Starting phenix.real_space_refine on Sat Jul 4 10:30:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3v_29710/07_2026/8g3v_29710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3v_29710/07_2026/8g3v_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_29710/07_2026/8g3v_29710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3v_29710/07_2026/8g3v_29710.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3v_29710/07_2026/8g3v_29710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3v_29710/07_2026/8g3v_29710.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g3v_29710/07_2026/8g3v_29710.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3v_29710/07_2026/8g3v_29710.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 4.66, per 1000 atoms: 0.23 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: 2.11 Conformation dependent library (CDL) restraints added in 866.1 milliseconds 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: 0.72 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: 3.73 Time building geometry restraints manager: 2.72 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 - 17.39: 10731 17.39 - 34.78: 744 34.78 - 52.17: 135 52.17 - 69.56: 63 69.56 - 86.95: 19 Dihedral angle restraints: 11692 sinusoidal: 4580 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 11689 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.180 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.190 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9301 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 : 13.678 86.949 7032 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (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 ARG 0.020 0.003 ARG G 156 TYR 0.060 0.013 TYR H 281 PHE 0.066 0.012 PHE G 205 TRP 0.094 0.016 TRP H 458 HIS 0.024 0.006 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.01388 / 0.98 (20492) covalent geometry : angle 1.61122 / 1.04 (27824) SS BOND : bond 0.06185 / 4.33 ( 44) SS BOND : angle 2.27667 / 1.58 ( 88) hydrogen bonds : bond 0.13550 / 8.97 ( 656) hydrogen bonds : angle 8.33451 / 5.91 ( 1728) link_ALPHA1-2 : bond 0.00384 / 0.18 ( 4) link_ALPHA1-2 : angle 5.62704 / 3.21 ( 12) link_ALPHA1-3 : bond 0.01399 / 0.82 ( 8) link_ALPHA1-3 : angle 3.16599 / 1.96 ( 24) link_ALPHA1-6 : bond 0.00930 / 0.56 ( 8) link_ALPHA1-6 : angle 2.39121 / 1.48 ( 24) link_BETA1-4 : bond 0.01402 / 0.87 ( 16) link_BETA1-4 : angle 4.05015 / 2.79 ( 48) link_NAG-ASN : bond 0.00720 / 0.44 ( 20) link_NAG-ASN : angle 4.25351 / 2.88 ( 60) *********************** 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 : 0.798 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: 0.7522 time to fit residues: 278.7840 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 : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3321 r_free = 0.3321 target = 0.098671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.070376 restraints weight = 28031.162| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.17 r_work: 0.2716 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20592 Z= 0.162 Angle : 0.655 6.598 28080 Z= 0.350 Chirality : 0.046 0.147 3196 Planarity : 0.004 0.033 3500 Dihedral : 6.197 21.585 2720 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.58 % Favored : 97.09 % Rotamer: Outliers : 1.46 % Allowed : 8.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2476 helix: -0.12 (0.92), residues: 24 sheet: 0.27 (0.15), residues: 1060 loop : -0.11 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 27 TYR 0.012 0.001 TYR J 121 PHE 0.012 0.002 PHE J 410 TRP 0.020 0.002 TRP J 178 HIS 0.005 0.001 HIS J 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (20492) covalent geometry : angle 0.63571 / 0.35 (27824) SS BOND : bond 0.00291 / 0.17 ( 44) SS BOND : angle 0.68721 / 0.47 ( 88) hydrogen bonds : bond 0.04495 / 3.04 ( 656) hydrogen bonds : angle 6.73068 / 4.80 ( 1728) link_ALPHA1-2 : bond 0.00366 / 0.17 ( 4) link_ALPHA1-2 : angle 1.93240 / 1.04 ( 12) link_ALPHA1-3 : bond 0.00472 / 0.27 ( 8) link_ALPHA1-3 : angle 1.69460 / 1.07 ( 24) link_ALPHA1-6 : bond 0.00628 / 0.38 ( 8) link_ALPHA1-6 : angle 1.33359 / 0.81 ( 24) link_BETA1-4 : bond 0.00366 / 0.21 ( 16) link_BETA1-4 : angle 1.77489 / 1.16 ( 48) link_NAG-ASN : bond 0.00133 / 0.08 ( 20) link_NAG-ASN : angle 2.71023 / 1.79 ( 60) *********************** 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 311 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.855 Fit side-chains REVERT: G 400 ARG cc_start: 0.8400 (ptm-80) cc_final: 0.7813 (ptm160) REVERT: A 62 