Starting phenix.real_space_refine on Tue May 20 16:28:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3v_29710/05_2025/8g3v_29710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3v_29710/05_2025/8g3v_29710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3v_29710/05_2025/8g3v_29710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3v_29710/05_2025/8g3v_29710.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3v_29710/05_2025/8g3v_29710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3v_29710/05_2025/8g3v_29710.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 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 5 9.91 5 S 116 5.16 5 C 12484 2.51 5 N 3416 2.21 5 O 4024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20045 Number of models: 1 Model: "" Number of chains: 28 Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "A" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: "I" 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: "J" 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: 13.12, per 1000 atoms: 0.65 Number of scatterers: 20045 At special positions: 0 Unit cell: (131.97, 131.97, 102.92, 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 5 19.99 S 116 16.00 O 4024 8.00 N 3416 7.00 C 12484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.06 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.07 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.08 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.11 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.11 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.10 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.10 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.15 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.06 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.07 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.11 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.11 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.10 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.10 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.15 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.05 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.07 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 417 " distance=2.06 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS I 129 " distance=2.07 Simple disulfide: pdb=" SG CYS I 175 " - pdb=" SG CYS I 193 " distance=2.03 Simple disulfide: pdb=" SG CYS I 183 " - pdb=" SG CYS I 230 " distance=2.08 Simple disulfide: pdb=" SG CYS I 232 " - pdb=" SG CYS I 237 " distance=2.11 Simple disulfide: pdb=" SG CYS I 278 " - pdb=" SG CYS I 291 " distance=2.11 Simple disulfide: pdb=" SG CYS I 280 " - pdb=" SG CYS I 289 " distance=2.10 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.10 Simple disulfide: pdb=" SG CYS I 421 " - pdb=" SG CYS I 447 " distance=2.15 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.07 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.06 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.07 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.08 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.11 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.11 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.10 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.15 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN Q 4 " - " MAN Q 5 " " MAN T 4 " - " MAN T 5 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 6 " - " MAN Q 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA W 3 " - " MAN W 4 " " MAN W 6 " - " MAN W 7 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " MAN F 6 " - " MAN F 8 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 6 " - " MAN Q 8 " " BMA T 3 " - " MAN T 6 " " MAN T 6 " - " MAN T 8 " " BMA W 3 " - " MAN W 6 " " MAN W 6 " - " MAN W 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN G 86 " " NAG F 1 " - " ASN G 200 " " NAG G1101 " - " ASN G 146 " " NAG G1102 " - " ASN G 367 " " NAG H1101 " - " ASN H 146 " " NAG H1102 " - " ASN H 367 " " NAG I1101 " - " ASN I 146 " " NAG I1102 " - " ASN I 367 " " NAG J1101 " - " ASN J 146 " " NAG J1102 " - " ASN J 367 " " NAG K 1 " - " ASN G 234 " " NAG P 1 " - " ASN H 86 " " NAG Q 1 " - " ASN H 200 " " NAG R 1 " - " ASN H 234 " " NAG S 1 " - " ASN I 86 " " NAG T 1 " - " ASN I 200 " " NAG U 1 " - " ASN I 234 " " NAG V 1 " - " ASN J 86 " " NAG W 1 " - " ASN J 200 " " NAG X 1 " - " ASN J 234 " Time building additional restraints: 5.70 Conformation dependent library (CDL) restraints added in 2.6 seconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.1% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.690A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.560A pdb=" N LYS A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.691A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.558A pdb=" N LYS B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.659A pdb=" N PHE M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.689A pdb=" N ASN I 146 " --> pdb=" O VAL I 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.561A pdb=" N LYS C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.679A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.561A pdb=" N LYS D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE O 83 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.802A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.796A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.116A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP G 213 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.527A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.381A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.082A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.497A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.487A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.241A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.249A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 40 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE A 117 