Starting phenix.real_space_refine on Wed Mar 4 15:53:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qto_53356/03_2026/9qto_53356.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qto_53356/03_2026/9qto_53356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qto_53356/03_2026/9qto_53356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qto_53356/03_2026/9qto_53356.map" model { file = "/net/cci-nas-00/data/ceres_data/9qto_53356/03_2026/9qto_53356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qto_53356/03_2026/9qto_53356.cif" } resolution = 2.16 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= 0.012 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8920 2.51 5 N 2265 2.21 5 O 3097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14352 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain: "B" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain: "C" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain: "D" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain: "E" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 950 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "G" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 950 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 950 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 950 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "J" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 950 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 3.47, per 1000 atoms: 0.24 Number of scatterers: 14352 At special positions: 0 Unit cell: (107.07, 106.425, 110.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 3097 8.00 N 2265 7.00 C 8920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 51 " - pdb=" SG CYS G 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 51 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 51 " - pdb=" SG CYS I 105 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 51 " - pdb=" SG CYS J 105 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA N 3 " - " MAN N 5 " " BMA Q 3 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 S 2 " - " BMA S 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG M 1 " - " FUC M 4 " " NAG O 1 " - " FUC O 3 " " NAG P 1 " - " FUC P 4 " " NAG R 1 " - " FUC R 3 " " NAG S 1 " - " FUC S 4 " " NAG U 1 " - " FUC U 3 " " NAG V 1 " - " FUC V 4 " " NAG X 1 " - " FUC X 3 " " NAG Y 1 " - " FUC Y 4 " NAG-ASN " NAG K 1 " - " ASN A 110 " " NAG L 1 " - " ASN A 67 " " NAG M 1 " - " ASN A 23 " " NAG N 1 " - " ASN B 110 " " NAG O 1 " - " ASN B 67 " " NAG P 1 " - " ASN B 23 " " NAG Q 1 " - " ASN C 110 " " NAG R 1 " - " ASN C 67 " " NAG S 1 " - " ASN C 23 " " NAG T 1 " - " ASN D 110 " " NAG U 1 " - " ASN D 67 " " NAG V 1 " - " ASN D 23 " " NAG W 1 " - " ASN E 110 " " NAG X 1 " - " ASN E 67 " " NAG Y 1 " - " ASN E 23 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 511.1 milliseconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 39 sheets defined 7.0% alpha, 54.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.518A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.726A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.728A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.690A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.757A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 108 through 112 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 108 through 112 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 108 through 112 Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'J' and resid 108 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117 removed outlier: 4.243A pdb=" N GLY A 113 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 117 removed outlier: 4.243A pdb=" N GLY A 113 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 48 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 42 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 50 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 38 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP A 54 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 36 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN A 56 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU A 34 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N SER A 58 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE A 32 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR A 60 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 30 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N HIS A 62 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 13.445A pdb=" N LEU A 28 " --> pdb=" O HIS A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.756A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.756A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 79 removed outlier: 4.233A pdb=" N GLY B 113 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 4.233A pdb=" N GLY B 113 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 48 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 42 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR B 50 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 38 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP B 54 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU B 36 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN B 56 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU B 34 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER B 58 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE B 32 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR B 60 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 30 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N HIS B 62 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 13.465A pdb=" N LEU B 28 " --> pdb=" O HIS B 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.763A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.763A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 112 through 117 removed outlier: 4.235A pdb=" N GLY C 113 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 117 removed outlier: 4.235A pdb=" N GLY C 113 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL C 48 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 42 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR C 50 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 38 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TRP C 54 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU C 36 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN C 56 