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7476 (tp-100) REVERT: L 61 ARG cc_start: 0.8837 (ptt-90) cc_final: 0.8615 (ptt-90) REVERT: L 82 ASP cc_start: 0.9093 (m-30) cc_final: 0.8781 (m-30) REVERT: L 101 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8381 (mm110) REVERT: H 400 ARG cc_start: 0.8401 (ptm-80) cc_final: 0.7804 (ptm160) REVERT: B 62 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7508 (tp-100) REVERT: M 61 ARG cc_start: 0.8848 (ptt-90) cc_final: 0.8625 (ptt-90) REVERT: M 82 ASP cc_start: 0.9091 (m-30) cc_final: 0.8778 (m-30) REVERT: M 101 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8385 (mm110) REVERT: I 400 ARG cc_start: 0.8386 (ptm-80) cc_final: 0.7843 (ptm160) REVERT: C 62 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7479 (tp-100) REVERT: N 61 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8631 (ptt-90) REVERT: N 82 ASP cc_start: 0.9100 (m-30) cc_final: 0.8800 (m-30) REVERT: N 101 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8377 (mm110) REVERT: J 400 ARG cc_start: 0.8378 (ptm-80) cc_final: 0.7836 (ptm160) REVERT: D 62 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7733 (mm-40) REVERT: O 61 ARG cc_start: 0.8858 (ptt-90) cc_final: 0.8642 (ptt-90) REVERT: O 82 ASP cc_start: 0.9101 (m-30) cc_final: 0.8795 (m-30) REVERT: O 101 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8381 (mm110) outliers start: 31 outliers final: 4 residues processed: 288 average time/residue: 0.6757 time to fit residues: 218.2833 Evaluate side-chains 257 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 253 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 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 117 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 141 ASN A 30 ASN A 65 GLN L 6 GLN H 141 ASN B 30 ASN B 65 GLN M 6 GLN I 141 ASN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.069444 restraints weight = 28127.102| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.18 r_work: 0.2704 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20592 Z= 0.167 Angle : 0.613 6.043 28080 Z= 0.327 Chirality : 0.046 0.154 3196 Planarity : 0.003 0.039 3500 Dihedral : 5.741 22.335 2720 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.79 % Favored : 96.89 % Rotamer: Outliers : 2.12 % Allowed : 10.14 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2476 helix: 0.30 (0.96), residues: 24 sheet: 0.37 (0.15), residues: 1060 loop : -0.08 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 85 TYR 0.014 0.001 TYR H 121 PHE 0.013 0.002 PHE G 410 TRP 0.017 0.002 TRP J 178 HIS 0.004 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (20492) covalent geometry : angle 0.59623 / 0.32 (27824) SS BOND : bond 0.00273 / 0.15 ( 44) SS BOND : angle 0.61390 / 0.42 ( 88) hydrogen bonds : bond 0.04359 / 2.92 ( 656) hydrogen bonds : angle 6.31458 / 4.49 ( 1728) link_ALPHA1-2 : bond 0.00298 / 0.14 ( 4) link_ALPHA1-2 : angle 2.20008 / 1.16 ( 12) link_ALPHA1-3 : bond 0.00432 / 0.25 ( 8) link_ALPHA1-3 : angle 1.53432 / 0.97 ( 24) link_ALPHA1-6 : bond 0.00452 / 0.28 ( 8) link_ALPHA1-6 : angle 1.44339 / 0.89 ( 24) link_BETA1-4 : bond 0.00462 / 0.28 ( 16) link_BETA1-4 : angle 1.57491 / 1.02 ( 48) link_NAG-ASN : bond 0.00095 / 0.06 ( 20) link_NAG-ASN : angle 2.42448 / 1.57 ( 60) *********************** 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 306 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.798 Fit side-chains REVERT: G 400 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.7825 (ptm160) REVERT: A 11 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8713 (t) REVERT: A 62 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7523 (tp-100) REVERT: L 61 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8484 (ptt-90) REVERT: L 101 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8485 (mm110) REVERT: H 400 ARG cc_start: 0.8466 (ptm-80) cc_final: 0.7833 (ptm160) REVERT: B 11 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8726 (t) REVERT: B 62 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7533 (tp-100) REVERT: M 61 ARG cc_start: 0.8852 (ptt-90) cc_final: 0.8487 (ptt-90) REVERT: M 101 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8491 (mm110) REVERT: I 400 ARG cc_start: 0.8452 (ptm-80) cc_final: 0.7827 (ptm160) REVERT: C 11 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8718 (t) REVERT: C 62 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7518 (tp-100) REVERT: N 61 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8486 (ptt-90) REVERT: N 101 