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER L 67 " --> pdb=" O GLN L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.474A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.804A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.797A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.121A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP H 213 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.381A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 353 through 356 removed outlier: 7.085A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.500A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.525A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.252A pdb=" N LEU B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE B 117 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AC5, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER M 67 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY I 96 " --> pdb=" O THR I 449 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL I 445 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS I 102 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE I 443 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG I 420 " --> pdb=" O GLY I 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 115 through 124 removed outlier: 4.795A pdb=" N TRP I 115 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR I 138 " --> pdb=" O TRP I 115 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR I 117 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN I 136 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU I 119 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU I 134 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR I 157 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS I 172 " --> pdb=" O MET I 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 179 through 184 removed outlier: 4.114A pdb=" N ASP I 197 " --> pdb=" O ASN I 200 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP I 213 " --> pdb=" O PHE I 205 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR I 207 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU I 211 " --> pdb=" O TYR I 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU I 258 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE I 262 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 276 through 283 removed outlier: 5.384A pdb=" N GLU I 277 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG I 292 " --> pdb=" O GLU I 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 353 through 356 removed outlier: 7.093A pdb=" N ASP I 402 " --> pdb=" O GLY I 373 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N GLU I 375 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N ARG I 400 " --> pdb=" O GLU I 375 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N PHE I 377 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 13.491A pdb=" N VAL I 398 " --> pdb=" O PHE I 377 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N VAL I 379 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL I 396 " --> pdb=" O VAL I 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.261A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE C 117 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER N 67 " --> pdb=" O GLN N 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.476A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.798A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.119A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP J 213 " --> pdb=" O PHE J 205 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 231 through 233 removed outlier: 6.525A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.383A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 353 through 356 removed outlier: 7.092A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.259A pdb=" N LEU D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE D 117 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AF2, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.850A pdb=" N GLN O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER O 67 " --> pdb=" O GLN O 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.477A pdb=" N LEU O 33 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 6.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3703 1.32 - 1.45: 5439 1.45 - 1.57: 11206 1.57 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 20492 Sorted by residual: bond pdb=" N VAL O 58 " pdb=" CA VAL O 58 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.00e+01 bond pdb=" CA SER J 457 " pdb=" CB SER J 457 " ideal model delta sigma weight residual 1.534 1.460 0.074 1.72e-02 3.38e+03 1.85e+01 bond pdb=" CA SER H 457 " pdb=" CB SER H 457 " ideal model delta sigma weight residual 1.534 1.463 0.070 1.72e-02 3.38e+03 1.67e+01 bond pdb=" N VAL G 165 " pdb=" CA VAL G 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 bond pdb=" N VAL I 165 " pdb=" CA VAL I 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 ... (remaining 20487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 24137 2.38 - 4.77: 3467 4.77 - 7.15: 203 7.15 - 9.53: 13 9.53 - 11.91: 4 Bond angle restraints: 27824 Sorted by residual: angle pdb=" C ARG I 430 " pdb=" N LYS I 431 " pdb=" CA LYS I 431 " ideal model delta sigma weight residual 121.54 133.45 -11.91 1.91e+00 2.74e-01 3.89e+01 angle pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta sigma weight residual 121.54 133.42 -11.88 1.91e+00 2.74e-01 3.87e+01 angle pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta sigma weight residual 121.54 133.41 -11.87 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.86e+01 angle pdb=" N ILE J 397 " pdb=" CA ILE J 397 " pdb=" C ILE J 397 " ideal model delta sigma weight residual 111.67 106.00 5.67 9.50e-01 1.11e+00 3.56e+01 ... (remaining 27819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.51: 12055 20.51 - 41.03: 576 41.03 - 61.54: 102 61.54 - 82.05: 63 82.05 - 102.56: 24 Dihedral angle restraints: 12820 sinusoidal: 5708 harmonic: 7112 Sorted by residual: dihedral pdb=" CA ARG G 430 " pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta harmonic sigma weight residual -180.00 -143.33 -36.67 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA ARG H 430 " pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta harmonic sigma weight residual -180.00 -143.45 -36.55 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA ARG J 430 " pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta harmonic sigma weight residual -180.00 -143.