Starting phenix.real_space_refine on Thu Sep 18 05:59:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvm_39608/09_2025/8yvm_39608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvm_39608/09_2025/8yvm_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_39608/09_2025/8yvm_39608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvm_39608/09_2025/8yvm_39608_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yvm_39608/09_2025/8yvm_39608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvm_39608/09_2025/8yvm_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-2.0-5805/lib/python3.9/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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.76, per 1000 atoms: 0.26 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: 1.53 Conformation dependent library (CDL) restraints added in 629.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 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: 0.43 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: 2.13 Time building geometry restraints manager: 1.96 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 2.510 nonbonded pdb=" O HIS D 347 " pdb="CA CA D 503 " model vdw 2.146 2.510 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.610 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 aren 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 covalent geometry : bond 0.01083 (14880) covalent geometry : angle 1.40563 (20186) SS BOND : bond 0.01013 ( 38) SS BOND : angle 2.21808 ( 76) hydrogen bonds : bond 0.12947 ( 426) hydrogen bonds : angle 7.79071 ( 1185) Misc. bond : bond 0.13816 ( 1) link_ALPHA1-2 : bond 0.00673 ( 4) link_ALPHA1-2 : angle 3.71695 ( 12) link_ALPHA1-3 : bond 0.01743 ( 8) link_ALPHA1-3 : angle 3.86081 ( 24) link_ALPHA1-6 : bond 0.00479 ( 8) link_ALPHA1-6 : angle 1.63677 ( 24) link_BETA1-4 : bond 0.00591 ( 24) link_BETA1-4 : angle 3.91960 ( 72) link_NAG-ASN : bond 0.01552 ( 24) link_NAG-ASN : angle 6.36401 ( 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 : 0.610 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: 0.7324 (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: 0.1612 time to fit residues: 78.6856 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 : 0.651 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3803 r_free = 0.3803 target = 0.137406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110837 restraints weight = 19418.849| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.44 r_work: 0.3343 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14987 Z= 0.158 Angle : 0.764 9.860 20466 Z= 0.369 Chirality : 0.048 0.243 2403 Planarity : 0.004 0.068 2508 Dihedral : 12.085 77.314 3310 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.56 % Allowed : 11.34 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.18), residues: 1766 helix: -1.21 (0.88), residues: 24 sheet: -0.07 (0.20), residues: 651 loop : -1.77 (0.16), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 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 covalent geometry : bond 0.00345 (14880) covalent geometry : angle 0.71735 (20186) SS BOND : bond 0.00306 ( 38) SS BOND : angle 1.02659 ( 76) hydrogen bonds : bond 0.03701 ( 426) hydrogen bonds : angle 6.54780 ( 1185) Misc. bond : bond 0.00010 ( 1) link_ALPHA1-2 : bond 0.00605 ( 4) link_ALPHA1-2 : angle 2.24591 ( 12) link_ALPHA1-3 : bond 0.01047 ( 8) link_ALPHA1-3 : angle 2.36643 ( 24) link_ALPHA1-6 : bond 0.00661 ( 8) link_ALPHA1-6 : angle 1.39995 ( 24) link_BETA1-4 : bond 0.00725 ( 24) link_BETA1-4 : angle 2.51406 ( 72) link_NAG-ASN : bond 0.00654 ( 24) link_NAG-ASN : angle 3.32557 ( 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 254 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.7555 (tttt) cc_final: 0.7314 (ttpp) REVERT: C 318 CYS cc_start: 0.6712 (m) cc_final: 0.6421 (m) REVERT: C 356 ASP cc_start: 0.6250 (t0) cc_final: 0.5968 (t0) REVERT: C 362 MET cc_start: 0.8404 (ptm) cc_final: 0.8203 (ptp) REVERT: D 339 ASP cc_start: 0.8366 (m-30) cc_final: 