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8485 (mm110) REVERT: J 400 ARG cc_start: 0.8447 (ptm-80) cc_final: 0.7825 (ptm160) REVERT: D 11 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8713 (t) REVERT: D 62 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7658 (tp-100) REVERT: O 61 ARG cc_start: 0.8866 (ptt-90) cc_final: 0.8509 (ptt-90) REVERT: O 101 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8484 (mm110) outliers start: 45 outliers final: 24 residues processed: 292 average time/residue: 0.5681 time to fit residues: 187.4484 Evaluate side-chains 278 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 11 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU 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 11 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 73 LEU 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 21 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 150 optimal weight: 0.0030 chunk 108 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN L 6 GLN L 70 GLN B 30 ASN B 65 GLN M 6 GLN M 70 GLN C 30 ASN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.068592 restraints weight = 28205.792| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.18 r_work: 0.2692 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20592 Z= 0.192 Angle : 0.616 6.895 28080 Z= 0.327 Chirality : 0.046 0.154 3196 Planarity : 0.004 0.042 3500 Dihedral : 5.674 22.565 2720 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.67 % Favored : 97.01 % Rotamer: Outliers : 2.22 % Allowed : 10.09 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2476 helix: 0.45 (0.92), residues: 24 sheet: 0.33 (0.15), residues: 1024 loop : -0.14 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 85 TYR 0.013 0.002 TYR H 121 PHE 0.013 0.002 PHE G 410 TRP 0.016 0.002 TRP G 178 HIS 0.004 0.001 HIS J 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (20492) covalent geometry : angle 0.59820 / 0.32 (27824) SS BOND : bond 0.00283 / 0.15 ( 44) SS BOND : angle 0.85583 / 0.58 ( 88) hydrogen bonds : bond 0.04380 / 2.93 ( 656) hydrogen bonds : angle 6.23919 / 4.44 ( 1728) link_ALPHA1-2 : bond 0.00169 / 0.08 ( 4) link_ALPHA1-2 : angle 2.23555 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00258 / 0.15 ( 8) link_ALPHA1-3 : angle 1.61046 / 1.01 ( 24) link_ALPHA1-6 : bond 0.00375 / 0.23 ( 8) link_ALPHA1-6 : angle 1.48201 / 0.91 ( 24) link_BETA1-4 : bond 0.00380 / 0.23 ( 16) link_BETA1-4 : angle 1.56379 / 1.00 ( 48) link_NAG-ASN : bond 0.00183 / 0.11 ( 20) link_NAG-ASN : angle 2.38489 / 1.53 ( 60) *********************** 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 296 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 0.722 Fit side-chains REVERT: G 400 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.7845 (ptm160) REVERT: A 62 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7527 (tp-100) REVERT: A 82 GLU cc_start: 0.8376 (tt0) cc_final: 0.8102 (tt0) REVERT: L 61 ARG cc_start: 0.8810 (ptt-90) cc_final: 0.8358 (ptt-90) REVERT: H 400 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.7840 (ptm160) REVERT: B 62 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7509 (tp-100) REVERT: B 82 GLU cc_start: 0.8373 (tt0) cc_final: 0.8098 (tt0) REVERT: M 61 ARG cc_start: 0.8805 (ptt-90) cc_final: 0.8355 (ptt-90) REVERT: I 400 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.7841 (ptm160) REVERT: C 62 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7527 (tp-100) REVERT: C 82 GLU cc_start: 0.8368 (tt0) cc_final: 0.8093 (tt0) REVERT: N 61 ARG cc_start: 0.8813 (ptt-90) cc_final: 0.8372 (ptt-90) REVERT: J 400 ARG cc_start: 0.8493 (ptm-80) cc_final: 0.7834 (ptm160) REVERT: D 62 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7678 (tp-100) REVERT: D 82 GLU cc_start: 0.8364 (tt0) cc_final: 0.8103 (tt0) REVERT: O 61 ARG cc_start: 0.8814 (ptt-90) cc_final: 0.8365 (ptt-90) outliers start: 47 outliers final: 35 residues processed: 273 average time/residue: 0.5900 time to fit residues: 182.1938 Evaluate side-chains 278 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 308 LYS 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 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 308 LYS 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 M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 308 LYS 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 175 optimal weight: 0.0270 chunk 79 optimal weight: 0.8980 chunk 189 optimal weight: 0.3980 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN L 6 GLN L 70 GLN B 30 ASN B 65 GLN M 6 GLN