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 12817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1388 0.056 - 0.113: 1105 0.113 - 0.169: 483 0.169 - 0.225: 185 0.225 - 0.282: 35 Chirality restraints: 3196 Sorted by residual: chirality pdb=" C1 MAN Q 4 " pdb=" O3 BMA Q 3 " pdb=" C2 MAN Q 4 " pdb=" O5 MAN Q 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.93e+01 chirality pdb=" C1 MAN W 4 " pdb=" O3 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.67e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.11e+01 ... (remaining 3193 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " -0.088 2.00e-02 2.50e+03 7.60e-02 7.21e+01 pdb=" C7 NAG Q 1 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " -0.078 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " 0.107 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.087 2.00e-02 2.50e+03 7.54e-02 7.11e+01 pdb=" C7 NAG F 1 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.077 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.087 2.00e-02 2.50e+03 7.48e-02 7.00e+01 pdb=" C7 NAG W 1 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.076 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.001 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2596 2.79 - 3.31: 19147 3.31 - 3.84: 35950 3.84 - 4.37: 46110 4.37 - 4.90: 73522 Nonbonded interactions: 177325 Sorted by model distance: nonbonded pdb=" O ASP G 293 " pdb="CA CA G1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP I 293 " pdb="CA CA I1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP H 293 " pdb="CA CA H1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP J 293 " pdb="CA CA J1103 " model vdw 2.265 2.510 nonbonded pdb=" O GLY J 345 " pdb="CA CA J1103 " model vdw 2.323 2.510 ... (remaining 177320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'T' selection = chain 'W' } ncs_group { reference = (chain 'G' and (resid 82 through 469 or resid 1101 through 1103)) selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 47.300 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 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 : 0.014 0.120 20592 Z= 0.989 Angle : 1.638 11.913 28080 Z= 1.045 Chirality : 0.092 0.282 3196 Planarity : 0.010 0.076 3500 Dihedral : 14.337 102.563 8160 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.88 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2476 helix: 0.14 (0.94), residues: 24 sheet: 0.03 (0.16), residues: 1012 loop : -0.88 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.016 TRP H 458 HIS 0.024 0.006 HIS H 168 PHE 0.066 0.012 PHE G 205 TYR 0.060 0.013 TYR H 281 ARG 0.020 0.003 ARG G 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 20) link_NAG-ASN : angle 4.25351 ( 60) link_ALPHA1-6 : bond 0.00930 ( 8) link_ALPHA1-6 : angle 2.39121 ( 24) link_BETA1-4 : bond 0.01402 ( 16) link_BETA1-4 : angle 4.05015 ( 48) link_ALPHA1-2 : bond 0.00384 ( 4) link_ALPHA1-2 : angle 5.62704 ( 12) link_ALPHA1-3 : bond 0.01399 ( 8) link_ALPHA1-3 : angle 3.16599 ( 24) hydrogen bonds : bond 0.13550 ( 656) hydrogen bonds : angle 8.33451 ( 1728) SS BOND : bond 0.06185 ( 44) SS BOND : angle 2.27667 ( 88) covalent geometry : bond 0.01388 (20492) covalent geometry : angle 1.61122 (27824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 2.322 Fit side-chains REVERT: G 400 ARG cc_start: 0.8987 (ptm-80) cc_final: 0.8568 (ptm160) REVERT: G 467 MET cc_start: 0.9081 (ptm) cc_final: 0.8878 (ptm) REVERT: A 10 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8503 (mt-10) REVERT: A 62 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8282 (tp-100) REVERT: L 61 ARG cc_start: 0.9078 (ptt-90) cc_final: 0.8828 (ptt-90) REVERT: L 82 ASP cc_start: 0.9266 (m-30) cc_final: 0.9047 (m-30) REVERT: H 400 ARG cc_start: 0.8991 (ptm-80) cc_final: 0.8573 (ptm160) REVERT: B 10 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8498 (mt-10) REVERT: B 62 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8268 (tp-100) REVERT: M 61 ARG cc_start: 0.9084 (ptt-90) cc_final: 0.8832 (ptt-90) REVERT: M 82 ASP cc_start: 0.9269 (m-30) cc_final: 0.9049 (m-30) REVERT: I 400 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8558 (ptm160) REVERT: C 10 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8497 (mt-10) REVERT: C 62 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8283 (tp-100) REVERT: N 61 ARG cc_start: 0.9081 (ptt-90) cc_final: 0.8831 (ptt-90) REVERT: N 82 ASP cc_start: 0.9267 (m-30) cc_final: 0.9046 (m-30) REVERT: J 247 THR cc_start: 0.7304 (m) cc_final: 0.6837 (p) REVERT: J 400 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8559 (ptm160) REVERT: D 10 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8501 (mt-10) REVERT: D 62 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8331 (tp-100) REVERT: O 61 ARG cc_start: 0.9085 (ptt-90) cc_final: 0.8826 (ptt-90) REVERT: O 82 ASP cc_start: 0.9270 (m-30) cc_final: 0.9045 (m-30) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 1.4912 time to fit residues: 551.8535 Evaluate side-chains 277 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS A 65 GLN L 6 GLN H 347 HIS B 65 GLN M 6 GLN I 347 HIS C 65 GLN N 6 GLN J 347 HIS O 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.069735 restraints weight = 27830.696| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.18 r_work: 0.2700 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20592 Z= 0.166 Angle : 0.680 7.178 28080 Z= 0.364 Chirality : 0.048 0.155 3196 Planarity : 0.004 0.033 3500 Dihedral : 9.310 78.798 3848 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.42 % Favored : 97.25 % Rotamer: Outliers : 1.27 % Allowed : 8.68 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2476 