) SS BOND : angle 0.78058 / 0.57 ( 76) hydrogen bonds : bond 0.03248 / 2.12 ( 426) hydrogen bonds : angle 6.24924 / 4.36 ( 1185) Misc. bond : bond 0.00075 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00268 / 0.14 ( 4) link_ALPHA1-2 : angle 2.26141 / 1.21 ( 12) link_ALPHA1-3 : bond 0.00944 / 0.53 ( 8) link_ALPHA1-3 : angle 2.11225 / 1.27 ( 24) link_ALPHA1-6 : bond 0.00636 / 0.35 ( 8) link_ALPHA1-6 : angle 1.39629 / 0.77 ( 24) link_BETA1-4 : bond 0.00564 / 0.30 ( 24) link_BETA1-4 : angle 1.72224 / 1.21 ( 72) link_NAG-ASN : bond 0.00199 / 0.10 ( 24) link_NAG-ASN : angle 2.63379 / 1.92 ( 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 234 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLU cc_start: 0.7252 (mp0) cc_final: 0.6843 (mp0) REVERT: B 257 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7803 (mt) REVERT: C 121 TYR cc_start: 0.8861 (p90) cc_final: 0.8539 (p90) REVERT: C 128 LYS cc_start: 0.7601 (ptmt) cc_final: 0.7276 (pttt) REVERT: C 257 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7471 (mt) REVERT: D 375 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: E 5 THR cc_start: 0.8327 (m) cc_final: 0.7860 (p) REVERT: E 38 GLN cc_start: 0.8565 (tt0) cc_final: 0.8081 (tt0) REVERT: E 105 GLU cc_start: 0.7562 (mp0) cc_final: 0.5861 (pp20) REVERT: F 38 ARG cc_start: 0.8172 (ptt-90) cc_final: 0.7944 (ttp80) REVERT: F 43 LYS cc_start: 0.7886 (mmmm) cc_final: 0.7241 (mppt) outliers start: 57 outliers final: 50 residues processed: 209 average time/residue: 0.1223 time to fit residues: 38.6684 Evaluate side-chains 227 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 53 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 347 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.131598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105004 restraints weight = 19977.397| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.44 r_work: 0.3256 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14987 Z= 0.200 Angle : 0.667 10.687 20466 Z= 0.330 Chirality : 0.047 0.354 2403 Planarity : 0.004 0.040 2508 Dihedral : 7.823 58.407 3304 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.58 % Allowed : 18.70 % Favored : 77.72 % 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 are not related in a simple way. whole: -1.23 (0.19), residues: 1766 helix: -0.98 (0.97), residues: 24 sheet: -0.01 (0.21), residues: 618 loop : -1.34 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.019 0.002 TYR B 121 PHE 0.016 0.002 PHE C 132 TRP 0.017 0.002 TRP C 178 HIS 0.011 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (14880) covalent geometry : angle 0.63161 / 0.32 (20186) SS BOND : bond 0.00384 / 0.23 ( 38) SS BOND : angle 1.01451 / 0.63 ( 76) hydrogen bonds : bond 0.03420 / 2.21 ( 426) hydrogen bonds : angle 6.33646 / 4.43 ( 1185) Misc. bond : bond 0.00079 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00190 / 0.10 ( 4) link_ALPHA1-2 : angle 2.35032 / 1.26 ( 12) link_ALPHA1-3 : bond 0.00875 / 0.49 ( 8) link_ALPHA1-3 : angle 2.23451 / 1.33 ( 24) link_ALPHA1-6 : bond 0.00603 / 0.33 ( 8) link_ALPHA1-6 : angle 1.40952 / 0.78 ( 24) link_BETA1-4 : bond 0.00551 / 0.28 ( 24) link_BETA1-4 : angle 1.77292 / 1.23 ( 72) link_NAG-ASN : bond 0.00231 / 0.12 ( 24) link_NAG-ASN : angle 2.66567 / 1.92 ( 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 228 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 173 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 432 GLU cc_start: 0.7322 (mp0) cc_final: 0.6898 (mp0) REVERT: B 257 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7855 (mt) REVERT: C 121 TYR cc_start: 0.8862 (p90) cc_final: 0.8549 (p90) REVERT: C 257 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7504 (mt) REVERT: D 375 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: E 5 THR cc_start: 0.8319 (m) cc_final: 0.7869 (p) REVERT: E 38 GLN cc_start: 0.8587 (tt0) cc_final: 0.8116 (tt0) REVERT: E 105 GLU cc_start: 0.7602 (mp0) cc_final: 0.5811 (pp20) REVERT: F 43 LYS cc_start: 0.7922 (mmmm) cc_final: 0.7278 (mppt) outliers start: 55 outliers final: 48 residues processed: 205 average time/residue: 0.1215 time to fit residues: 37.6414 Evaluate side-chains 221 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 171 