0.8080 (p0) REVERT: D 375 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: D 402 ASP cc_start: 0.8065 (m-30) cc_final: 0.7863 (m-30) outliers start: 24 outliers final: 15 residues processed: 243 average time/residue: 0.1385 time to fit residues: 48.9458 Evaluate side-chains 207 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 24 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 347 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 441 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109553 restraints weight = 19690.980| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.45 r_work: 0.3320 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14987 Z= 0.147 Angle : 0.676 9.736 20466 Z= 0.330 Chirality : 0.047 0.235 2403 Planarity : 0.004 0.065 2508 Dihedral : 9.811 65.544 3304 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.41 % Allowed : 14.79 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.19), residues: 1766 helix: -0.74 (0.99), residues: 24 sheet: -0.10 (0.20), residues: 664 loop : -1.61 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 327 TYR 0.018 0.001 TYR C 121 PHE 0.013 0.002 PHE B 354 TRP 0.021 0.001 TRP C 178 HIS 0.004 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00328 (14880) covalent geometry : angle 0.63886 (20186) SS BOND : bond 0.00281 ( 38) SS BOND : angle 0.78944 ( 76) hydrogen bonds : bond 0.03424 ( 426) hydrogen bonds : angle 6.32156 ( 1185) Misc. bond : bond 0.00807 ( 1) link_ALPHA1-2 : bond 0.00422 ( 4) link_ALPHA1-2 : angle 2.27408 ( 12) link_ALPHA1-3 : bond 0.01023 ( 8) link_ALPHA1-3 : angle 2.22419 ( 24) link_ALPHA1-6 : bond 0.00627 ( 8) link_ALPHA1-6 : angle 1.39884 ( 24) link_BETA1-4 : bond 0.00683 ( 24) link_BETA1-4 : angle 2.22373 ( 72) link_NAG-ASN : bond 0.00359 ( 24) link_NAG-ASN : angle 2.57307 ( 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 246 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ASP cc_start: 0.6958 (t70) cc_final: 0.6718 (p0) REVERT: A 432 GLU cc_start: 0.7297 (mp0) cc_final: 0.6791 (mp0) REVERT: A 463 ASP cc_start: 0.8313 (t70) cc_final: 0.8101 (t70) REVERT: C 318 CYS cc_start: 0.6457 (m) cc_final: 0.6103 (m) REVERT: C 338 LEU cc_start: 0.7915 (mt) cc_final: 0.7378 (pt) REVERT: C 356 ASP cc_start: 0.6218 (t0) cc_final: 0.5919 (t0) REVERT: C 362 MET cc_start: 0.8446 (ptm) cc_final: 0.8204 (ptp) REVERT: D 339 ASP cc_start: 0.8287 (m-30) cc_final: 0.8067 (p0) REVERT: F 82 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7277 (tm-30) outliers start: 37 outliers final: 25 residues processed: 224 average time/residue: 0.1218 time to fit residues: 40.8783 Evaluate side-chains 215 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 381 GLU 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 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 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: 0.9990 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 167 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 294 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 ** 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 = 0.3770 r_free = 0.3770 target = 0.134658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108106 restraints weight = 19678.431| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.44 r_work: 0.3299 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2648 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 : 0.653 9.542 20466 Z= 0.322 Chirality : 0.046 0.231 2403 Planarity : 0.004 0.117 2508 Dihedral : 8.726 58.747 3304 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.48 % Allowed : 17.13 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.19), residues: 1766 helix: -0.78 (0.98), residues: 24 sheet: -0.04 (0.20), residues: 652 loop : -1.51 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 400 TYR 0.022 0.002 TYR C 121 PHE 0.013 0.002 PHE B 354 TRP 0.018 0.001 TRP C 178 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00353 (14880) covalent geometry : angle 0.61974 (20186) SS BOND : bond 