helix: -0.43 (0.84), residues: 24 sheet: 0.24 (0.15), residues: 1080 loop : -0.10 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 178 HIS 0.005 0.001 HIS J 347 PHE 0.013 0.002 PHE J 410 TYR 0.014 0.002 TYR J 121 ARG 0.003 0.001 ARG I 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 20) link_NAG-ASN : angle 3.04093 ( 60) link_ALPHA1-6 : bond 0.00674 ( 8) link_ALPHA1-6 : angle 1.40869 ( 24) link_BETA1-4 : bond 0.00565 ( 16) link_BETA1-4 : angle 1.98224 ( 48) link_ALPHA1-2 : bond 0.00486 ( 4) link_ALPHA1-2 : angle 2.46145 ( 12) link_ALPHA1-3 : bond 0.00964 ( 8) link_ALPHA1-3 : angle 2.01438 ( 24) hydrogen bonds : bond 0.04907 ( 656) hydrogen bonds : angle 6.84166 ( 1728) SS BOND : bond 0.00319 ( 44) SS BOND : angle 0.74589 ( 88) covalent geometry : bond 0.00356 (20492) covalent geometry : angle 0.65575 (27824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 2.255 Fit side-chains REVERT: G 400 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.7850 (ptm160) REVERT: A 62 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7509 (tp-100) REVERT: L 61 ARG cc_start: 0.8881 (ptt-90) cc_final: 0.8517 (ptt-90) REVERT: L 82 ASP cc_start: 0.9105 (m-30) cc_final: 0.8794 (m-30) REVERT: L 101 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8329 (mm110) REVERT: H 400 ARG cc_start: 0.8453 (ptm-80) cc_final: 0.7871 (ptm160) REVERT: B 62 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7540 (tp-100) REVERT: M 61 ARG cc_start: 0.8889 (ptt-90) cc_final: 0.8522 (ptt-90) REVERT: M 82 ASP cc_start: 0.9098 (m-30) cc_final: 0.8786 (m-30) REVERT: M 101 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8334 (mm110) REVERT: I 400 ARG cc_start: 0.8405 (ptm-80) cc_final: 0.7863 (ptm160) REVERT: C 62 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7512 (tp-100) REVERT: N 61 ARG cc_start: 0.8895 (ptt-90) cc_final: 0.8532 (ptt-90) REVERT: N 82 ASP cc_start: 0.9104 (m-30) cc_final: 0.8798 (m-30) REVERT: N 101 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8326 (mm110) REVERT: J 400 ARG cc_start: 0.8395 (ptm-80) cc_final: 0.7856 (ptm160) REVERT: D 62 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7736 (mm-40) REVERT: O 61 ARG cc_start: 0.8889 (ptt-90) cc_final: 0.8528 (ptt-90) REVERT: O 82 ASP cc_start: 0.9110 (m-30) cc_final: 0.8803 (m-30) REVERT: O 101 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8319 (mm110) outliers start: 27 outliers final: 8 residues processed: 285 average time/residue: 1.4046 time to fit residues: 449.2910 Evaluate side-chains 264 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 256 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 190 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 0.2980 chunk 197 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 65 GLN L 6 GLN B 65 GLN M 6 GLN C 30 ASN C 65 GLN N 6 GLN J 141 ASN D 30 ASN O 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.068525 restraints weight = 28118.441| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.18 r_work: 0.2685 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20592 Z= 0.203 Angle : 0.645 6.364 28080 Z= 0.342 Chirality : 0.047 0.171 3196 Planarity : 0.004 0.040 3500 Dihedral : 8.549 70.923 3848 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.99 % Favored : 96.69 % Rotamer: Outliers : 1.93 % Allowed : 9.86 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2476 helix: 0.22 (0.93), residues: 24 sheet: 0.41 (0.16), residues: 1012 loop : -0.12 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 115 HIS 0.004 0.001 HIS H 168 PHE 0.013 0.002 PHE J 410 TYR 0.015 0.002 TYR H 121 ARG 0.004 0.000 ARG I 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 20) link_NAG-ASN : angle 2.76087 ( 60) link_ALPHA1-6 : bond 0.00454 ( 8) link_ALPHA1-6 : angle 1.41629 ( 24) link_BETA1-4 : bond 0.00415 ( 16) link_BETA1-4 : angle 1.85477 ( 48) link_ALPHA1-2 : bond 0.00158 ( 4) link_ALPHA1-2 : angle 2.65131 ( 12) link_ALPHA1-3 : bond 0.00631 ( 8) link_ALPHA1-3 : angle 2.10368 ( 24) hydrogen bonds : bond 0.04599 ( 656) hydrogen bonds : angle 6.38792 ( 1728) SS BOND : bond 0.00295 ( 44) SS BOND : angle 0.65006 ( 88) covalent geometry : bond 0.00458 (20492) covalent geometry : angle 0.62237 (27824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 2.158 Fit side-chains REVERT: G 400 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.7862 (ptm160) REVERT: A 62 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7557 (tp-100) REVERT: L 61 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8471 (ptt-90) REVERT: L 70 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8024 (mm110) REVERT: L 101 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8489 (mm110) REVERT: H 400 ARG cc_start: 0.8506 (ptm-80) cc_final: 0.7863 (ptm160) REVERT: B 62 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7538 (tp-100) REVERT: M 61 ARG cc_start: 0.8849 (ptt-90) cc_final: 0.8470 (ptt-90) REVERT: M 70 GLN cc_start: 0.8258 (mm-40) cc_final: 0.8023 (mm110) REVERT: M 101 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8493 (mm110) REVERT: I 400 ARG cc_start: 0.8486 (ptm-80) cc_final: 0.7849 (ptm160) REVERT: C 62 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7561 (tp-100) REVERT: N 61 ARG cc_start: 0.8856 (ptt-90) cc_final: 0.8478 (ptt-90) REVERT: N 70 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8030 (mm110) REVERT: N 101 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8486 (mm110) REVERT: J 400 ARG cc_start: 0.8485 (ptm-80) cc_final: 0.7850 (ptm160) REVERT: D 62 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7691 (tp-100) REVERT: O 61 ARG cc_start: 0.8844 (ptt-90) cc_final: 0.8476 (ptt-90) REVERT: O 70 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8028 (mm110) REVERT: O 101 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8473 (mm110) outliers start: 41 outliers final: 21 residues processed: 278 average time/residue: 1.2718 time to fit residues: 400.1172 Evaluate side-chains 266 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 175 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 150 optimal weight: 0.0470 