M 70 GLN C 30 ASN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.071943 restraints weight = 27984.578| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.19 r_work: 0.2762 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20592 Z= 0.105 Angle : 0.551 8.121 28080 Z= 0.291 Chirality : 0.043 0.143 3196 Planarity : 0.003 0.041 3500 Dihedral : 5.150 21.825 2720 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.63 % Favored : 97.21 % Rotamer: Outliers : 1.32 % Allowed : 10.99 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2476 helix: -1.68 (0.63), residues: 52 sheet: 0.30 (0.15), residues: 1040 loop : -0.07 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 85 TYR 0.012 0.001 TYR H 121 PHE 0.013 0.002 PHE G 354 TRP 0.017 0.001 TRP J 178 HIS 0.003 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (20492) covalent geometry : angle 0.53863 / 0.29 (27824) SS BOND : bond 0.00192 / 0.10 ( 44) SS BOND : angle 0.56319 / 0.39 ( 88) hydrogen bonds : bond 0.03583 / 2.39 ( 656) hydrogen bonds : angle 5.82506 / 4.15 ( 1728) link_ALPHA1-2 : bond 0.00500 / 0.23 ( 4) link_ALPHA1-2 : angle 1.65688 / 0.87 ( 12) link_ALPHA1-3 : bond 0.00551 / 0.33 ( 8) link_ALPHA1-3 : angle 1.31551 / 0.84 ( 24) link_ALPHA1-6 : bond 0.00505 / 0.30 ( 8) link_ALPHA1-6 : angle 1.36800 / 0.84 ( 24) link_BETA1-4 : bond 0.00469 / 0.28 ( 16) link_BETA1-4 : angle 1.25308 / 0.79 ( 48) link_NAG-ASN : bond 0.00065 / 0.04 ( 20) link_NAG-ASN : angle 1.93440 / 1.24 ( 60) *********************** 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 291 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 0.727 Fit side-chains REVERT: G 362 MET cc_start: 0.9244 (ptp) cc_final: 0.9040 (ptp) REVERT: G 400 ARG cc_start: 0.8433 (ptm-80) cc_final: 0.7753 (ptm160) REVERT: A 62 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7438 (tp-100) REVERT: A 82 GLU cc_start: 0.8418 (tt0) cc_final: 0.8140 (tt0) REVERT: L 61 ARG cc_start: 0.8780 (ptt-90) cc_final: 0.8370 (ptt-90) REVERT: H 362 MET cc_start: 0.9240 (ptp) cc_final: 0.9036 (ptp) REVERT: H 400 ARG cc_start: 0.8453 (ptm-80) cc_final: 0.7778 (ptm160) REVERT: B 62 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7441 (tp-100) REVERT: B 82 GLU cc_start: 0.8413 (tt0) cc_final: 0.8134 (tt0) REVERT: M 61 ARG cc_start: 0.8775 (ptt-90) cc_final: 0.8369 (ptt-90) REVERT: I 362 MET cc_start: 0.9243 (ptp) cc_final: 0.9040 (ptp) REVERT: I 400 ARG cc_start: 0.8413 (ptm-80) cc_final: 0.7745 (ptm160) REVERT: C 62 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7405 (tp-100) REVERT: C 82 GLU cc_start: 0.8410 (tt0) cc_final: 0.8129 (tt0) REVERT: N 61 ARG cc_start: 0.8783 (ptt-90) cc_final: 0.8386 (ptt-90) REVERT: J 362 MET cc_start: 0.9245 (ptp) cc_final: 0.9039 (ptp) REVERT: J 400 ARG cc_start: 0.8410 (ptm-80) cc_final: 0.7745 (ptm160) REVERT: D 62 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7629 (tp-100) REVERT: D 82 GLU cc_start: 0.8404 (tt0) cc_final: 0.8123 (tt0) REVERT: O 61 ARG cc_start: 0.8793 (ptt-90) cc_final: 0.8487 (ptt-90) outliers start: 28 outliers final: 14 residues processed: 272 average time/residue: 0.5775 time to fit residues: 176.6901 Evaluate side-chains 267 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 390 LEU 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 I residue 247 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 230 optimal weight: 0.0370 chunk 19 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3312 r_free = 0.3312 target = 0.097686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.069463 restraints weight = 27945.734| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.18 r_work: 0.2710 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2210 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= 0.173 Angle : 0.588 7.651 28080 Z= 0.310 Chirality : 0.045 0.150 3196 Planarity : 0.003 0.043 3500 Dihedral : 5.336 22.733 2720 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.07 % Favored : 96.77 % Rotamer: Outliers : 1.51 % Allowed : 11.60 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2476 helix: -1.71 (0.63), residues: 52 sheet: 0.35 (0.16), residues: 940 loop : -0.07 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 85 TYR 0.013 0.001 TYR I 121 PHE 0.013 0.002 PHE J 410 TRP 0.013 0.002 TRP H 178 HIS 0.002 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (20492) covalent geometry : angle 0.57268 / 0.31 (27824) SS BOND : bond 0.00249 / 0.14 ( 44) SS BOND : angle 0.57137 / 0.39 ( 88) hydrogen bonds : bond 0.04140 / 2.76 ( 656) hydrogen bonds : angle 6.00266 / 4.28 ( 