0.00274 ( 38) SS BOND : angle 0.73994 ( 76) hydrogen bonds : bond 0.03342 ( 426) hydrogen bonds : angle 6.30220 ( 1185) Misc. bond : bond 0.00712 ( 1) link_ALPHA1-2 : bond 0.00404 ( 4) link_ALPHA1-2 : angle 2.20366 ( 12) link_ALPHA1-3 : bond 0.00907 ( 8) link_ALPHA1-3 : angle 2.19832 ( 24) link_ALPHA1-6 : bond 0.00624 ( 8) link_ALPHA1-6 : angle 1.38175 ( 24) link_BETA1-4 : bond 0.00634 ( 24) link_BETA1-4 : angle 2.00868 ( 72) link_NAG-ASN : bond 0.00293 ( 24) link_NAG-ASN : angle 2.40372 ( 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 241 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8810 (t0) cc_final: 0.8556 (t0) REVERT: A 432 GLU cc_start: 0.7333 (mp0) cc_final: 0.6855 (mp0) REVERT: C 257 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7423 (mp) REVERT: C 338 LEU cc_start: 0.8022 (mt) cc_final: 0.7467 (pt) REVERT: C 362 MET cc_start: 0.8426 (ptm) cc_final: 0.8181 (ptp) REVERT: D 375 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: E 105 GLU cc_start: 0.7574 (mp0) cc_final: 0.5856 (pp20) REVERT: F 82 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7230 (tm-30) outliers start: 38 outliers final: 29 residues processed: 222 average time/residue: 0.1206 time to fit residues: 40.4410 Evaluate side-chains 218 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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 257 ILE 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 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: 0.8980 chunk 53 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** 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 274 HIS ** D 347 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 = 0.3764 r_free = 0.3764 target = 0.134130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107451 restraints weight = 19801.860| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.46 r_work: 0.3284 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14987 Z= 0.157 Angle : 0.639 9.610 20466 Z= 0.315 Chirality : 0.046 0.229 2403 Planarity : 0.004 0.038 2508 Dihedral : 8.156 57.205 3304 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.74 % Allowed : 17.98 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.19), residues: 1766 helix: -0.94 (0.97), residues: 24 sheet: -0.05 (0.20), residues: 660 loop : -1.44 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.016 0.001 TYR B 121 PHE 0.012 0.002 PHE B 354 TRP 0.017 0.001 TRP C 178 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00355 (14880) covalent geometry : angle 0.60625 (20186) SS BOND : bond 0.00261 ( 38) SS BOND : angle 0.69455 ( 76) hydrogen bonds : bond 0.03345 ( 426) hydrogen bonds : angle 6.29270 ( 1185) Misc. bond : bond 0.00383 ( 1) link_ALPHA1-2 : bond 0.00350 ( 4) link_ALPHA1-2 : angle 2.23819 ( 12) link_ALPHA1-3 : bond 0.00973 ( 8) link_ALPHA1-3 : angle 2.16063 ( 24) link_ALPHA1-6 : bond 0.00654 ( 8) link_ALPHA1-6 : angle 1.39047 ( 24) link_BETA1-4 : bond 0.00576 ( 24) link_BETA1-4 : angle 1.86795 ( 72) link_NAG-ASN : bond 0.00203 ( 24) link_NAG-ASN : angle 2.43256 ( 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 229 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8837 (t0) cc_final: 0.8535 (t0) REVERT: A 432 GLU cc_start: 0.7306 (mp0) cc_final: 0.6870 (mp0) REVERT: C 338 LEU cc_start: 0.7973 (mt) cc_final: 0.7414 (pt) REVERT: C 362 MET cc_start: 0.8304 (ptm) cc_final: 0.8066 (ptp) REVERT: E 105 GLU cc_start: 0.7597 (mp0) cc_final: 0.5886 (pp20) outliers start: 42 outliers final: 34 residues processed: 205 average time/residue: 0.1245 time to fit residues: 37.9072 Evaluate side-chains 211 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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 314 SER Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain C residue 117 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 314 SER Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 369 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 441 ASN ** 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 