chunk 215 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN B 30 ASN B 65 GLN M 6 GLN C 65 GLN N 6 GLN O 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.071048 restraints weight = 28117.624| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.17 r_work: 0.2739 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20592 Z= 0.119 Angle : 0.580 7.439 28080 Z= 0.304 Chirality : 0.045 0.183 3196 Planarity : 0.003 0.040 3500 Dihedral : 7.683 61.414 3848 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.42 % Favored : 97.25 % Rotamer: Outliers : 1.32 % Allowed : 10.38 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2476 helix: -0.49 (0.84), residues: 28 sheet: 0.41 (0.16), residues: 976 loop : -0.09 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 178 HIS 0.003 0.001 HIS H 274 PHE 0.013 0.002 PHE G 410 TYR 0.012 0.001 TYR H 121 ARG 0.002 0.000 ARG J 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 20) link_NAG-ASN : angle 2.39657 ( 60) link_ALPHA1-6 : bond 0.00595 ( 8) link_ALPHA1-6 : angle 1.36310 ( 24) link_BETA1-4 : bond 0.00526 ( 16) link_BETA1-4 : angle 1.55149 ( 48) link_ALPHA1-2 : bond 0.00395 ( 4) link_ALPHA1-2 : angle 2.24951 ( 12) link_ALPHA1-3 : bond 0.00893 ( 8) link_ALPHA1-3 : angle 1.80214 ( 24) hydrogen bonds : bond 0.03855 ( 656) hydrogen bonds : angle 6.03459 ( 1728) SS BOND : bond 0.00187 ( 44) SS BOND : angle 0.64810 ( 88) covalent geometry : bond 0.00252 (20492) covalent geometry : angle 0.56093 (27824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 2.048 Fit side-chains REVERT: G 400 ARG cc_start: 0.8449 (ptm-80) cc_final: 0.7786 (ptm160) REVERT: A 62 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7462 (tp-100) REVERT: L 61 ARG cc_start: 0.8866 (ptt-90) cc_final: 0.8473 (ptt-90) REVERT: L 101 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8562 (mm110) REVERT: H 400 ARG cc_start: 0.8458 (ptm-80) cc_final: 0.7798 (ptm160) REVERT: B 62 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7460 (tp-100) REVERT: M 61 ARG cc_start: 0.8862 (ptt-90) cc_final: 0.8471 (ptt-90) REVERT: M 101 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8554 (mm110) REVERT: I 400 ARG cc_start: 0.8433 (ptm-80) cc_final: 0.7783 (ptm160) REVERT: C 62 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7460 (tp-100) REVERT: N 61 ARG cc_start: 0.8864 (ptt-90) cc_final: 0.8475 (ptt-90) REVERT: N 101 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8553 (mm110) REVERT: J 249 LYS cc_start: 0.7017 (tptp) cc_final: 0.6154 (tptt) REVERT: J 400 ARG cc_start: 0.8427 (ptm-80) cc_final: 0.7781 (ptm160) REVERT: D 62 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7671 (tp-100) REVERT: O 61 ARG cc_start: 0.8871 (ptt-90) cc_final: 0.8472 (ptt-90) REVERT: O 101 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8555 (mm110) outliers start: 28 outliers final: 13 residues processed: 271 average time/residue: 1.3132 time to fit residues: 400.6246 Evaluate side-chains 262 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 70 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.067315 restraints weight = 28283.554| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.17 r_work: 0.2667 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20592 Z= 0.269 Angle : 0.663 7.390 28080 Z= 0.348 Chirality : 0.048 0.193 3196 Planarity : 0.004 0.044 3500 Dihedral : 8.304 67.928 3848 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.15 % Favored : 96.53 % Rotamer: Outliers : 1.98 % Allowed : 10.38 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2476 helix: 0.31 (0.91), residues: 24 sheet: 0.34 (0.15), residues: 1016 loop : -0.09 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 115 HIS 0.004 0.001 HIS G 168 PHE 0.015 0.002 PHE J 410 TYR 0.014 0.002 TYR G 121 ARG 0.003 0.000 ARG H 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 20) link_NAG-ASN : angle 2.78568 ( 60) link_ALPHA1-6 : bond 0.00315 ( 8) link_ALPHA1-6 : angle 1.53747 ( 24) link_BETA1-4 : bond 0.00372 ( 16) link_BETA1-4 : angle 1.84623 ( 48) link_ALPHA1-2 : bond 0.00093 ( 4) link_ALPHA1-2 : angle 2.77772 ( 12) link_ALPHA1-3 : bond 0.00417 ( 8) link_ALPHA1-3 : angle 2.31955 ( 24) hydrogen bonds : bond 0.04765 ( 656) hydrogen bonds : angle 6.31736 ( 1728) SS BOND : bond 0.00340 ( 44) SS BOND : angle 0.79411 ( 88) covalent geometry : bond 0.00610 (20492) covalent geometry : angle 0.63996 (27824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 2.415 Fit side-chains REVERT: G 400 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.7859 (ptm160) REVERT: G 430 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8130 (mmt180) REVERT: A 62 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7584 (tp-100) REVERT: L 61 ARG cc_start: 0.8806 (ptt-90) cc_final: 0.8310 (ptt-90) REVERT: H 400 ARG cc_start: 0.8580 (ptm-80) cc_final: 0.7867 (ptm160) REVERT: H 430 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8119 (mmt180) REVERT: B 62 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7593 (tp-100) REVERT: M 61 ARG cc_start: 0.8806 (ptt-90) cc_final: 0.8313 (ptt-90) REVERT: I 400 ARG cc_start: 0.8566 (ptm-80) cc_final: 0.7860 (ptm160) REVERT: I 430 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8138 (mmt180) REVERT: C 62 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7566 (tp-100) REVERT: N 61 ARG cc_start: 0.8813 (ptt-90) cc_final: 0.8320 (ptt-90) REVERT: J 400 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.7848 (ptm160) REVERT: J 430 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8135 (mmt180) REVERT: D 62 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7689 (tp-100) REVERT: O 61 ARG cc_start: 0.8819 (ptt-90) cc_final: 0.8446 (ptt-90) outliers start: 42 outliers final: 29 residues processed: 263 average time/residue: 1.3793 time to fit residues: 409.6656 Evaluate side-chains 274 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 430 ARG Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 430 ARG Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 430 ARG Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 430 ARG Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.070280 