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU C 34 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N SER C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE C 32 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR C 60 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL C 30 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N HIS C 62 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 13.502A pdb=" N LEU C 28 " --> pdb=" O HIS C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.766A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.766A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 117 removed outlier: 4.255A pdb=" N GLY D 113 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 117 removed outlier: 4.255A pdb=" N GLY D 113 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL D 48 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL D 42 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR D 50 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN D 38 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP D 54 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU D 36 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN D 56 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 34 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER D 58 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE D 32 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N THR D 60 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL D 30 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 11.238A pdb=" N HIS D 62 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 13.454A pdb=" N LEU D 28 " --> pdb=" O HIS D 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AB9, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.742A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.742A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 117 removed outlier: 4.229A pdb=" N GLY E 113 " --> pdb=" O ASP E 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 112 through 117 removed outlier: 4.229A pdb=" N GLY E 113 " --> pdb=" O ASP E 61 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL E 48 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL E 42 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR E 50 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN E 38 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TRP E 54 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU E 36 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN E 56 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU E 34 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 58 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE E 32 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N THR E 60 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL E 30 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N HIS E 62 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 13.509A pdb=" N LEU E 28 " --> pdb=" O HIS E 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC5, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.800A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.800A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 12 through 13 removed outlier: 6.777A pdb=" N ILE F 35 " --> pdb=" O CYS F 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N CYS F 51 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AC9, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AD1, first strand: chain 'G' and resid 12 through 13 removed outlier: 6.786A pdb=" N ILE G 35 " --> pdb=" O CYS G 51 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS G 51 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AD3, first strand: chain 'G' and resid 19 through 22 Processing sheet with id=AD4, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.780A pdb=" N ILE H 35 " --> pdb=" O CYS H 51 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS H 51 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AD6, first strand: chain 'H' and resid 19 through 22 Processing sheet with id=AD7, first strand: chain 'I' and resid 12 through 13 removed outlier: 6.704A pdb=" N ILE I 35 " --> pdb=" O CYS I 51 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS I 51 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP I 37 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN I 60 " --> pdb=" O CYS I 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AD9, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AE1, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.743A pdb=" N ILE J 35 " --> pdb=" O CYS J 51 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS J 51 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 12 through 13 Processing sheet with id=AE3, first strand: chain 'J' and resid 19 through 22 518 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4297 1.34 - 1.46: 3428 1.46 - 1.58: 6605 1.58 - 1.70: 0 1.70 - 1.81: 95 Bond restraints: 14425 Sorted by residual: bond pdb=" CB ASN C 67 " pdb=" CG ASN C 67 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.68e+00 bond pdb=" CA ASN C 23 " pdb=" CB ASN C 23 " ideal model delta sigma weight residual 1.516 1.536 -0.021 1.65e-02 3.67e+03 1.56e+00 bond pdb=" CA ASN C 23 " pdb=" C ASN C 23 " ideal model delta sigma weight residual 1.533 1.521 0.012 9.60e-03 1.09e+04 1.56e+00 bond pdb=" CB ASN C 23 " pdb=" CG ASN C 23 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 bond pdb=" N PRO A 20 " pdb=" CA PRO A 20 " ideal model delta sigma weight residual 1.469 1.484 -0.016 1.28e-02 6.10e+03 1.50e+00 ... (remaining 14420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 19254 2.04 - 4.09: 304 4.09 - 6.13: 32 6.13 - 8.17: 3 8.17 - 10.21: 7 Bond angle restraints: 19600 Sorted by residual: angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 134.77 -10.21 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C2 NAG S 1 " pdb=" N2 NAG S 1 " pdb=" C7 NAG S 1 " ideal model delta sigma weight residual 124.56 134.56 -10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C2 NAG Y 1 " pdb=" N2 NAG Y 1 " pdb=" C7 NAG Y 1 " ideal model delta sigma weight residual 124.56 134.52 -9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C2 NAG V 1 " pdb=" N2 NAG V 1 " pdb=" C7 NAG V 1 " ideal model delta sigma weight residual 124.56 133.67 -9.11 3.00e+00 1.11e-01 9.23e+00 angle pdb=" C2 NAG M 1 " pdb=" N2 NAG M 1 " pdb=" C7 NAG M 1 " ideal model delta sigma weight residual 124.56 133.49 -8.93 3.00e+00 1.11e-01 8.87e+00 ... (remaining 