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103660 restraints weight = 19914.725| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.42 r_work: 0.3236 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14987 Z= 0.249 Angle : 0.718 9.676 20466 Z= 0.357 Chirality : 0.048 0.252 2403 Planarity : 0.004 0.038 2508 Dihedral : 8.421 59.135 3304 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.58 % Allowed : 17.46 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.19), residues: 1766 helix: -1.02 (0.98), residues: 24 sheet: -0.24 (0.20), residues: 652 loop : -1.52 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 18 TYR 0.023 0.002 TYR C 121 PHE 0.018 0.002 PHE D 410 TRP 0.016 0.002 TRP C 178 HIS 0.008 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00571 (14880) covalent geometry : angle 0.68246 (20186) SS BOND : bond 0.00370 ( 38) SS BOND : angle 0.89434 ( 76) hydrogen bonds : bond 0.03742 ( 426) hydrogen bonds : angle 6.60746 ( 1185) Misc. bond : bond 0.00109 ( 1) link_ALPHA1-2 : bond 0.00209 ( 4) link_ALPHA1-2 : angle 2.58732 ( 12) link_ALPHA1-3 : bond 0.00787 ( 8) link_ALPHA1-3 : angle 2.53238 ( 24) link_ALPHA1-6 : bond 0.00552 ( 8) link_ALPHA1-6 : angle 1.46891 ( 24) link_BETA1-4 : bond 0.00556 ( 24) link_BETA1-4 : angle 1.98780 ( 72) link_NAG-ASN : bond 0.00318 ( 24) link_NAG-ASN : angle 2.69362 ( 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 235 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8797 (t0) cc_final: 0.8479 (t0) REVERT: A 432 GLU cc_start: 0.7325 (mp0) cc_final: 0.6919 (mp0) REVERT: B 257 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7853 (mt) REVERT: C 257 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7488 (mt) REVERT: C 362 MET cc_start: 0.8401 (ptm) cc_final: 0.8147 (ptp) REVERT: D 336 HIS cc_start: 0.7633 (t-90) cc_final: 0.7378 (t-90) REVERT: D 375 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: E 38 GLN cc_start: 0.8595 (tt0) cc_final: 0.8126 (tt0) REVERT: F 43 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7366 (mppt) outliers start: 55 outliers final: 42 residues processed: 212 average time/residue: 0.1262 time to fit residues: 40.2952 Evaluate side-chains 216 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 229 GLU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 314 SER 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 356 ASP 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 338 LEU 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: 4.9990 chunk 146 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** 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 310 HIS D 347 HIS 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 = 0.3753 r_free = 0.3753 target = 0.133178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106826 restraints weight = 19696.583| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.42 r_work: 0.3281 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14987 Z= 0.132 Angle : 0.632 9.830 20466 Z= 0.312 Chirality : 0.046 0.341 2403 Planarity : 0.004 0.038 2508 Dihedral : 7.874 58.495 3304 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.00 % Allowed : 18.57 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.19), residues: 1766 helix: -1.03 (0.93), residues: 24 sheet: 0.10 (0.21), residues: 616 loop : -1.31 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 150 TYR 0.012 0.001 TYR D 121 PHE 0.014 0.002 PHE D 354 TRP 0.021 0.001 TRP C 178 HIS 0.002 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00292 (14880) covalent geometry : angle 0.59896 (20186) SS BOND : bond 0.00276 ( 38) SS BOND : angle 0.90967 ( 76) hydrogen bonds : bond 0.03214 ( 426) hydrogen bonds : angle 6.30548 ( 1185) Misc. bond : bond 0.00093 ( 1) link_ALPHA1-2 : bond 0.00270 ( 4) link_ALPHA1-2 : angle 2.30738 ( 12) link_ALPHA1-3 : bond 0.01037 ( 8) link_ALPHA1-3 : angle 2.05663 ( 24) link_ALPHA1-6 : bond 0.00665 ( 8) link_ALPHA1-6 : angle 1.38987 ( 24) link_BETA1-4 : bond 0.00597 ( 24) link_BETA1-4 : angle 1.70497 ( 72) link_NAG-ASN : bond 0.00172 ( 24) link_NAG-ASN : angle 2.52001 ( 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 228 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8846 (t0) cc_final: 0.8583 (t0) REVERT: A 432 GLU cc_start: 0.7247 (mp0) cc_final: 0.6784 (mp0) REVERT: B 406 TYR cc_start: 0.8707 (m-10) cc_final: 0.8464 (m-80) REVERT: C 121 TYR cc_start: 0.8762 (p90) cc_final: 0.8536 (p90) REVERT: C 257 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7412 (mp) REVERT: C 338 LEU cc_start: 0.7984 (mt) cc_final: 0.7441 (pt) REVERT: C 362 MET cc_start: 0.8354 (ptm) cc_final: 0.8096 (ptp) REVERT: D 375 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: D 381 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7103 (mt-10) REVERT: E 5 THR cc_start: 0.8259 (m) cc_final: 0.7813 (p) REVERT: E 38 GLN cc_start: 0.8557 (tt0) cc_final: 0.8067 (tt0) REVERT: E 105 GLU cc_start: 0.7464 (mp0) cc_final: 0.5548 (pp20) outliers start: 46 outliers final: 38 residues processed: 208 average time/residue: 0.1165 time to fit residues: 36.9101 Evaluate side-chains 215 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 229 GLU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 314 SER 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 313 VAL Chi-restraints excluded: chain C residue 356 ASP 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 338 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 149 optimal weight: 0.0770 chunk 97 optimal weight: 0.9980 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 274 HIS ** D 347 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 = 0.3735 r_free = 0.3735 target = 0.131852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105416 restraints weight = 19887.158| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.43 r_work: 0.3260 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.004 0.042 14987 Z= 0.178 Angle : 0.652 9.884 20466 Z= 0.323 Chirality : 0.047 0.292 2403 Planarity : 0.004 0.039 2508 Dihedral : 7.810 58.291 3304 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.39 % Allowed : 18.96 % 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 aren not related in a simple way. whole: -1.26 (0.19), residues: 1766 helix: -1.03 (0.95), residues: 24 sheet: -0.07 (0.21), residues: 598 loop : -1.31 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 18 TYR 0.016 0.002 TYR B 121 PHE 0.015 0.002 PHE C 132 TRP 0.018 0.002 TRP C 178 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00410 (14880) covalent geometry : angle 0.61883 (20186) SS BOND : bond 0.00332 ( 38) SS BOND : angle 0.97673 ( 76) hydrogen bonds : bond 0.03368 ( 426) hydrogen bonds : angle 6.36035 ( 1185) Misc. bond : bond 0.00092 ( 1) link_ALPHA1-2 : bond 0.00207 ( 4) link_ALPHA1-2 : angle 2.32904 ( 12) link_ALPHA1-3 : bond 0.00903 ( 8) link_ALPHA1-3 : angle 2.20109 ( 24) link_ALPHA1-6 : bond 0.00608 ( 8) link_ALPHA1-6 : angle 1.41922 ( 24) link_BETA1-4 : bond 0.00547 ( 24) link_BETA1-4 : angle 1.75465 ( 72) link_NAG-ASN : bond 0.00214 ( 24) link_NAG-ASN : angle 2.51728 ( 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 226 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8452 (ttt90) REVERT: A 147 ASN cc_start: 0.8804 (t0) cc_final: 0.8514 (t0) REVERT: A 432 GLU cc_start: 0.7262 (mp0) cc_final: 0.6842 (mp0) REVERT: C 121 TYR cc_start: 0.8881 (p90) cc_final: 0.8605 (p90) REVERT: C 257 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7444 (mt) REVERT: C 362 MET cc_start: 0.8347 (ptm) cc_final: 0.8070 (ptp) REVERT: D 336 HIS cc_start: 0.7675 (t-90) cc_final: 0.7308 (t-90) REVERT: D 375 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: D 381 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7105 (mt-10) REVERT: D 465 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7955 (m-40) REVERT: E 5 THR cc_start: 0.8299 (m) cc_final: 0.7848 (p) REVERT: E 38 GLN cc_start: 0.8573 (tt0) cc_final: 0.8133 (tt0) REVERT: E 105 GLU cc_start: 0.7484 (mp0) cc_final: 0.5471 (pp20) outliers start: 52 outliers final: 41 residues