restraints weight = 28090.443| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.18 r_work: 0.2726 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20592 Z= 0.130 Angle : 0.583 8.281 28080 Z= 0.306 Chirality : 0.045 0.187 3196 Planarity : 0.003 0.042 3500 Dihedral : 7.547 59.924 3848 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 1.75 % Allowed : 11.08 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2476 helix: -0.57 (0.84), residues: 28 sheet: 0.27 (0.16), residues: 940 loop : -0.05 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 178 HIS 0.002 0.001 HIS H 274 PHE 0.013 0.002 PHE H 410 TYR 0.011 0.001 TYR H 121 ARG 0.002 0.000 ARG I 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 20) link_NAG-ASN : angle 2.33487 ( 60) link_ALPHA1-6 : bond 0.00532 ( 8) link_ALPHA1-6 : angle 1.38104 ( 24) link_BETA1-4 : bond 0.00501 ( 16) link_BETA1-4 : angle 1.49883 ( 48) link_ALPHA1-2 : bond 0.00295 ( 4) link_ALPHA1-2 : angle 2.29616 ( 12) link_ALPHA1-3 : bond 0.00872 ( 8) link_ALPHA1-3 : angle 1.83270 ( 24) hydrogen bonds : bond 0.03877 ( 656) hydrogen bonds : angle 5.95706 ( 1728) SS BOND : bond 0.00203 ( 44) SS BOND : angle 0.51161 ( 88) covalent geometry : bond 0.00280 (20492) covalent geometry : angle 0.56570 (27824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 2.266 Fit side-chains REVERT: G 400 ARG cc_start: 0.8502 (ptm-80) cc_final: 0.7789 (ptm160) REVERT: A 62 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7489 (tp-100) REVERT: A 89 GLU cc_start: 0.8967 (pm20) cc_final: 0.8745 (pm20) REVERT: L 61 ARG cc_start: 0.8789 (ptt-90) cc_final: 0.8453 (ptt-90) REVERT: H 400 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.7784 (ptm160) REVERT: B 62 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7530 (tp-100) REVERT: B 89 GLU cc_start: 0.8969 (pm20) cc_final: 0.8739 (pm20) REVERT: M 61 ARG cc_start: 0.8786 (ptt-90) cc_final: 0.8450 (ptt-90) REVERT: I 230 CYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8926 (p) REVERT: I 400 ARG cc_start: 0.8475 (ptm-80) cc_final: 0.7775 (ptm160) REVERT: C 62 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7463 (tp-100) REVERT: C 65 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: C 89 GLU cc_start: 0.8966 (pm20) cc_final: 0.8746 (pm20) REVERT: N 61 ARG cc_start: 0.8790 (ptt-90) cc_final: 0.8458 (ptt-90) REVERT: J 400 ARG cc_start: 0.8475 (ptm-80) cc_final: 0.7774 (ptm160) REVERT: D 62 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7658 (tp-100) REVERT: D 89 GLU cc_start: 0.8969 (pm20) cc_final: 0.8749 (pm20) REVERT: O 61 ARG cc_start: 0.8799 (ptt-90) cc_final: 0.8467 (ptt-90) outliers start: 37 outliers final: 22 residues processed: 271 average time/residue: 1.2867 time to fit residues: 394.9335 Evaluate side-chains 270 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 230 CYS Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 105 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 220 ASN A 65 GLN L 6 GLN L 70 GLN H 220 ASN B 65 GLN M 6 GLN M 70 GLN I 220 ASN N 6 GLN N 70 GLN J 220 ASN O 6 GLN O 70 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.069229 restraints weight = 27979.846| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.18 r_work: 0.2703 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20592 Z= 0.175 Angle : 0.607 8.076 28080 Z= 0.316 Chirality : 0.046 0.196 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.589 60.368 3848 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.19 % Favored : 96.65 % Rotamer: Outliers : 1.42 % Allowed : 11.98 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2476 helix: -0.56 (0.84), residues: 28 sheet: 0.39 (0.16), residues: 928 loop : -0.08 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 178 HIS 0.002 0.001 HIS G 184 PHE 0.013 0.002 PHE J 410 TYR 0.013 0.001 TYR G 121 ARG 0.004 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 20) link_NAG-ASN : angle 2.44979 ( 60) link_ALPHA1-6 : bond 0.00454 ( 8) link_ALPHA1-6 : angle 1.46735 ( 24) link_BETA1-4 : bond 0.00425 ( 16) link_BETA1-4 : angle 1.59423 ( 48) link_ALPHA1-2 : bond 0.00137 ( 4) link_ALPHA1-2 : angle 2.42951 ( 12) link_ALPHA1-3 : bond 0.00656 ( 8) link_ALPHA1-3 : angle 2.01433 ( 24) hydrogen bonds : bond 0.04136 ( 656) hydrogen bonds : angle 6.03416 ( 1728) SS BOND : bond 0.00275 ( 44) SS BOND : angle 0.86434 ( 88) covalent geometry : bond 0.00391 (20492) covalent geometry : angle 0.58708 (27824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 2.122 Fit side-chains REVERT: G 400 ARG cc_start: 0.8517 (ptm-80) cc_final: 0.7791 (ptm160) REVERT: A 19 ARG cc_start: 0.9093 (ttt-90) cc_final: 0.8786 (ttt-90) REVERT: A 62 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7528 (tp-100) REVERT: A 65 GLN cc_start: 0.7654 (tt0) cc_final: 0.7452 (tt0) REVERT: A 82 GLU cc_start: 0.8184 (tt0) cc_final: 0.7627 (mm-30) REVERT: L 61 ARG cc_start: 0.8789 (ptt-90) cc_final: 0.8429 (ptt-90) REVERT: H 400 ARG cc_start: 0.8537 (ptm-80) cc_final: 0.7808 (ptm160) REVERT: B 19 ARG cc_start: 0.9103 (ttt-90) cc_final: 0.8863 (ttt90) REVERT: B 62 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7527 (tp-100) REVERT: B 65 GLN cc_start: 0.7640 (tt0) cc_final: 0.7428 (tt0) REVERT: B 82 GLU cc_start: 0.8222 (tt0) cc_final: 0.7920 (tp30) REVERT: M 61 ARG cc_start: 0.8785 (ptt-90) cc_final: 0.8426 (ptt-90) REVERT: I 400 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.7796 (ptm160) REVERT: C 19 ARG cc_start: 0.9094 (ttt-90) cc_final: 0.8775 (ttt-90) REVERT: C 62 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7543 (tp-100) REVERT: C 82 GLU cc_start: 0.8202 (tt0) cc_final: 0.7634 (mm-30) REVERT: N 61 ARG cc_start: 0.8791 (ptt-90) cc_final: 0.8436 (ptt-90) REVERT: J 400 ARG cc_start: 0.8513 (ptm-80) cc_final: 0.7790 (ptm160) REVERT: D 19 ARG cc_start: 0.9100 (ttt-90) cc_final: 0.8859 (ttt90) REVERT: D 62 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7672 (tp-100) REVERT: D 82 GLU cc_start: 0.8197 (tt0) cc_final: 0.7885 (tp30) REVERT: O 61 ARG cc_start: 0.8800 (ptt-90) cc_final: 0.8437 (ptt-90) outliers start: 30 outliers final: 22 residues