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106972 restraints weight = 19682.804| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.44 r_work: 0.3285 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14987 Z= 0.133 Angle : 0.625 10.633 20466 Z= 0.310 Chirality : 0.046 0.297 2403 Planarity : 0.004 0.042 2508 Dihedral : 7.565 59.074 3304 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.13 % Allowed : 19.22 % Favored : 77.65 % 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 are not related in a simple way. whole: -0.99 (0.19), residues: 1766 helix: -0.95 (0.95), residues: 24 sheet: 0.26 (0.22), residues: 590 loop : -1.21 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.014 0.001 TYR C 121 PHE 0.013 0.002 PHE D 354 TRP 0.021 0.001 TRP C 178 HIS 0.006 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14880) covalent geometry : angle 0.59345 / 0.30 (20186) SS BOND : bond 0.00278 / 0.17 ( 38) SS BOND : angle 0.90735 / 0.57 ( 76) hydrogen bonds : bond 0.03150 / 2.06 ( 426) hydrogen bonds : angle 6.19393 / 4.32 ( 1185) Misc. bond : bond 0.00073 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00252 / 0.13 ( 4) link_ALPHA1-2 : angle 2.22494 / 1.19 ( 12) link_ALPHA1-3 : bond 0.00999 / 0.56 ( 8) link_ALPHA1-3 : angle 1.99323 / 1.21 ( 24) link_ALPHA1-6 : bond 0.00659 / 0.36 ( 8) link_ALPHA1-6 : angle 1.39012 / 0.76 ( 24) link_BETA1-4 : bond 0.00573 / 0.30 ( 24) link_BETA1-4 : angle 1.62680 / 1.14 ( 72) link_NAG-ASN : bond 0.00163 / 0.08 ( 24) link_NAG-ASN : angle 2.42397 / 1.74 ( 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 231 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLU cc_start: 0.7214 (mp0) cc_final: 0.6799 (mp0) REVERT: C 121 TYR cc_start: 0.8854 (p90) cc_final: 0.8556 (p90) REVERT: C 257 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7438 (mp) REVERT: D 306 ASN cc_start: 0.7635 (t0) cc_final: 0.7322 (t0) REVERT: D 375 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: D 465 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7968 (m-40) REVERT: E 5 THR cc_start: 0.8297 (m) cc_final: 0.7864 (p) REVERT: E 38 GLN cc_start: 0.8571 (tt0) cc_final: 0.8092 (tt0) REVERT: E 105 GLU cc_start: 0.7562 (mp0) cc_final: 0.5805 (pp20) REVERT: F 38 ARG cc_start: 0.8131 (ptt-90) cc_final: 0.7914 (ttp80) outliers start: 48 outliers final: 40 residues processed: 208 average time/residue: 0.1231 time to fit residues: 38.3742 Evaluate side-chains 219 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 19 optimal weight: 0.0010 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 347 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107808 restraints weight = 19680.024| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.44 r_work: 0.3295 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14987 Z= 0.128 Angle : 0.607 10.436 20466 Z= 0.302 Chirality : 0.045 0.257 2403 Planarity : 0.004 0.042 2508 Dihedral : 7.267 59.181 3304 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.13 % Allowed : 19.35 % Favored : 77.52 % 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 are not related in a simple way. whole: -0.94 (0.19), residues: 1766 helix: -0.92 (0.96), residues: 24 sheet: 0.25 (0.21), residues: 606 loop : -1.16 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.016 0.001 TYR A 121 PHE 0.012 0.002 PHE D 354 TRP 0.022 0.001 TRP C 178 HIS 0.013 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14880) covalent geometry : angle 0.57782 / 0.30 (20186) SS BOND : bond 0.00269 / 0.17 ( 38) SS BOND : angle 0.86004 / 0.55 ( 76) hydrogen bonds : bond 0.03073 / 2.00 ( 426) hydrogen bonds : angle 6.09031 / 4.24 ( 1185) Misc. bond : bond 0.00079 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00287 / 0.14 ( 4) link_ALPHA1-2 : angle 2.11573 / 1.12 ( 12) link_ALPHA1-3 : bond 0.01038 / 0.59 ( 8) link_ALPHA1-3 : angle 1.92200 / 1.16 ( 24) link_ALPHA1-6 : bond 0.00677 / 0.37 ( 8) link_ALPHA1-6 : angle 1.38236 / 0.76 ( 24) link_BETA1-4 : bond 0.00578 / 0.30 ( 24) link_BETA1-4 : angle 1.55344 / 1.10 ( 72) link_NAG-ASN : bond 0.00152 / 0.08 ( 24) link_NAG-ASN : angle 2.27186 / 1.62 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3754.58 seconds wall clock time: 65 minutes 38.08 seconds (3938.08 seconds total)