processed: 206 average time/residue: 0.1231 time to fit residues: 37.7510 Evaluate side-chains 212 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 118 ARG 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 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 238 THR Chi-restraints excluded: chain B residue 314 SER 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 183 CYS Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 356 ASP 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 338 LEU 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 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 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: 0.9980 chunk 162 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106482 restraints weight = 19898.175| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.43 r_work: 0.3277 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14987 Z= 0.148 Angle : 0.630 9.947 20466 Z= 0.313 Chirality : 0.046 0.251 2403 Planarity : 0.004 0.042 2508 Dihedral : 7.652 58.385 3304 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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 aren not related in a simple way. whole: -1.06 (0.19), residues: 1766 helix: -1.01 (0.95), residues: 24 sheet: 0.18 (0.21), residues: 598 loop : -1.23 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.014 0.001 TYR B 121 PHE 0.015 0.002 PHE B 410 TRP 0.021 0.001 TRP C 178 HIS 0.003 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00337 (14880) covalent geometry : angle 0.59958 (20186) SS BOND : bond 0.00275 ( 38) SS BOND : angle 0.86327 ( 76) hydrogen bonds : bond 0.03232 ( 426) hydrogen bonds : angle 6.25691 ( 1185) Misc. bond : bond 0.00083 ( 1) link_ALPHA1-2 : bond 0.00230 ( 4) link_ALPHA1-2 : angle 2.26102 ( 12) link_ALPHA1-3 : bond 0.00979 ( 8) link_ALPHA1-3 : angle 2.06670 ( 24) link_ALPHA1-6 : bond 0.00635 ( 8) link_ALPHA1-6 : angle 1.39690 ( 24) link_BETA1-4 : bond 0.00562 ( 24) link_BETA1-4 : angle 1.66397 ( 72) link_NAG-ASN : bond 0.00171 ( 24) link_NAG-ASN : angle 2.36588 ( 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 224 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8819 (t0) cc_final: 0.8535 (t0) REVERT: A 432 GLU cc_start: 0.7250 (mp0) cc_final: 0.6818 (mp0) REVERT: B 406 TYR cc_start: 0.8749 (m-10) cc_final: 0.8532 (m-80) REVERT: C 121 TYR cc_start: 0.8867 (p90) cc_final: 0.8553 (p90) REVERT: C 257 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7469 (mp) REVERT: C 362 MET cc_start: 0.8330 (ptm) cc_final: 0.8042 (ptp) REVERT: D 306 ASN cc_start: 0.7641 (t0) cc_final: 0.7329 (t0) REVERT: D 336 HIS cc_start: 0.7721 (t-90) cc_final: 0.7346 (t-90) REVERT: D 375 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: E 5 THR cc_start: 0.8277 (m) cc_final: 0.7842 (p) REVERT: E 38 GLN cc_start: 0.8590 (tt0) cc_final: 0.8152 (tt0) REVERT: E 105 GLU cc_start: 0.7416 (mp0) cc_final: 0.5468 (pp20) REVERT: F 38 ARG cc_start: 0.8163 (ptt-90) cc_final: 0.7924 (ttp80) outliers start: 48 outliers final: 41 residues processed: 203 average time/residue: 0.1282 time to fit residues: 38.7310 Evaluate side-chains 216 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 183 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 314 SER 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 183 CYS Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 356 ASP 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 338 LEU 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 440 SER 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: 1.