processed: 274 average time/residue: 1.3012 time to fit residues: 403.0099 Evaluate side-chains 267 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 92 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 84 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 235 optimal weight: 0.0970 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 70 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.070103 restraints weight = 28280.674| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.18 r_work: 0.2723 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20592 Z= 0.145 Angle : 0.594 8.164 28080 Z= 0.309 Chirality : 0.045 0.198 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.337 57.134 3848 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.83 % Favored : 97.01 % Rotamer: Outliers : 1.08 % Allowed : 12.69 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2476 helix: -1.78 (0.61), residues: 52 sheet: 0.33 (0.16), residues: 940 loop : -0.08 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 178 HIS 0.002 0.001 HIS I 184 PHE 0.013 0.002 PHE I 410 TYR 0.012 0.001 TYR H 121 ARG 0.004 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 20) link_NAG-ASN : angle 2.32781 ( 60) link_ALPHA1-6 : bond 0.00500 ( 8) link_ALPHA1-6 : angle 1.43605 ( 24) link_BETA1-4 : bond 0.00449 ( 16) link_BETA1-4 : angle 1.48964 ( 48) link_ALPHA1-2 : bond 0.00205 ( 4) link_ALPHA1-2 : angle 2.28605 ( 12) link_ALPHA1-3 : bond 0.00766 ( 8) link_ALPHA1-3 : angle 1.90386 ( 24) hydrogen bonds : bond 0.03945 ( 656) hydrogen bonds : angle 5.93222 ( 1728) SS BOND : bond 0.00226 ( 44) SS BOND : angle 0.81398 ( 88) covalent geometry : bond 0.00320 (20492) covalent geometry : angle 0.57581 (27824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 2.349 Fit side-chains REVERT: G 400 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.7772 (ptm160) REVERT: A 19 ARG cc_start: 0.9117 (ttt-90) cc_final: 0.8804 (ttt-90) REVERT: A 62 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7559 (tp-100) REVERT: A 65 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: A 82 GLU cc_start: 0.8187 (tt0) cc_final: 0.7659 (mm-30) REVERT: L 61 ARG cc_start: 0.8772 (ptt-90) cc_final: 0.8407 (ptt-90) REVERT: H 400 ARG cc_start: 0.8517 (ptm-80) cc_final: 0.7780 (ptm160) REVERT: B 19 ARG cc_start: 0.9129 (ttt-90) cc_final: 0.8815 (ttt-90) REVERT: B 62 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7555 (tp-100) REVERT: B 65 GLN cc_start: 0.7680 (tt0) cc_final: 0.7454 (tt0) REVERT: B 82 GLU cc_start: 0.8191 (tt0) cc_final: 0.7634 (mm-30) REVERT: M 61 ARG cc_start: 0.8771 (ptt-90) cc_final: 0.8406 (ptt-90) REVERT: I 400 ARG cc_start: 0.8495 (ptm-80) cc_final: 0.7769 (ptm160) REVERT: C 19 ARG cc_start: 0.9123 (ttt-90) cc_final: 0.8811 (ttt-90) REVERT: C 62 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7533 (tp-100) REVERT: C 65 GLN cc_start: 0.7651 (tt0) cc_final: 0.7402 (tt0) REVERT: C 82 GLU cc_start: 0.8173 (tt0) cc_final: 0.7618 (mm-30) REVERT: N 61 ARG cc_start: 0.8770 (ptt-90) cc_final: 0.8407 (ptt-90) REVERT: J 400 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.7777 (ptm160) REVERT: D 19 ARG cc_start: 0.9130 (ttt-90) cc_final: 0.8811 (ttt-90) REVERT: D 62 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7677 (tp-100) REVERT: D 82 GLU cc_start: 0.8174 (tt0) cc_final: 0.7617 (mm-30) REVERT: O 61 ARG cc_start: 0.8791 (ptt-90) cc_final: 0.8423 (ptt-90) outliers start: 23 outliers final: 22 residues processed: 264 average time/residue: 1.3276 time to fit residues: 399.4556 Evaluate side-chains 272 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 108 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 229 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 70 GLN M 6 GLN M 70 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.069423 restraints weight = 27978.505| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.18 r_work: 0.2710 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20592 Z= 0.169 Angle : 0.606 8.040 28080 Z= 0.315 Chirality : 0.046 0.201 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.392 57.515 3848 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 1.13 % Allowed : 13.11 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2476 helix: -1.79 (0.61), residues: 52 sheet: 0.27 (0.15), residues: 1048 loop : -0.09 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 178 HIS 0.002 0.001 HIS G 184 PHE 0.013 0.002 PHE O 83 TYR 0.012 0.001 TYR G 121 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 20) link_NAG-ASN : angle 2.40387 ( 60) link_ALPHA1-6 : bond 0.00439 ( 8) link_ALPHA1-6 : angle 1.47856 ( 24) link_BETA1-4 : bond 0.00430 ( 16) link_BETA1-4 : angle 1.53621 ( 48) link_ALPHA1-2 : bond 0.00106 ( 4) link_ALPHA1-2 : angle 2.31775 ( 12) link_ALPHA1-3 : bond 0.00666 ( 8) link_ALPHA1-3 : angle 2.00719 ( 24) hydrogen bonds : bond 0.04108 ( 656) hydrogen bonds : angle 5.99003 ( 1728) SS BOND : bond 0.00259 ( 44) SS BOND : angle 0.79608 ( 88) covalent geometry : bond 0.00377 (20492) covalent geometry : angle 0.58700 (27824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 2.234 Fit side-chains REVERT: G 400 ARG cc_start: 0.8533 (ptm-80) cc_final: 0.7786 (ptm160) REVERT: A 19 ARG cc_start: 0.9110 (ttt-90) cc_final: 0.8783 (ttt-90) REVERT: A 62 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7587 (tp-100) REVERT: A 65 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: A 82 GLU cc_start: 0.8206 (tt0) cc_final: 0.7642 (mm-30) REVERT: L 61 ARG cc_start: 0.8776 (ptt-90) cc_final: 0.8395 (ptt-90) REVERT: H 400 ARG cc_start: 0.8541 (ptm-80) cc_final: 0.7801 (ptm160) REVERT: B 19 ARG cc_start: 0.9135 (ttt-90) cc_final: 0.8822 (ttt-90) REVERT: B 62 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7579 (tp-100) REVERT: B 65 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: B 82 GLU cc_start: 0.8212 (tt0) cc_final: 0.7651 (mm-30) REVERT: M 61 ARG cc_start: 0.8773 (ptt-90) cc_final: 0.8392 (ptt-90) REVERT: I 400 ARG cc_start: 0.8526 (ptm-80) cc_final: 0.7786 (ptm160) REVERT: C 19 ARG cc_start: 0.9123 (ttt-90) cc_final: 0.8809 (ttt-90) REVERT: C 62 