19595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 8052 17.42 - 34.85: 779 34.85 - 52.27: 290 52.27 - 69.70: 76 69.70 - 87.12: 13 Dihedral angle restraints: 9210 sinusoidal: 4410 harmonic: 4800 Sorted by residual: dihedral pdb=" CB CYS F 51 " pdb=" SG CYS F 51 " pdb=" SG CYS F 105 " pdb=" CB CYS F 105 " ideal model delta sinusoidal sigma weight residual 93.00 153.93 -60.93 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CB CYS H 51 " pdb=" SG CYS H 51 " pdb=" SG CYS H 105 " pdb=" CB CYS H 105 " ideal model delta sinusoidal sigma weight residual 93.00 153.31 -60.31 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS J 51 " pdb=" SG CYS J 51 " pdb=" SG CYS J 105 " pdb=" CB CYS J 105 " ideal model delta sinusoidal sigma weight residual 93.00 153.20 -60.20 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 9207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1863 0.051 - 0.102: 277 0.102 - 0.153: 92 0.153 - 0.205: 7 0.205 - 0.256: 6 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C2 NAG P 1 " pdb=" C1 NAG P 1 " pdb=" C3 NAG P 1 " pdb=" N2 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.24 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C2 NAG S 1 " pdb=" C1 NAG S 1 " pdb=" C3 NAG S 1 " pdb=" N2 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.24 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C2 NAG Y 1 " pdb=" C1 NAG Y 1 " pdb=" C3 NAG Y 1 " pdb=" N2 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2242 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 134 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO E 135 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 135 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 135 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 134 " -0.036 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 135 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 135 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 135 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 134 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO D 135 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 135 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 135 " 0.030 5.00e-02 4.00e+02 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 335 2.65 - 3.21: 11986 3.21 - 3.78: 22659 3.78 - 4.34: 33536 4.34 - 4.90: 52535 Nonbonded interactions: 121051 Sorted by model distance: nonbonded pdb=" O LEU I 82 " pdb=" O HOH I 201 " model vdw 2.088 3.040 nonbonded pdb=" OH TYR F 112 " pdb=" O HOH F 201 " model vdw 2.101 3.040 nonbonded pdb=" OH TYR J 112 " pdb=" O HOH J 201 " model vdw 2.107 3.040 nonbonded pdb=" OH TYR G 112 " pdb=" O HOH G 201 " model vdw 2.112 3.040 nonbonded pdb=" O LEU J 82 " pdb=" O HOH J 202 " model vdw 2.119 3.040 ... (remaining 121046 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.880 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 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 : 0.003 0.044 14500 Z= 0.125 Angle : 0.633 10.215 19810 Z= 0.310 Chirality : 0.045 0.256 2245 Planarity : 0.005 0.054 2425 Dihedral : 15.844 87.119 6115 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.44 % Allowed : 24.05 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.19), residues: 1640 helix: -0.74 (0.69), residues: 55 sheet: 0.40 (0.19), residues: 630 loop : -1.00 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.014 0.001 TYR D 128 PHE 0.010 0.001 PHE H 28 TRP 0.033 0.002 TRP E 133 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00270 (14425) covalent geometry : angle 0.61452 (19600) SS BOND : bond 0.00460 ( 15) SS BOND : angle 1.00548 ( 30) hydrogen bonds : bond 0.14286 ( 412) hydrogen bonds : angle 6.07197 ( 1278) link_ALPHA1-3 : bond 0.00899 ( 5) link_ALPHA1-3 : angle 1.33436 ( 15) link_ALPHA1-6 : bond 0.00490 ( 5) link_ALPHA1-6 : angle 1.35724 ( 15) link_BETA1-4 : bond 0.00484 ( 25) link_BETA1-4 : angle 1.69851 ( 75) link_BETA1-6 : bond 0.00850 ( 10) link_BETA1-6 : angle 1.19035 ( 30) link_NAG-ASN : bond 0.01324 ( 15) link_NAG-ASN : angle 2.09069 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 299 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 96 ASP cc_start: 0.8694 (t0) cc_final: 0.8419 (t0) REVERT: A 124 LYS cc_start: 0.9252 (mttt) cc_final: 0.8923 (mttp) REVERT: A 185 ARG cc_start: 0.8374 (ttt90) cc_final: 0.8147 (ttt90) REVERT: B 96 ASP cc_start: 0.8570 (t0) cc_final: 0.8295 (t0) REVERT: B 142 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8806 (mtpp) REVERT: B 174 ASP cc_start: 0.8703 (t0) cc_final: 0.8380 (t70) REVERT: C 92 TYR cc_start: 0.9335 (m-80) cc_final: 0.9127 (m-10) REVERT: D 56 GLN cc_start: 0.8802 (mt0) cc_final: 0.8554 (mt0) REVERT: D 96 ASP cc_start: 0.8893 (t0) cc_final: 0.8660 (t0) REVERT: D 191 LYS cc_start: 0.9131 (mtpp) cc_final: 0.8805 (ttmm) REVERT: E 130 ASP cc_start: 0.8814 (t70) cc_final: 0.8529 (t0) REVERT: F 74 ASP cc_start: 0.9086 (t70) cc_final: 0.8693 (t70) REVERT: G 74 ASP cc_start: 0.8818 (t70) cc_final: 0.8404 (t70) REVERT: H 74 ASP cc_start: 0.8995 (t70) cc_final: 0.8748 (t70) REVERT: I 74 ASP cc_start: 0.8923 (t70) cc_final: 0.8672 (t70) REVERT: I 88 LYS cc_start: 0.8777 (mttt) cc_final: 0.8510 (mttp) REVERT: J 74 ASP cc_start: 0.9102 (t70) cc_final: 0.8893 (t70) outliers start: 21 outliers final: 15 residues processed: 313 average time/residue: 0.7612 time to fit residues: 256.6852 Evaluate side-chains 289 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 274 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN B 46 ASN B 65 GLN C 46 ASN C 65 GLN D 46 ASN E 46 ASN E 65 GLN H 60 ASN I 60 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.062547 restraints weight = 20816.508| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.88 r_work: 0.2570 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14500 Z= 0.236 Angle : 0.670 9.824 19810 Z= 0.329 Chirality : 0.047 0.261 2245 Planarity : 0.005 0.047 2425 Dihedral : 6.547 57.366 3030 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.12 % Allowed : 20.89 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.19), residues: 1640 helix: -0.26 (0.72), residues: 50 sheet: 0.34 (0.19), residues: 695 loop : -0.94 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 185 TYR 0.017 0.001 TYR A 128 PHE 0.010 0.001 PHE D 2 TRP 0.017 0.001 TRP E 133 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00544 (14425) covalent geometry : angle 0.65065 (19600) SS BOND : bond 0.00603 ( 15) SS BOND : angle 1.04782 ( 30) hydrogen bonds : bond 0.03793 ( 412) hydrogen bonds : angle 5.17621 ( 1278) link_ALPHA1-3 : bond 0.00776 ( 5) link_ALPHA1-3 : angle 1.43605 ( 15) link_ALPHA1-6 : bond 0.00473 ( 5) link_ALPHA1-6 : angle 1.32861 ( 15) link_BETA1-4 : bond 0.00463 ( 25) link_BETA1-4 : angle 1.60196 ( 75) link_BETA1-6 : bond 0.00769 ( 10) link_BETA1-6 : angle 1.30259 ( 30) link_NAG-ASN : bond 0.01268 ( 15) link_NAG-ASN : angle 2.36889 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 0.558 Fit side-chains REVERT: A 96 ASP cc_start: 0.8978 (t0) cc_final: 0.8657 (t0) REVERT: A 124 LYS cc_start: 0.9240 (mttt) cc_final: 0.8889 (mttp) REVERT: B 96 ASP cc_start: 0.8706 (t0) cc_final: 0.8392 (t0) REVERT: B 118 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8742 (mt) REVERT: C 92 TYR cc_start: 0.9399 (m-80) cc_final: 0.9078 (m-10) REVERT: D 56 GLN cc_start: 0.8693 (mt0) cc_final: 0.8387 (mt0) REVERT: D 191 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8649 (ttmm) REVERT: E 130 ASP cc_start: 0.8847 (t70) cc_final: 0.8524 (t0) REVERT: F 46 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7759 (mtm180) REVERT: F 74 ASP cc_start: 0.8869 (t70) cc_final: 0.8298 (t70) REVERT: G 74 ASP cc_start: 0.8692 (t70) cc_final: 0.8169 (t70) REVERT: H 20 ARG cc_start: 0.8894 (ttt90) cc_final: 0.8676 (ttt180) REVERT: H 74 ASP cc_start: 0.8827 (t70) cc_final: 0.8487 (t70) REVERT: I 46 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8156 (mtm180) REVERT: I 73 ARG cc_start: 0.9036 (ttp-170) cc_final: 0.8429 (ttm170) REVERT: I 74 ASP cc_start: 0.8873 (t70) cc_final: 0.8565 (t70) REVERT: I 88 LYS cc_start: 0.8370 (mttt) cc_final: 0.8074 (mttp) REVERT: J 44 LYS cc_start: 0.8180 (mttt) cc_final: 0.7940 (mppt) REVERT: J 47 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: J 74 ASP cc_start: 0.9086 (t70) cc_final: 0.8574 (t70) outliers start: 60 outliers final: 20 residues processed: 315 average time/residue: 0.7630 time to fit residues: 257.5623 Evaluate side-chains 289 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 46 ARG Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 46 ARG Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 46 ASN B 3 GLN B 46 ASN B 170 ASN C 3 GLN C 46 ASN C 170 ASN D 3 GLN D 46 ASN E 3 GLN E 46 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.064842 restraints weight = 20755.794| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.86 r_work: 0.2609 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14500 Z= 0.142 Angle : 0.597 10.027 19810 Z= 0.292 Chirality : 0.044 0.281 2245 Planarity : 0.004 0.046 2425 Dihedral : 6.292 59.276 3028 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.26 % Allowed : 20.89 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.19), residues: 1640 helix: -0.15 (0.71), residues: 50 sheet: 0.38 (0.19), residues: 695 loop : -0.96 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 206 TYR 0.007 0.001 TYR E 92 PHE 0.012 0.001 PHE C 136 TRP 0.013 0.001 TRP B 133 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00322 (14425) covalent geometry : angle 0.57916 (19600) SS BOND : bond 0.00408 ( 15) SS BOND : angle 0.96538 ( 30) hydrogen bonds : bond 0.03290 ( 412) hydrogen bonds : angle 4.82598 ( 1278) link_ALPHA1-3 : bond 0.00803 ( 5) link_ALPHA1-3 : angle 1.41484 ( 15) link_ALPHA1-6 : bond 0.00496 ( 5) link_ALPHA1-6 : angle 1.34548 ( 15) link_BETA1-4 : bond 0.00389 ( 25) link_BETA1-4 : angle 1.45014 ( 75) link_BETA1-6 : bond 0.00590 ( 10) link_BETA1-6 : angle 1.18242 ( 30) link_NAG-ASN : bond 0.00962 ( 15) link_NAG-ASN : angle 2.06874 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 285 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.8964 (t0) cc_final: 0.8657 (t0) REVERT: A 124 LYS cc_start: 0.9243 (mttt) cc_final: 0.8907 (mttp) REVERT: A 142 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8631 (ptpt) REVERT: B 96 ASP cc_start: 0.8657 (t0) cc_final: 0.8315 (t0) REVERT: B 118 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8692 (mt) REVERT: B 185 ARG cc_start: 0.8433 (ptm160) cc_final: 0.8158 (ptm160) REVERT: C 92 TYR cc_start: 0.9396 (m-80) cc_final: 0.9053 (m-10) REVERT: C 206 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7910 (ttm-80) REVERT: D 56 GLN cc_start: 0.8719 (mt0) cc_final: 0.8416 (mt0) REVERT: D 130 ASP cc_start: 0.8354 (t70) cc_final: 0.8152 (t0) REVERT: D 191 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8600 (ttmm) REVERT: D 205 ARG cc_start: 0.8715 (ttp-170) cc_final: 0.8280 (ttm-80) REVERT: E 118 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8718 (mp) REVERT: E 124 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8514 (mttm) REVERT: E 130 ASP cc_start: 0.8814 (t70) cc_final: 0.8539 (t0) REVERT: E 187 TYR cc_start: 0.7569 (m-10) cc_final: 0.7295 (m-10) REVERT: E 204 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7560 (ttp80) REVERT: F 74 ASP cc_start: 0.8880 (t70) cc_final: 0.8313 (t70) REVERT: G 18 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8560 (m) REVERT: G 74 ASP cc_start: 0.8706 (t70) cc_final: 0.8179 (t70) REVERT: H 20 ARG cc_start: 0.8893 (ttt90) cc_final: 0.8655 (ttt180) REVERT: H 74 ASP cc_start: 0.8844 (t70) cc_final: 0.8490 (t70) REVERT: I 73 ARG cc_start: 0.8998 (ttp-170) cc_final: 0.8384 (ttm170) REVERT: I 74 ASP cc_start: 0.8858 (t70) cc_final: 0.8539 (t70) REVERT: I 88 LYS cc_start: 0.8302 (mttt) cc_final: 0.8023 (mttp) REVERT: J 47 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: J 74 ASP cc_start: 0.9086 (t70) cc_final: 0.8586 (t70) outliers start: 62 outliers final: 25 residues processed: 327 average time/residue: 0.7310 time to fit residues: 256.8998 Evaluate side-chains 305 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 94 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 142 optimal weight: 0.1980 chunk 129 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN B 46 ASN B 170 ASN C 3 GLN C 46 ASN C 56 GLN C 170 ASN D 3 GLN D 46 ASN E 3 GLN E 46 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.065782 restraints weight = 20585.087| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.85 r_work: 0.2630 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14500 Z= 0.123 Angle : 0.575 9.875 19810 Z= 0.280 Chirality : 0.044 0.318 2245 Planarity : 0.004 0.047 2425 Dihedral : 6.040 58.633 3027 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.12 % Allowed : 21.03 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.19), residues: 1640 helix: 0.03 (0.71), residues: 50 sheet: 0.51 (0.19), residues: 665 loop : -1.01 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 204 TYR 0.019 0.001 TYR A 128 PHE 