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106195 restraints weight = 19806.103| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.46 r_work: 0.3273 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14987 Z= 0.156 Angle : 0.632 9.869 20466 Z= 0.314 Chirality : 0.046 0.240 2403 Planarity : 0.004 0.042 2508 Dihedral : 7.530 59.279 3304 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.93 % Allowed : 19.48 % Favored : 77.59 % 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 aren not related in a simple way. whole: -1.06 (0.19), residues: 1766 helix: -1.04 (0.95), residues: 24 sheet: 0.15 (0.21), residues: 598 loop : -1.22 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.015 0.001 TYR B 121 PHE 0.016 0.002 PHE B 410 TRP 0.020 0.001 TRP C 178 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00357 (14880) covalent geometry : angle 0.60210 (20186) SS BOND : bond 0.00281 ( 38) SS BOND : angle 0.86292 ( 76) hydrogen bonds : bond 0.03244 ( 426) hydrogen bonds : angle 6.24572 ( 1185) Misc. bond : bond 0.00087 ( 1) link_ALPHA1-2 : bond 0.00203 ( 4) link_ALPHA1-2 : angle 2.23672 ( 12) link_ALPHA1-3 : bond 0.00927 ( 8) link_ALPHA1-3 : angle 2.04928 ( 24) link_ALPHA1-6 : bond 0.00632 ( 8) link_ALPHA1-6 : angle 1.39968 ( 24) link_BETA1-4 : bond 0.00554 ( 24) link_BETA1-4 : angle 1.63712 ( 72) link_NAG-ASN : bond 0.00178 ( 24) link_NAG-ASN : angle 2.32671 ( 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 225 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8794 (t0) cc_final: 0.8518 (t0) REVERT: A 245 SER cc_start: 0.7753 (t) cc_final: 0.7411 (p) REVERT: A 432 GLU cc_start: 0.7250 (mp0) cc_final: 0.6810 (mp0) REVERT: B 406 TYR cc_start: 0.8749 (m-10) cc_final: 0.8526 (m-80) REVERT: C 121 TYR cc_start: 0.8864 (p90) cc_final: 0.8558 (p90) REVERT: C 257 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7478 (mp) REVERT: C 362 MET cc_start: 0.8405 (ptm) cc_final: 0.8133 (ptp) REVERT: D 306 ASN cc_start: 0.7650 (t0) cc_final: 0.7340 (t0) REVERT: D 336 HIS cc_start: 0.7693 (t-90) cc_final: 0.7256 (t-90) REVERT: D 375 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: E 5 THR cc_start: 0.8323 (m) cc_final: 0.7904 (p) REVERT: E 38 GLN cc_start: 0.8601 (tt0) cc_final: 0.8167 (tt0) REVERT: E 105 GLU cc_start: 0.7459 (mp0) cc_final: 0.5585 (pp20) REVERT: F 38 ARG cc_start: 0.8149 (ptt-90) cc_final: 0.7915 (ttp80) outliers start: 45 outliers final: 42 residues processed: 206 average time/residue: 0.1241 time to fit residues: 38.3564 Evaluate side-chains 221 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 183 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 314 SER 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 183 CYS Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 356 ASP 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 338 LEU 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 440 SER 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: 0.0670 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3743 r_free = 0.3743 target = 0.132409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.105814 restraints weight = 19878.710| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.44 r_work: 0.3263 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14987 Z= 0.166 Angle : 0.636 10.391 20466 Z= 0.317 Chirality : 0.047 0.238 2403 Planarity : 0.004 0.042 2508 Dihedral : 7.486 58.680 3304 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.06 % Allowed : 19.61 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.19), residues: 1766 helix: -0.99 (0.96), residues: 24 sheet: 0.12 (0.21), residues: 598 loop : -1.23 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.016 0.001 TYR B 121 PHE 0.016 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 covalent geometry : bond 0.00380 (14880) covalent geometry : angle 0.60683 (20186) SS BOND : bond 0.00289 ( 38) SS BOND : angle 0.85469 ( 76) hydrogen bonds : bond 0.03274 ( 426) hydrogen bonds : angle 6.25800 ( 1185) Misc. bond : bond 0.00093 ( 1) link_ALPHA1-2 : bond 0.00177 ( 4) link_ALPHA1-2 : angle 2.26282 ( 12) link_ALPHA1-3 : bond 0.00930 ( 8) link_ALPHA1-3 : angle 2.07876 ( 24) link_ALPHA1-6 : bond 0.00616 ( 8) link_ALPHA1-6 : angle 1.40302 ( 24) link_BETA1-4 : bond 0.00551 ( 24) link_BETA1-4 : angle 1.63597 ( 72) link_NAG-ASN : bond 0.00184 ( 24) link_NAG-ASN : angle 2.31764 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3645.93 seconds wall clock time: 63 minutes 37.76 seconds (3817.76 seconds total)