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7588 (tp-100) REVERT: C 65 GLN cc_start: 0.7728 (tt0) cc_final: 0.7467 (tt0) REVERT: C 82 GLU cc_start: 0.8189 (tt0) cc_final: 0.7607 (mm-30) REVERT: N 61 ARG cc_start: 0.8776 (ptt-90) cc_final: 0.8398 (ptt-90) REVERT: J 400 ARG cc_start: 0.8531 (ptm-80) cc_final: 0.7790 (ptm160) REVERT: D 19 ARG cc_start: 0.9134 (ttt-90) cc_final: 0.8818 (ttt-90) REVERT: D 62 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7693 (tp-100) REVERT: D 82 GLU cc_start: 0.8192 (tt0) cc_final: 0.7625 (mm-30) REVERT: O 61 ARG cc_start: 0.8814 (ptt-90) cc_final: 0.8448 (ptt-90) outliers start: 24 outliers final: 22 residues processed: 266 average time/residue: 1.3305 time to fit residues: 399.3439 Evaluate side-chains 270 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 0.0670 chunk 8 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 215 optimal weight: 0.0000 chunk 185 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 70 GLN M 6 GLN M 70 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.073630 restraints weight = 28061.549| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.18 r_work: 0.2795 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20592 Z= 0.099 Angle : 0.557 8.513 28080 Z= 0.288 Chirality : 0.044 0.192 3196 Planarity : 0.003 0.042 3500 Dihedral : 6.541 46.551 3848 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.71 % Favored : 97.13 % Rotamer: Outliers : 0.71 % Allowed : 13.58 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2476 helix: -1.77 (0.59), residues: 52 sheet: 0.37 (0.16), residues: 956 loop : -0.06 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 178 HIS 0.002 0.001 HIS H 274 PHE 0.013 0.001 PHE O 83 TYR 0.011 0.001 TYR H 121 ARG 0.004 0.000 ARG D 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 20) link_NAG-ASN : angle 1.96181 ( 60) link_ALPHA1-6 : bond 0.00709 ( 8) link_ALPHA1-6 : angle 1.34050 ( 24) link_BETA1-4 : bond 0.00560 ( 16) link_BETA1-4 : angle 1.23193 ( 48) link_ALPHA1-2 : bond 0.00471 ( 4) link_ALPHA1-2 : angle 1.98783 ( 12) link_ALPHA1-3 : bond 0.01036 ( 8) link_ALPHA1-3 : angle 1.51348 ( 24) hydrogen bonds : bond 0.03350 ( 656) hydrogen bonds : angle 5.61423 ( 1728) SS BOND : bond 0.00185 ( 44) SS BOND : angle 0.66198 ( 88) covalent geometry : bond 0.00212 (20492) covalent geometry : angle 0.54381 (27824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 2.195 Fit side-chains REVERT: G 362 MET cc_start: 0.9267 (ptp) cc_final: 0.8979 (ptp) REVERT: G 400 ARG cc_start: 0.8430 (ptm-80) cc_final: 0.7722 (ptm160) REVERT: A 19 ARG cc_start: 0.9100 (ttt-90) cc_final: 0.8877 (ttt-90) REVERT: A 62 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7497 (tp-100) REVERT: A 82 GLU cc_start: 0.8245 (tt0) cc_final: 0.7673 (mm-30) REVERT: L 61 ARG cc_start: 0.8745 (ptt-90) cc_final: 0.8436 (ptt-90) REVERT: H 362 MET cc_start: 0.9269 (ptp) cc_final: 0.8981 (ptp) REVERT: H 400 ARG cc_start: 0.8448 (ptm-80) cc_final: 0.7745 (ptm160) REVERT: B 19 ARG cc_start: 0.9107 (ttt-90) cc_final: 0.8843 (ttt-90) REVERT: B 62 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7493 (tp-100) REVERT: B 82 GLU cc_start: 0.8231 (tt0) cc_final: 0.7672 (mm-30) REVERT: M 61 ARG cc_start: 0.8746 (ptt-90) cc_final: 0.8438 (ptt-90) REVERT: I 362 MET cc_start: 0.9267 (ptp) cc_final: 0.8981 (ptp) REVERT: I 400 ARG cc_start: 0.8434 (ptm-80) cc_final: 0.7728 (ptm160) REVERT: C 19 ARG cc_start: 0.9111 (ttt-90) cc_final: 0.8883 (ttt-90) REVERT: C 62 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7474 (tp-100) REVERT: C 65 GLN cc_start: 0.7605 (tt0) cc_final: 0.7330 (tt0) REVERT: C 82 GLU cc_start: 0.8214 (tt0) cc_final: 0.7650 (mm-30) REVERT: N 61 ARG cc_start: 0.8748 (ptt-90) cc_final: 0.8443 (ptt-90) REVERT: J 362 MET cc_start: 0.9258 (ptp) cc_final: 0.8979 (ptp) REVERT: J 400 ARG cc_start: 0.8433 (ptm-80) cc_final: 0.7727 (ptm160) REVERT: D 19 ARG cc_start: 0.9103 (ttt-90) cc_final: 0.8895 (ttt-90) REVERT: D 62 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7612 (tp-100) REVERT: D 82 GLU cc_start: 0.8214 (tt0) cc_final: 0.7649 (mm-30) REVERT: O 61 ARG cc_start: 0.8790 (ptt-90) cc_final: 0.8494 (ptt-90) outliers start: 15 outliers final: 9 residues processed: 271 average time/residue: 1.4554 time to fit residues: 441.7625 Evaluate side-chains 261 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 252 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain D residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 110 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN M 6 GLN ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 70 GLN O 6 GLN ** O 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.072245 restraints weight = 28087.138| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.18 r_work: 0.2768 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20592 Z= 0.121 Angle : 0.576 7.946 28080 Z= 0.298 Chirality : 0.045 0.207 3196 Planarity : 0.003 0.042 3500 Dihedral : 6.554 46.612 3848 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.83 % Favored : 97.01 % Rotamer: Outliers : 0.71 % Allowed : 14.10 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2476 helix: -1.71 (0.61), residues: 52 sheet: 0.43 (0.16), residues: 940 loop : -0.04 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 178 HIS 0.002 0.001 HIS H 274 PHE 0.012 0.001 PHE G 410 TYR 0.012 0.001 TYR H 121 ARG 0.004 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 20) link_NAG-ASN : angle 2.10858 ( 60) link_ALPHA1-6 : bond 0.00602 ( 8) link_ALPHA1-6 : angle 1.43565 ( 24) link_BETA1-4 : bond 0.00457 ( 16) link_BETA1-4 : angle 1.30759 ( 48) link_ALPHA1-2 : bond 0.00280 ( 4) link_ALPHA1-2 : angle 2.04403 ( 12) link_ALPHA1-3 : bond 0.00837 ( 8) link_ALPHA1-3 : angle 1.73380 ( 24) hydrogen bonds : bond 0.03598 ( 656) hydrogen bonds : angle 5.71909 ( 1728) SS BOND : bond 0.00213 ( 44) SS BOND : angle 0.71628 ( 88) covalent geometry : bond 0.00265 (20492) covalent geometry : angle 0.56124 (27824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16002.41 seconds wall clock time: 276 minutes 13.10 seconds (16573.10 seconds total)