1728) link_ALPHA1-2 : bond 0.00168 / 0.08 ( 4) link_ALPHA1-2 : angle 2.00083 / 1.05 ( 12) link_ALPHA1-3 : bond 0.00281 / 0.16 ( 8) link_ALPHA1-3 : angle 1.58311 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00348 / 0.21 ( 8) link_ALPHA1-6 : angle 1.48857 / 0.92 ( 24) link_BETA1-4 : bond 0.00374 / 0.22 ( 16) link_BETA1-4 : angle 1.46872 / 0.92 ( 48) link_NAG-ASN : bond 0.00125 / 0.07 ( 20) link_NAG-ASN : angle 2.16123 / 1.36 ( 60) *********************** 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 288 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.770 Fit side-chains REVERT: G 400 ARG cc_start: 0.8516 (ptm-80) cc_final: 0.7805 (ptm160) REVERT: A 62 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7527 (tp-100) REVERT: A 82 GLU cc_start: 0.8433 (tt0) cc_final: 0.8147 (tt0) REVERT: A 89 GLU cc_start: 0.9005 (pm20) cc_final: 0.8763 (pm20) REVERT: L 61 ARG cc_start: 0.8772 (ptt-90) cc_final: 0.8429 (ptt-90) REVERT: H 400 ARG cc_start: 0.8515 (ptm-80) cc_final: 0.7804 (ptm160) REVERT: B 62 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7524 (tp-100) REVERT: B 82 GLU cc_start: 0.8430 (tt0) cc_final: 0.8128 (tt0) REVERT: B 89 GLU cc_start: 0.9005 (pm20) cc_final: 0.8763 (pm20) REVERT: M 61 ARG cc_start: 0.8771 (ptt-90) cc_final: 0.8432 (ptt-90) REVERT: I 400 ARG cc_start: 0.8495 (ptm-80) cc_final: 0.7800 (ptm160) REVERT: C 62 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7505 (tp-100) REVERT: C 82 GLU cc_start: 0.8429 (tt0) cc_final: 0.8125 (tt0) REVERT: C 89 GLU cc_start: 0.9004 (pm20) cc_final: 0.8765 (pm20) REVERT: N 61 ARG cc_start: 0.8798 (ptt-90) cc_final: 0.8473 (ptt-90) REVERT: J 400 ARG cc_start: 0.8491 (ptm-80) cc_final: 0.7797 (ptm160) REVERT: D 62 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7669 (tp-100) REVERT: D 82 GLU cc_start: 0.8418 (tt0) cc_final: 0.8126 (tt0) REVERT: D 89 GLU cc_start: 0.9010 (pm20) cc_final: 0.8771 (pm20) REVERT: O 61 ARG cc_start: 0.8789 (ptt-90) cc_final: 0.8435 (ptt-90) outliers start: 32 outliers final: 19 residues processed: 279 average time/residue: 0.6327 time to fit residues: 199.2602 Evaluate side-chains 268 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 I residue 148 THR 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 N residue 73 LEU 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 13 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3340 r_free = 0.3340 target = 0.099545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.071580 restraints weight = 28124.121| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.18 r_work: 0.2754 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.2353 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= 0.112 Angle : 0.551 7.917 28080 Z= 0.289 Chirality : 0.043 0.143 3196 Planarity : 0.003 0.042 3500 Dihedral : 5.085 22.011 2720 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 1.13 % Allowed : 12.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2476 helix: -1.70 (0.62), residues: 52 sheet: 0.30 (0.16), residues: 956 loop : 0.02 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 85 TYR 0.012 0.001 TYR H 121 PHE 0.013 0.001 PHE G 410 TRP 0.016 0.001 TRP G 178 HIS 0.002 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (20492) covalent geometry : angle 0.53795 / 0.29 (27824) SS BOND : bond 0.00216 / 0.12 ( 44) SS BOND : angle 0.85046 / 0.57 ( 88) hydrogen bonds : bond 0.03642 / 2.43 ( 656) hydrogen bonds : angle 5.77429 / 4.11 ( 1728) link_ALPHA1-2 : bond 0.00403 / 0.19 ( 4) link_ALPHA1-2 : angle 1.68837 / 0.89 ( 12) link_ALPHA1-3 : bond 0.00508 / 0.30 ( 8) link_ALPHA1-3 : angle 1.40157 / 0.89 ( 24) link_ALPHA1-6 : bond 0.00463 / 0.28 ( 8) link_ALPHA1-6 : angle 1.40599 / 0.87 ( 24) link_BETA1-4 : bond 0.00447 / 0.27 ( 16) link_BETA1-4 : angle 1.27737 / 0.80 ( 48) link_NAG-ASN : bond 0.00026 / 0.02 ( 20) link_NAG-ASN : angle 1.89683 / 1.19 ( 60) *********************** 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 290 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.773 Fit side-chains REVERT: G 362 MET cc_start: 0.9255 (ptp) cc_final: 0.9046 (ptp) REVERT: G 400 ARG cc_start: 0.8461 (ptm-80) cc_final: 0.7766 (ptm160) REVERT: A 12 LYS cc_start: 0.9111 (mmtp) cc_final: 0.8907 (mmtm) REVERT: A 62 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7475 (tp-100) REVERT: A 65 GLN cc_start: 0.7558 (tt0) cc_final: 0.7350 (tt0) REVERT: A 82 GLU cc_start: 0.8457 (tt0) cc_final: 0.8148 (tt0) REVERT: L 61 ARG cc_start: 0.8772 (ptt-90) cc_final: 0.8475 (ptt-90) REVERT: H 400 ARG cc_start: 0.8467 (ptm-80) cc_final: 0.7771 (ptm160) REVERT: B 62 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7471 (tp-100) REVERT: B 65 GLN cc_start: 0.7553 (tt0) cc_final: 0.7339 (tt0) REVERT: B 82 GLU cc_start: 0.8447 (tt0) cc_final: 0.8149 (tt0) REVERT: M 61 ARG cc_start: 0.8763 (ptt-90) cc_final: 0.8464 (ptt-90) REVERT: I 400 ARG cc_start: 0.8443 (ptm-80) cc_final: 0.7761 (ptm160) REVERT: C 62 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7470 (tp-100) REVERT: C 65 GLN cc_start: 0.7545 (tt0) cc_final: 0.7335 (tt0) REVERT: C 82 GLU cc_start: 0.8446 (tt0) cc_final: 0.8146 (tt0) REVERT: N 61 ARG cc_start: 0.8765 (ptt-90) cc_final: 0.8468 (ptt-90) REVERT: J 400 ARG cc_start: 0.8446 (ptm-80) cc_final: 0.7758 (ptm160) REVERT: D 62 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7595 (tp-100) REVERT: D 82 GLU cc_start: 0.8434 (tt0) cc_final: 0.8142 (tt0) REVERT: O 61 ARG cc_start: 0.8780 (ptt-90) cc_final: 0.8459 (ptt-90) outliers start: 24 outliers final: 20 residues processed: 281 average time/residue: 0.6500 time to fit residues: 205.3774 Evaluate side-chains 276 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 73 LEU 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 I residue 148 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 73 LEU 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 85 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 33 optimal weight: 0.1980 overall best weight: 1.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 220 ASN L 6 GLN L 70 GLN H 220 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.068577 restraints weight = 28188.759| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.18 r_work: 0.2693 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20592 Z= 0.220 Angle : 0.623 7.791 28080 Z= 0.326 Chirality : 0.046 0.160 3196 Planarity : 0.004 0.043 3500 Dihedral : 5.406 22.940 2720 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Rotamer: Outliers : 1.27 % Allowed : 12.69 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2476 helix: -1.81 (0.61), residues: 52 sheet: 0.32 (0.15), residues: 1056 loop : -0.04 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 85 TYR 0.013 0.002 TYR H 121 PHE 0.014 0.002 PHE G 410 TRP 0.012 0.002 TRP H 115 HIS 0.003 0.001 HIS G 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (20492) covalent geometry : angle 0.60658 / 0.32 (27824) SS BOND : bond 0.00305 / 0.17 ( 44) SS BOND : angle 0.91417 / 0.62 ( 88) hydrogen bonds : bond 0.04355 / 2.90 ( 656) hydrogen bonds : angle 6.04926 / 4.31 ( 1728) link_ALPHA1-2 : bond 0.00034 / 0.02 ( 4) link_ALPHA1-2 : angle 1.99803 / 1.05 ( 12) link_ALPHA1-3 : bond 0.00174 / 0.10 ( 8) link_ALPHA1-3 : angle 1.68015 / 1.05 ( 24) link_ALPHA1-6 : bond 0.00295 / 0.18 ( 8) link_ALPHA1-6 : angle 1.51319 / 0.93 ( 24) link_BETA1-4 : bond 0.00329 / 0.20 ( 16) link_BETA1-4 : angle 1.51701 / 0.95 ( 48) link_NAG-ASN : bond 0.00197 / 0.12 ( 20) link_NAG-ASN : angle 2.23520 / 1.39 ( 60) *********************** 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 280 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.794 Fit side-chains REVERT: G 400 ARG cc_start: 0.8548 (ptm-80) cc_final: 0.7808 (ptm160) REVERT: A 62 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7582 (tp-100) REVERT: A 65 GLN cc_start: 0.7682 (tt0) cc_final: 0.7459 (tt0) REVERT: A 82 GLU cc_start: 0.8465 (tt0) cc_final: 0.8169 (tt0) REVERT: L 61 ARG cc_start: 0.8783 (ptt-90) cc_final: 0.8380 (ptt-90) REVERT: H 400 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.7812 (ptm160) REVERT: B 62 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7595 (tp-100) REVERT: B 65 GLN cc_start: 0.7632 (tt0) cc_final: 0.7398 (tt0) REVERT: B 82 GLU cc_start: 0.8445 (tt0) cc_final: 0.8140 (tt0) REVERT: M 61 ARG cc_start: 0.8777 (ptt-90) cc_final: 0.8376 (ptt-90) REVERT: I 400 ARG cc_start: 0.8545 (ptm-80) cc_final: 0.7808 (ptm160) REVERT: C 62 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7570 (tp-100) REVERT: C 65 GLN cc_start: 0.7664 (tt0) cc_final: 0.7438 (tt0) REVERT: C 82 GLU cc_start: 0.8450 (tt0) cc_final: 0.8144 (tt0) REVERT: N 61 ARG cc_start: 0.8787 (ptt-90) cc_final: 0.8400 (ptt-90) REVERT: J 400 ARG cc_start: 0.8543 (ptm-80) cc_final: 0.7805 (ptm160) REVERT: D 62 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7656 (tp-100) REVERT: D 82 GLU cc_start: 0.8443 (tt0) cc_final: 0.8137 (tt0) REVERT: O 61 ARG cc_start: 0.8800 (ptt-90) cc_final: 0.8394 (ptt-90) outliers start: 27 outliers final: 26 residues processed: 270 average time/residue: 0.5999 time to fit