0.008 0.001 PHE C 136 TRP 0.011 0.001 TRP B 133 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00279 (14425) covalent geometry : angle 0.55739 (19600) SS BOND : bond 0.00312 ( 15) SS BOND : angle 0.95369 ( 30) hydrogen bonds : bond 0.03023 ( 412) hydrogen bonds : angle 4.56266 ( 1278) link_ALPHA1-3 : bond 0.00827 ( 5) link_ALPHA1-3 : angle 1.39551 ( 15) link_ALPHA1-6 : bond 0.00508 ( 5) link_ALPHA1-6 : angle 1.35799 ( 15) link_BETA1-4 : bond 0.00377 ( 25) link_BETA1-4 : angle 1.36791 ( 75) link_BETA1-6 : bond 0.00564 ( 10) link_BETA1-6 : angle 1.17430 ( 30) link_NAG-ASN : bond 0.00930 ( 15) link_NAG-ASN : angle 2.11430 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 294 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.8931 (t0) cc_final: 0.8618 (t0) REVERT: A 124 LYS cc_start: 0.9232 (mttt) cc_final: 0.8894 (mttp) REVERT: A 142 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8609 (ptpt) REVERT: B 96 ASP cc_start: 0.8619 (t0) cc_final: 0.8244 (t0) REVERT: B 118 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8665 (mt) REVERT: B 185 ARG cc_start: 0.8436 (ptm160) cc_final: 0.8142 (ptm160) REVERT: C 92 TYR cc_start: 0.9385 (m-80) cc_final: 0.9025 (m-10) REVERT: C 128 TYR cc_start: 0.8535 (t80) cc_final: 0.8053 (t80) REVERT: D 96 ASP cc_start: 0.9044 (t0) cc_final: 0.8735 (t0) REVERT: D 191 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8703 (mttm) REVERT: D 205 ARG cc_start: 0.8751 (ttp-170) cc_final: 0.8322 (ttm-80) REVERT: E 118 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8713 (mp) REVERT: E 130 ASP cc_start: 0.8812 (t70) cc_final: 0.8577 (t0) REVERT: E 142 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8904 (mtpp) REVERT: F 45 GLU cc_start: 0.8468 (pm20) cc_final: 0.8135 (pm20) REVERT: F 74 ASP cc_start: 0.8878 (t70) cc_final: 0.8338 (t70) REVERT: G 74 ASP cc_start: 0.8721 (t70) cc_final: 0.8191 (t70) REVERT: H 20 ARG cc_start: 0.8881 (ttt90) cc_final: 0.8633 (ttt180) REVERT: H 74 ASP cc_start: 0.8833 (t70) cc_final: 0.8441 (t70) REVERT: I 73 ARG cc_start: 0.8964 (ttp-170) cc_final: 0.8420 (ttm170) REVERT: I 74 ASP cc_start: 0.8865 (t70) cc_final: 0.8562 (t70) REVERT: I 88 LYS cc_start: 0.8250 (mttt) cc_final: 0.7990 (mttm) REVERT: J 29 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8605 (t) REVERT: J 44 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7363 (mtmm) REVERT: J 47 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: J 74 ASP cc_start: 0.9083 (t70) cc_final: 0.8560 (t70) outliers start: 60 outliers final: 24 residues processed: 327 average time/residue: 0.7129 time to fit residues: 250.5199 Evaluate side-chains 314 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 44 LYS Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 93 optimal weight: 0.1980 chunk 126 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN B 46 ASN B 170 ASN C 3 GLN C 46 ASN D 3 GLN D 46 ASN E 46 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.089826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.060820 restraints weight = 20865.476| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.88 r_work: 0.2536 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 14500 Z= 0.302 Angle : 0.687 9.930 19810 Z= 0.337 Chirality : 0.048 0.290 2245 Planarity : 0.005 0.049 2425 Dihedral : 6.361 58.496 3026 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.02 % Allowed : 20.07 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.19), residues: 1640 helix: -1.65 (0.50), residues: 80 sheet: 0.20 (0.19), residues: 695 loop : -1.03 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 204 TYR 0.015 0.001 TYR E 92 PHE 0.013 0.002 PHE I 69 TRP 0.009 0.001 TRP C 133 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00699 (14425) covalent geometry : angle 0.66474 (19600) SS BOND : bond 0.00391 ( 15) SS BOND : angle 1.07377 ( 30) hydrogen bonds : bond 0.03674 ( 412) hydrogen bonds : angle 4.92843 ( 1278) link_ALPHA1-3 : bond 0.00755 ( 5) link_ALPHA1-3 : angle 1.39244 ( 15) link_ALPHA1-6 : bond 0.00415 ( 5) link_ALPHA1-6 : angle 1.39451 ( 15) link_BETA1-4 : bond 0.00348 ( 25) link_BETA1-4 : angle 1.47740 ( 75) link_BETA1-6 : bond 0.00379 ( 10) link_BETA1-6 : angle 1.36600 ( 30) link_NAG-ASN : bond 0.01197 ( 15) link_NAG-ASN : angle 2.87755 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 276 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.9247 (mttt) cc_final: 0.8887 (mttp) REVERT: A 185 ARG cc_start: 0.8598 (ttt90) cc_final: 0.8006 (ttt90) REVERT: B 96 ASP cc_start: 0.8793 (t0) cc_final: 0.8474 (t0) REVERT: B 118 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8762 (mt) REVERT: B 185 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8126 (ptm160) REVERT: C 92 TYR cc_start: 0.9410 (m-80) cc_final: 0.9085 (m-10) REVERT: D 191 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8774 (mttm) REVERT: D 205 ARG cc_start: 0.8701 (ttp-170) cc_final: 0.8247 (ttm-80) REVERT: E 118 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8786 (mp) REVERT: E 191 LYS cc_start: 0.8809 (mtpp) cc_final: 0.8595 (mtpp) REVERT: F 12 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8823 (tm) REVERT: F 45 GLU cc_start: 0.8559 (pm20) cc_final: 0.8202 (pm20) REVERT: F 74 ASP cc_start: 0.8881 (t70) cc_final: 0.8315 (t70) REVERT: G 18 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8701 (m) REVERT: G 39 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.6344 (ptp-170) REVERT: G 74 ASP cc_start: 0.8717 (t70) cc_final: 0.8260 (t70) REVERT: H 20 ARG cc_start: 0.8935 (ttt90) cc_final: 0.8690 (ttt180) REVERT: H 74 ASP cc_start: 0.8890 (t70) cc_final: 0.8489 (t70) REVERT: I 73 ARG cc_start: 0.9023 (ttp-170) cc_final: 0.8505 (ttm170) REVERT: I 74 ASP cc_start: 0.8879 (t70) cc_final: 0.8626 (t70) REVERT: I 88 LYS cc_start: 0.8229 (mttt) cc_final: 0.7975 (mttm) REVERT: J 44 LYS cc_start: 0.8222 (mppt) cc_final: 0.7459 (mtmm) REVERT: J 47 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: J 74 ASP cc_start: 0.9093 (t70) cc_final: 0.8580 (t70) outliers start: 73 outliers final: 33 residues processed: 329 average time/residue: 0.7574 time to fit residues: 267.9388 Evaluate side-chains 314 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 22 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN B 46 ASN C 3 GLN C 46 ASN C 170 ASN D 3 GLN D 46 ASN E 3 GLN E 46 ASN H 60 ASN H 118 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.092138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.063310 restraints weight = 20679.668| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.89 r_work: 0.2588 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14500 Z= 0.148 Angle : 0.602 9.846 19810 Z= 0.296 Chirality : 0.044 0.281 2245 Planarity : 0.004 0.049 2425 Dihedral : 6.173 59.069 3025 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.85 % Allowed : 21.86 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.19), residues: 1640 helix: -0.21 (0.70), residues: 50 sheet: 0.21 (0.19), residues: 695 loop : -0.93 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 204 TYR 0.020 0.001 TYR C 128 PHE 0.010 0.001 PHE E 2 TRP 0.010 0.001 TRP E 133 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00338 (14425) covalent geometry : angle 0.58237 (19600) SS BOND : bond 0.00622 ( 15) SS BOND : angle 1.06820 ( 30) hydrogen bonds : bond 0.03164 ( 412) hydrogen bonds : angle 4.64173 ( 1278) link_ALPHA1-3 : bond 0.00829 ( 5) link_ALPHA1-3 : angle 1.40730 ( 15) link_ALPHA1-6 : bond 0.00490 ( 5) link_ALPHA1-6 : angle 1.38726 ( 15) link_BETA1-4 : bond 0.00370 ( 25) link_BETA1-4 : angle 1.39920 ( 75) link_BETA1-6 : bond 0.00498 ( 10) link_BETA1-6 : angle 1.22543 ( 30) link_NAG-ASN : bond 0.00949 ( 15) link_NAG-ASN : angle 2.31854 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.9049 (t0) cc_final: 0.8765 (t0) REVERT: A 124 LYS cc_start: 0.9224 (mttt) cc_final: 0.8880 (mttp) REVERT: A 142 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8622 (ptpt) REVERT: A 185 ARG cc_start: 0.8584 (ttt90) cc_final: 0.7995 (ttt90) REVERT: B 96 ASP cc_start: 0.8716 (t0) cc_final: 0.8355 (t0) REVERT: B 118 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8683 (mt) REVERT: C 92 TYR cc_start: 0.9405 (m-80) cc_final: 0.9098 (m-10) REVERT: D 185 ARG cc_start: 0.8150 (ttp-170) cc_final: 0.7762 (ptm-80) REVERT: D 191 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8769 (mttm) REVERT: D 205 ARG cc_start: 0.8708 (ttp-170) cc_final: 0.8278 (ttm-80) REVERT: E 118 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8716 (mp) REVERT: E 204 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7481 (ttp80) REVERT: F 12 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8778 (tm) REVERT: F 45 GLU cc_start: 0.8557 (pm20) cc_final: 0.8206 (pm20) REVERT: F 74 ASP cc_start: 0.8868 (t70) cc_final: 0.8298 (t70) REVERT: G 18 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8689 (m) REVERT: G 74 ASP cc_start: 0.8693 (t70) cc_final: 0.8183 (t70) REVERT: H 20 ARG cc_start: 0.8903 (ttt90) cc_final: 0.8642 (ttt180) REVERT: H 74 ASP cc_start: 0.8857 (t70) cc_final: 0.8482 (t70) REVERT: I 73 ARG cc_start: 0.8972 (ttp-170) cc_final: 0.8509 (ttm170) REVERT: I 74 ASP cc_start: 0.8860 (t70) cc_final: 0.8605 (t70) REVERT: I 88 LYS cc_start: 0.8138 (mttt) cc_final: 0.7914 (mttm) REVERT: J 44 LYS cc_start: 0.8244 (mppt) cc_final: 0.7795 (mppt) REVERT: J 47 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: J 74 ASP cc_start: 0.9056 (t70) cc_final: 0.8568 (t70) outliers start: 56 outliers final: 30 residues processed: 324 average time/residue: 0.7668 time to fit residues: 267.1016 Evaluate side-chains 316 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.0370 chunk 140 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.0770 chunk 48 optimal weight: 0.8980 overall best weight: 0.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 46 ASN C 3 GLN C 46 ASN C 170 ASN D 56 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 46 ASN H 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.064795 restraints weight = 20571.315| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.87 r_work: 0.2623 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14500 Z= 0.123 Angle : 0.589 10.040 19810 Z= 0.288 Chirality : 0.044 0.266 2245 Planarity : 0.004 0.049 2425 Dihedral : 5.996 58.807 3025 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.64 % Allowed : 22.06 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.19), residues: 1640 helix: -0.02 (0.71), residues: 50 sheet: 0.40 (0.19), residues: 665 loop : -1.03 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 204 TYR 0.013 0.001 TYR B 128 PHE 0.008 0.001 PHE J 69 TRP 0.010 0.001 TRP C 66 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00282 (14425) covalent geometry : angle 0.57180 (19600) SS BOND : bond 0.00332 ( 15) SS BOND : angle 0.90237 ( 30) hydrogen bonds : bond 0.02945 ( 412) hydrogen bonds : angle 4.43047 ( 1278) link_ALPHA1-3 : bond 0.00847 ( 5) link_ALPHA1-3 : angle 1.38168 ( 15) link_ALPHA1-6 : bond 0.00505 ( 5) link_ALPHA1-6 : angle 1.37780 ( 15) link_BETA1-4 : bond 0.00366 ( 25) link_BETA1-4 : angle 1.38469 ( 75) link_BETA1-6 : bond 0.00560 ( 10) link_BETA1-6 : angle 1.13197 ( 30) link_NAG-ASN : bond 0.00829 ( 15) link_NAG-ASN : angle 2.10799 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 291 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.8988 (t0) cc_final: 0.8683 (t0) REVERT: A 124 LYS cc_start: 0.9227 (mttt) cc_final: 0.8884 (mttp) REVERT: A 142 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8587 (ptpt) REVERT: A 185 ARG cc_start: 0.8575 (ttt90) cc_final: 0.7973 (ttt90) REVERT: B 96 ASP cc_start: 0.8670 (t0) cc_final: 0.8300 (t0) REVERT: B 118 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 185 ARG cc_start: 0.8523 (ptm160) cc_final: 0.8114 (ptm160) REVERT: C 92 TYR cc_start: 0.9373 (m-80) cc_final: 0.9045 (m-10) REVERT: C 191 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8728 (mtpp) REVERT: D 142 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8636 (ptpp) REVERT: D 185 ARG cc_start: 0.8159 (ttp-170) cc_final: 0.7794 (ptm-80) REVERT: D 188 GLU cc_start: 0.8204 (mp0) cc_final: 0.7954 (mp0) REVERT: D 191 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8744 (mttm) REVERT: D 205 ARG cc_start: 0.8722 (ttp-170) cc_final: 0.8500 (ttm-80) REVERT: E 142 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8883 (mtpp) REVERT: E 204 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7507 (ttp80) REVERT: F 12 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8778 (tm) REVERT: F 45 GLU cc_start: 0.8546 (pm20) cc_final: 0.8231 (pm20) REVERT: F 74 ASP cc_start: 0.8864 (t70) cc_final: 0.8337 (t70) REVERT: G 18 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8664 (m) REVERT: G 74 ASP cc_start: 0.8689 (t70) cc_final: 0.8198 (t70) REVERT: H 74 ASP cc_start: 0.8856 (t70) cc_final: 0.8420 (t70) REVERT: I 73 ARG cc_start: 0.8953 (ttp-170) cc_final: 0.8544 (ttm170) REVERT: I 74 ASP cc_start: 0.8843 (t70) cc_final: 0.8568 (t70) REVERT: I 88 LYS cc_start: 0.8125 (mttt) cc_final: 0.7901 (mttm) REVERT: J 29 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8648 (t) REVERT: J 44 LYS cc_start: 0.8275 (mppt) cc_final: 0.7360 (mtmm) REVERT: J 47 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: J 74 ASP cc_start: 0.9065 (t70) cc_final: 0.8590 (t70) outliers start: 53 outliers final: 29 residues processed: 324 average time/residue: 0.7510 time to fit residues: 261.7605 Evaluate side-chains 316 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 89 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 46 ASN C 3 GLN C 46 ASN C 170 ASN D 3 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN H 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.064522 restraints weight = 20675.990| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.87 r_work: 0.2606 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14500 Z= 0.152 Angle : 0.601 9.613 19810 Z= 0.294 Chirality : 0.044 0.300 2245 Planarity : 0.004 0.050 2425 Dihedral : 5.996 58.021 3025 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.85 % Allowed : 22.06 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.19), residues: 1640 helix: -0.04 (0.71), residues: 50 sheet: 0.25 (0.19), residues: 690 loop : -0.94 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 204 TYR 0.019 0.001 TYR A 128 PHE 0.008 0.001 PHE D 2 TRP 0.008 0.001 TRP E 133 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00351 (14425) covalent geometry : angle 0.58407 (19600) SS BOND : bond 0.00315 ( 15) SS BOND : angle 0.90259 ( 30) hydrogen bonds : bond 0.03023 ( 412) hydrogen bonds : angle 4.46202 ( 1278) link_ALPHA1-3 : bond 0.00840 ( 5) link_ALPHA1-3 : angle 1.37861 ( 15) link_ALPHA1-6 : bond 0.00492 ( 5) link_ALPHA1-6 : angle 1.38115 ( 15) link_BETA1-4 : bond 0.00357 ( 25) link_BETA1-4 : angle 1.39227 ( 75) link_BETA1-6 : bond 0.00523 ( 10) link_BETA1-6 : angle 1.17899 ( 30) link_NAG-ASN : bond 0.00866 ( 15) link_NAG-ASN : angle 2.13004 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 279 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.8993 (t0) cc_final: 0.8684 (t0) REVERT: A 124 LYS cc_start: 0.9224 (mttt) cc_final: 0.8879 (mttp) REVERT: A 142 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8598 (ptpt) REVERT: B 96 ASP cc_start: 0.8695 (t0) cc_final: 0.8311 (t0) REVERT: B 118 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8666 (mt) REVERT: B 142 LYS cc_start: 0.9032 (ptpp) cc_final: 0.8733 (mtpp) REVERT: B 185 ARG cc_start: 0.8510 (ptm160) cc_final: 0.8211 (ptm160) REVERT: C 128 TYR cc_start: 0.8547 (t80) cc_final: 0.8343 (t80) REVERT: C 170 ASN cc_start: 0.8955 (t0) cc_final: 0.8409 (t0) REVERT: C 172 GLU cc_start: 0.8939 (tt0) cc_final: 0.8617 (tt0) REVERT: D 142 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8634 (ptpp) REVERT: D 185 ARG cc_start: 0.8159 (ttp-170) cc_final: 0.7790 (ptm-80) REVERT: D 191 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8740 (mttm) REVERT: D 205 ARG cc_start: 0.8711 (ttp-170) cc_final: 0.8481 (ttm-80) REVERT: E 118 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8710 (mp) REVERT: E 142 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8885 (mtpp) REVERT: F 12 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8775 (tm) REVERT: F 45 GLU cc_start: 0.8571 (pm20) cc_final: 0.8251 (pm20) REVERT: F 74 ASP cc_start: 0.8872 (t70) cc_final: 0.8352 (t70) REVERT: G 18 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8673 (m) REVERT: G 74 ASP cc_start: 0.8702 (t70) cc_final: 0.8216 (t70) REVERT: H 20 ARG cc_start: 0.8896 (ttt90) cc_final: 0.8624 (ttt180) REVERT: H 74 ASP cc_start: 0.8855 (t70) cc_final: 0.8374 (t70) REVERT: H 90 GLU cc_start: 0.8918 (mp0) cc_final: 0.8711 (pm20) REVERT: I 73 ARG cc_start: 0.8960 (ttp-170) cc_final: 0.8560 (ttm170) REVERT: I 74 ASP cc_start: 0.8844 (t70) cc_final: 0.8567 (t70) REVERT: I 88 LYS cc_start: 0.8122 (mttt) cc_final: 0.7898 (mttm) REVERT: J 44 LYS cc_start: 0.8268 (mppt) cc_final: 0.7525 (mtmm) REVERT: J 47 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: J 74 ASP cc_start: 0.9068 (t70) cc_final: 0.8570 (t70) outliers start: 56 outliers final: 35 residues processed: 314 average time/residue: 0.7563 time to fit residues: 255.5290 Evaluate side-chains 322 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 157 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 46 ASN C 3 GLN C 46 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN F 4 GLN H 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.063025 restraints weight = 20769.592| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.88 r_work: 0.2573 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14500 Z= 0.199 Angle : 0.638 9.571 19810 Z= 0.312 Chirality : 0.045 0.285 2245 Planarity : 0.004 0.050 2425 Dihedral : 6.092 56.278 3025 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.92 % Allowed : 21.92 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.19), residues: 1640 helix: -1.55 (0.50), residues: 80 sheet: 0.18 (0.19), residues: 695 loop : -1.06 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 204 TYR 0.013 0.001 TYR E 92 PHE 0.010 0.001 PHE D 2 TRP 0.009 0.001 TRP E 133 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00461 (14425) covalent geometry : angle 0.61999 (19600) SS BOND : bond 0.00326 ( 15) SS BOND : angle 0.99106 ( 30) hydrogen bonds : bond 0.03237 ( 412) hydrogen bonds : angle 4.61459 ( 1278) link_ALPHA1-3 : bond 0.00817 ( 5) link_ALPHA1-3 : angle 1.38868 ( 15) link_ALPHA1-6 : bond 0.00461 ( 5) link_ALPHA1-6 : angle 1.39415 ( 15) link_BETA1-4 : bond 0.00344 ( 25) link_BETA1-4 : angle 1.42278 ( 75) link_BETA1-6 : bond 0.00468 ( 10) link_BETA1-6 : angle 1.25216 ( 30) link_NAG-ASN : bond 0.00981 ( 15) link_NAG-ASN : angle 2.33237 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.9052 (t0) cc_final: 0.8743 (t0) REVERT: A 124 LYS cc_start: 0.9224 (mttt) cc_final: 0.8881 (mttp) REVERT: A 142 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8615 (ptpt) REVERT: B 96 ASP cc_start: 0.8725 (t0) cc_final: 0.8381 (t0) REVERT: B 118 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8696 (mt) REVERT: B 185 ARG cc_start: 0.8500 (ptm160) cc_final: 0.8186 (ptm160) REVERT: C 191 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8761 (mtpp) REVERT: D 185 ARG cc_start: 0.8173 (ttp-170) cc_final: 0.7627 (ptm160) REVERT: D 188 GLU cc_start: 0.8197 (mp0) cc_final: 0.7925 (mp0) REVERT: D 191 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8741 (mttm) REVERT: D 205 ARG cc_start: 0.8712 (ttp-170) cc_final: 0.8457 (ttm-80) REVERT: E 118 