residues: 183.0852 Evaluate side-chains 276 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 247 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 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 232 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 117 optimal weight: 0.0770 chunk 128 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3308 r_free = 0.3308 target = 0.097361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.069122 restraints weight = 28044.600| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.18 r_work: 0.2703 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20592 Z= 0.178 Angle : 0.605 8.082 28080 Z= 0.318 Chirality : 0.045 0.149 3196 Planarity : 0.003 0.042 3500 Dihedral : 5.361 22.644 2720 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.99 % Favored : 96.85 % Rotamer: Outliers : 1.37 % Allowed : 12.74 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2476 helix: -1.79 (0.61), residues: 52 sheet: 0.30 (0.15), residues: 1056 loop : -0.05 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 85 TYR 0.012 0.001 TYR H 121 PHE 0.013 0.002 PHE J 410 TRP 0.014 0.001 TRP J 178 HIS 0.002 0.001 HIS I 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (20492) covalent geometry : angle 0.59034 / 0.32 (27824) SS BOND : bond 0.00255 / 0.14 ( 44) SS BOND : angle 0.76284 / 0.52 ( 88) hydrogen bonds : bond 0.04170 / 2.78 ( 656) hydrogen bonds : angle 5.98955 / 4.27 ( 1728) link_ALPHA1-2 : bond 0.00100 / 0.05 ( 4) link_ALPHA1-2 : angle 1.86458 / 0.98 ( 12) link_ALPHA1-3 : bond 0.00290 / 0.17 ( 8) link_ALPHA1-3 : angle 1.57922 / 0.99 ( 24) link_ALPHA1-6 : bond 0.00354 / 0.22 ( 8) link_ALPHA1-6 : angle 1.47149 / 0.90 ( 24) link_BETA1-4 : bond 0.00364 / 0.22 ( 16) link_BETA1-4 : angle 1.43822 / 0.90 ( 48) link_NAG-ASN : bond 0.00155 / 0.10 ( 20) link_NAG-ASN : angle 2.12769 / 1.33 ( 60) *********************** 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 280 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.732 Fit side-chains REVERT: G 400 ARG cc_start: 0.8543 (ptm-80) cc_final: 0.7794 (ptm160) REVERT: A 62 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7606 (tp-100) REVERT: A 65 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: A 82 GLU cc_start: 0.8454 (tt0) cc_final: 0.8154 (tt0) REVERT: L 61 ARG cc_start: 0.8782 (ptt-90) cc_final: 0.8370 (ptt-90) REVERT: H 400 ARG cc_start: 0.8543 (ptm-80) cc_final: 0.7800 (ptm160) REVERT: B 62 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7602 (tp-100) REVERT: B 65 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: B 82 GLU cc_start: 0.8449 (tt0) cc_final: 0.8143 (tt0) REVERT: M 61 ARG cc_start: 0.8780 (ptt-90) cc_final: 0.8368 (ptt-90) REVERT: I 400 ARG cc_start: 0.8530 (ptm-80) cc_final: 0.7787 (ptm160) REVERT: C 62 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7594 (tp-100) REVERT: C 65 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: C 82 GLU cc_start: 0.8450 (tt0) cc_final: 0.8143 (tt0) REVERT: N 61 ARG cc_start: 0.8781 (ptt-90) cc_final: 0.8386 (ptt-90) REVERT: J 400 ARG cc_start: 0.8532 (ptm-80) cc_final: 0.7789 (ptm160) REVERT: D 62 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7661 (tp-100) REVERT: D 82 GLU cc_start: 0.8444 (tt0) cc_final: 0.8137 (tt0) REVERT: O 61 ARG cc_start: 0.8803 (ptt-90) cc_final: 0.8390 (ptt-90) outliers start: 29 outliers final: 26 residues processed: 267 average time/residue: 0.6085 time to fit residues: 183.8780 Evaluate side-chains 280 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 390 LEU 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 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 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3293 r_free = 0.3293 target = 0.096363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.068070 restraints weight = 28185.166| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.18 r_work: 0.2682 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2225 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= 0.228 Angle : 0.639 7.963 28080 Z= 0.335 Chirality : 0.046 0.159 3196 Planarity : 0.004 0.043 3500 Dihedral : 5.516 23.078 2720 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.19 % Favored : 96.65 % Rotamer: Outliers : 1.37 % Allowed : 13.02 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.16), residues: 2476 helix: -1.48 (0.63), residues: 48 sheet: 0.24 (0.15), residues: 1060 loop : -0.03 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 85 TYR 0.013 0.002 TYR H 121 PHE 0.014 0.002 PHE G 410 TRP 0.012 0.002 TRP H 