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8740 (mp) REVERT: E 204 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7481 (ttp80) REVERT: F 12 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8794 (tm) REVERT: F 45 GLU cc_start: 0.8606 (pm20) cc_final: 0.8274 (pm20) REVERT: F 74 ASP cc_start: 0.8889 (t70) cc_final: 0.8323 (t70) REVERT: G 74 ASP cc_start: 0.8717 (t70) cc_final: 0.8242 (t70) REVERT: H 20 ARG cc_start: 0.8903 (ttt90) cc_final: 0.8634 (ttt180) REVERT: H 74 ASP cc_start: 0.8866 (t70) cc_final: 0.8397 (t70) REVERT: H 90 GLU cc_start: 0.8941 (mp0) cc_final: 0.8735 (pm20) REVERT: I 73 ARG cc_start: 0.8973 (ttp-170) cc_final: 0.8569 (ttm170) REVERT: I 74 ASP cc_start: 0.8837 (t70) cc_final: 0.8581 (t70) REVERT: I 88 LYS cc_start: 0.8115 (mttt) cc_final: 0.7883 (mttm) REVERT: J 44 LYS cc_start: 0.8265 (mppt) cc_final: 0.7415 (mtmm) REVERT: J 47 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: J 74 ASP cc_start: 0.9076 (t70) cc_final: 0.8576 (t70) outliers start: 57 outliers final: 40 residues processed: 317 average time/residue: 0.7626 time to fit residues: 260.0052 Evaluate side-chains 322 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN B 46 ASN C 3 GLN C 46 ASN C 170 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN F 4 GLN H 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.092692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.064129 restraints weight = 20686.786| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.87 r_work: 0.2609 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14500 Z= 0.135 Angle : 0.607 9.743 19810 Z= 0.297 Chirality : 0.044 0.308 2245 Planarity : 0.004 0.052 2425 Dihedral : 6.004 58.396 3025 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.37 % Allowed : 22.41 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.19), residues: 1640 helix: -0.07 (0.71), residues: 50 sheet: 0.22 (0.19), residues: 695 loop : -0.94 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.019 0.001 TYR A 128 PHE 0.009 0.001 PHE E 2 TRP 0.010 0.001 TRP E 133 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00312 (14425) covalent geometry : angle 0.59019 (19600) SS BOND : bond 0.00322 ( 15) SS BOND : angle 1.08050 ( 30) hydrogen bonds : bond 0.02994 ( 412) hydrogen bonds : angle 4.45686 ( 1278) link_ALPHA1-3 : bond 0.00830 ( 5) link_ALPHA1-3 : angle 1.37912 ( 15) link_ALPHA1-6 : bond 0.00491 ( 5) link_ALPHA1-6 : angle 1.39121 ( 15) link_BETA1-4 : bond 0.00364 ( 25) link_BETA1-4 : angle 1.39598 ( 75) link_BETA1-6 : bond 0.00548 ( 10) link_BETA1-6 : angle 1.16662 ( 30) link_NAG-ASN : bond 0.00857 ( 15) link_NAG-ASN : angle 2.03678 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 283 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.9005 (t0) cc_final: 0.8697 (t0) REVERT: A 124 LYS cc_start: 0.9226 (mttt) cc_final: 0.8880 (mttp) REVERT: A 142 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8600 (ptpt) REVERT: B 96 ASP cc_start: 0.8707 (t0) cc_final: 0.8319 (t0) REVERT: B 118 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8664 (mt) REVERT: B 142 LYS cc_start: 0.9023 (ptpp) cc_final: 0.8724 (mtpp) REVERT: B 185 ARG cc_start: 0.8503 (ptm160) cc_final: 0.8186 (ptm160) REVERT: B 206 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7604 (mtm-85) REVERT: C 170 ASN cc_start: 0.8936 (t0) cc_final: 0.8427 (t0) REVERT: C 191 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8722 (mtpp) REVERT: D 142 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8627 (ptpp) REVERT: D 185 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7835 (ptm-80) REVERT: D 188 GLU cc_start: 0.8208 (mp0) cc_final: 0.7937 (mp0) REVERT: D 191 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8727 (mttm) REVERT: D 205 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.8264 (ttm-80) REVERT: E 118 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8694 (mp) REVERT: E 204 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7449 (ttp80) REVERT: F 12 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8752 (tm) REVERT: F 45 GLU cc_start: 0.8591 (pm20) cc_final: 0.8256 (pm20) REVERT: F 74 ASP cc_start: 0.8866 (t70) cc_final: 0.8311 (t70) REVERT: G 74 ASP cc_start: 0.8695 (t70) cc_final: 0.8095 (t70) REVERT: H 20 ARG cc_start: 0.8885 (ttt90) cc_final: 0.8607 (ttt180) REVERT: H 74 ASP cc_start: 0.8849 (t70) cc_final: 0.8351 (t70) REVERT: I 73 ARG cc_start: 0.8926 (ttp-170) cc_final: 0.8547 (ttm170) REVERT: I 74 ASP cc_start: 0.8826 (t70) cc_final: 0.8568 (t70) REVERT: I 88 LYS cc_start: 0.8100 (mttt) cc_final: 0.7868 (mttm) REVERT: J 44 LYS cc_start: 0.8298 (mppt) cc_final: 0.7527 (mppt) REVERT: J 47 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: J 74 ASP cc_start: 0.9062 (t70) cc_final: 0.8559 (t70) outliers start: 49 outliers final: 34 residues processed: 314 average time/residue: 0.7608 time to fit residues: 257.0911 Evaluate side-chains 320 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 118 GLN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 46 ASN C 3 GLN C 46 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN F 4 GLN H 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.065075 restraints weight = 20750.652| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.87 r_work: 0.2625 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14500 Z= 0.123 Angle : 0.603 10.152 19810 Z= 0.294 Chirality : 0.044 0.302 2245 Planarity : 0.004 0.051 2425 Dihedral : 5.921 59.813 3025 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.37 % Allowed : 22.61 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.20), residues: 1640 helix: -0.00 (0.71), residues: 50 sheet: 0.23 (0.19), residues: 715 loop : -0.93 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.012 0.001 TYR A 187 PHE 0.010 0.001 PHE A 186 TRP 0.010 0.001 TRP E 133 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00284 (14425) covalent geometry : angle 0.58717 (19600) SS BOND : bond 0.00324 ( 15) SS BOND : angle 1.00815 ( 30) hydrogen bonds : bond 0.02890 ( 412) hydrogen bonds : angle 4.35264 ( 1278) link_ALPHA1-3 : bond 0.00850 ( 5) link_ALPHA1-3 : angle 1.37407 ( 15) link_ALPHA1-6 : bond 0.00501 ( 5) link_ALPHA1-6 : angle 1.38571 ( 15) link_BETA1-4 : bond 0.00365 ( 25) link_BETA1-4 : angle 1.38078 ( 75) link_BETA1-6 : bond 0.00568 ( 10) link_BETA1-6 : angle 1.13139 ( 30) link_NAG-ASN : bond 0.00799 ( 15) link_NAG-ASN : angle 1.94990 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7227.59 seconds wall clock time: 123 minutes 18.99 seconds (7398.99 seconds total)