115 HIS 0.003 0.001 HIS I 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (20492) covalent geometry : angle 0.62289 / 0.33 (27824) SS BOND : bond 0.00310 / 0.17 ( 44) SS BOND : angle 0.88923 / 0.60 ( 88) hydrogen bonds : bond 0.04465 / 2.97 ( 656) hydrogen bonds : angle 6.13207 / 4.37 ( 1728) link_ALPHA1-2 : bond 0.00087 / 0.04 ( 4) link_ALPHA1-2 : angle 1.93791 / 1.02 ( 12) link_ALPHA1-3 : bond 0.00157 / 0.09 ( 8) link_ALPHA1-3 : angle 1.71319 / 1.07 ( 24) link_ALPHA1-6 : bond 0.00293 / 0.18 ( 8) link_ALPHA1-6 : angle 1.51803 / 0.93 ( 24) link_BETA1-4 : bond 0.00327 / 0.20 ( 16) link_BETA1-4 : angle 1.54070 / 0.96 ( 48) link_NAG-ASN : bond 0.00244 / 0.15 ( 20) link_NAG-ASN : angle 2.28400 / 1.42 ( 60) ********************** 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 283 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.879 Fit side-chains REVERT: G 400 ARG cc_start: 0.8559 (ptm-80) cc_final: 0.7814 (ptm160) REVERT: A 10 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8068 (mt-10) REVERT: A 62 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7640 (tp-100) REVERT: A 65 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: A 82 GLU cc_start: 0.8450 (tt0) cc_final: 0.8142 (tt0) REVERT: L 61 ARG cc_start: 0.8796 (ptt-90) cc_final: 0.8364 (ptt-90) REVERT: H 400 ARG cc_start: 0.8568 (ptm-80) cc_final: 0.7814 (ptm160) REVERT: B 10 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8112 (mt-10) REVERT: B 62 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7635 (tp-100) REVERT: B 65 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: B 82 GLU cc_start: 0.8445 (tt0) cc_final: 0.8127 (tt0) REVERT: M 61 ARG cc_start: 0.8794 (ptt-90) cc_final: 0.8362 (ptt-90) REVERT: I 400 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.7809 (ptm160) REVERT: C 10 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8104 (mt-10) REVERT: C 62 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7628 (tp-100) REVERT: C 65 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: C 82 GLU cc_start: 0.8445 (tt0) cc_final: 0.8126 (tt0) REVERT: N 61 ARG cc_start: 0.8798 (ptt-90) cc_final: 0.8385 (ptt-90) REVERT: J 400 ARG cc_start: 0.8557 (ptm-80) cc_final: 0.7810 (ptm160) REVERT: D 10 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8100 (mt-10) REVERT: D 62 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7664 (tp-100) REVERT: D 82 GLU cc_start: 0.8426 (tt0) cc_final: 0.8121 (tt0) REVERT: O 61 ARG cc_start: 0.8815 (ptt-90) cc_final: 0.8382 (ptt-90) outliers start: 29 outliers final: 26 residues processed: 270 average time/residue: 0.6583 time to fit residues: 200.4258 Evaluate side-chains 283 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 390 LEU 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 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 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 18 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3316 r_free = 0.3316 target = 0.097796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.069708 restraints weight = 28243.079| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.18 r_work: 0.2713 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20592 Z= 0.159 Angle : 0.598 8.377 28080 Z= 0.313 Chirality : 0.045 0.143 3196 Planarity : 0.003 0.042 3500 Dihedral : 5.323 22.476 2720 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 1.27 % Allowed : 13.40 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.16), residues: 2476 helix: -1.79 (0.61), residues: 52 sheet: 0.30 (0.15), residues: 1056 loop : -0.06 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 85 TYR 0.012 0.001 TYR H 121 PHE 0.013 0.002 PHE G 410 TRP 0.015 0.001 TRP H 178 HIS 0.002 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (20492) covalent geometry : angle 0.58495 / 0.31 (27824) SS BOND : bond 0.00234 / 0.13 ( 44) SS BOND : angle 0.72428 / 0.49 ( 88) hydrogen bonds : bond 0.04042 / 2.69 ( 656) hydrogen bonds : angle 5.95616 / 4.25 ( 1728) link_ALPHA1-2 : bond 0.00138 / 0.06 ( 4) link_ALPHA1-2 : angle 1.75090 / 0.92 ( 12) link_ALPHA1-3 : bond 0.00361 / 0.21 ( 8) link_ALPHA1-3 : angle 1.53957 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00383 / 0.23 ( 8) link_ALPHA1-6 : angle 1.45084 / 0.89 ( 24) link_BETA1-4 : bond 0.00378 / 0.23 ( 16) link_BETA1-4 : angle 1.39314 / 0.87 ( 48) link_NAG-ASN : bond 0.00135 / 0.08 ( 20) link_NAG-ASN : angle 2.04624 / 1.27 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7954.49 seconds wall clock time: 136 minutes 24.51 seconds (8184.51 seconds total)