Starting phenix.real_space_refine on Sun Jul 5 19:09:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v12_64680/07_2026/9v12_64680_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v12_64680/07_2026/9v12_64680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v12_64680/07_2026/9v12_64680_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v12_64680/07_2026/9v12_64680_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v12_64680/07_2026/9v12_64680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v12_64680/07_2026/9v12_64680.map" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 40 5.49 5 S 96 5.16 5 C 18520 2.51 5 N 5152 2.21 5 O 5504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29320 Number of models: 1 Model: "" Number of chains: 32 Chain: "I" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1395 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1395 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1395 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1395 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1395 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1395 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1395 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1395 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2195 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "j" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2195 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "k" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2195 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "l" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2195 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "m" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2195 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "n" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2195 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "o" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2195 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "p" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2195 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.93, per 1000 atoms: 0.20 Number of scatterers: 29320 At special positions: 0 Unit cell: (173.55, 169.65, 120.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 96 16.00 P 40 15.00 O 5504 8.00 N 5152 7.00 C 18520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.2 seconds 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 16 sheets defined 52.3% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'I' and resid 11 through 22 removed outlier: 3.582A pdb=" N ARG I 16 " --> pdb=" O SER I 12 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 59 removed outlier: 3.804A pdb=" N ILE I 52 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA I 57 " --> pdb=" O ALA I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 81 Processing helix chain 'I' and resid 82 through 89 removed outlier: 3.610A pdb=" N GLU I 87 " --> pdb=" O LYS I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 95 Processing helix chain 'I' and resid 158 through 163 Processing helix chain 'I' and resid 164 through 166 No H-bonds generated for 'chain 'I' and resid 164 through 166' Processing helix chain 'I' and resid 167 through 180 removed outlier: 4.895A pdb=" N THR I 173 " --> pdb=" O GLY I 169 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 22 removed outlier: 3.582A pdb=" N ARG K 16 " --> pdb=" O SER K 12 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL K 21 " --> pdb=" O GLU K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 59 removed outlier: 3.804A pdb=" N ILE K 52 " --> pdb=" O ARG K 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 81 Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.611A pdb=" N GLU K 87 " --> pdb=" O LYS K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'K' and resid 158 through 163 Processing helix chain 'K' and resid 164 through 166 No H-bonds generated for 'chain 'K' and resid 164 through 166' Processing helix chain 'K' and resid 167 through 180 removed outlier: 4.895A pdb=" N THR K 173 " --> pdb=" O GLY K 169 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG K 174 " --> pdb=" O ARG K 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 22 removed outlier: 3.582A pdb=" N ARG M 16 " --> pdb=" O SER M 12 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL M 21 " --> pdb=" O GLU M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 59 removed outlier: 3.804A pdb=" N ILE M 52 " --> pdb=" O ARG M 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 81 Processing helix chain 'M' and resid 82 through 89 removed outlier: 3.610A pdb=" N GLU M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 95 Processing helix chain 'M' and resid 158 through 163 Processing helix chain 'M' and resid 164 through 166 No H-bonds generated for 'chain 'M' and resid 164 through 166' Processing helix chain 'M' and resid 167 through 180 removed outlier: 4.895A pdb=" N THR M 173 " --> pdb=" O GLY M 169 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG M 174 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 22 removed outlier: 3.582A pdb=" N ARG O 16 " --> pdb=" O SER O 12 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL O 21 " --> pdb=" O GLU O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 59 removed outlier: 3.804A pdb=" N ILE O 52 " --> pdb=" O ARG O 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA O 53 " --> pdb=" O ALA O 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 81 Processing helix chain 'O' and resid 82 through 89 removed outlier: 3.610A pdb=" N GLU O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 95 Processing helix chain 'O' and resid 158 through 163 Processing helix chain 'O' and resid 164 through 166 No H-bonds generated for 'chain 'O' and resid 164 through 166' Processing helix chain 'O' and resid 167 through 180 removed outlier: 4.894A pdb=" N THR O 173 " --> pdb=" O GLY O 169 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG O 174 " --> pdb=" O ARG O 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 22 removed outlier: 3.582A pdb=" N ARG R 16 " --> pdb=" O SER R 12 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL R 21 " --> pdb=" O GLU R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 59 removed outlier: 3.804A pdb=" N ILE R 52 " --> pdb=" O ARG R 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA R 53 " --> pdb=" O ALA R 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA R 57 " --> pdb=" O ALA R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 81 Processing helix chain 'R' and resid 82 through 89 removed outlier: 3.610A pdb=" N GLU R 87 " --> pdb=" O LYS R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 158 through 163 Processing helix chain 'R' and resid 164 through 166 No H-bonds generated for 'chain 'R' and resid 164 through 166' Processing helix chain 'R' and resid 167 through 180 removed outlier: 4.895A pdb=" N THR R 173 " --> pdb=" O GLY R 169 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG R 174 " --> pdb=" O ARG R 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 22 removed outlier: 3.582A pdb=" N ARG T 16 " --> pdb=" O SER T 12 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL T 21 " --> pdb=" O GLU T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 59 removed outlier: 3.804A pdb=" N ILE T 52 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA T 53 " --> pdb=" O ALA T 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA T 57 " --> pdb=" O ALA T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 81 Processing helix chain 'T' and resid 82 through 89 removed outlier: 3.611A pdb=" N GLU T 87 " --> pdb=" O LYS T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 95 Processing helix chain 'T' and resid 158 through 163 Processing helix chain 'T' and resid 164 through 166 No H-bonds generated for 'chain 'T' and resid 164 through 166' Processing helix chain 'T' and resid 167 through 180 removed outlier: 4.895A pdb=" N THR T 173 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG T 174 " --> pdb=" O ARG T 170 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 22 removed outlier: 3.581A pdb=" N ARG V 16 " --> pdb=" O SER V 12 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL V 21 " --> pdb=" O GLU V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 59 removed outlier: 3.804A pdb=" N ILE V 52 " --> pdb=" O ARG V 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA V 53 " --> pdb=" O ALA V 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA V 57 " --> pdb=" O ALA V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 78 through 81 Processing helix chain 'V' and resid 82 through 89 removed outlier: 3.610A pdb=" N GLU V 87 " --> pdb=" O LYS V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 95 Processing helix chain 'V' and resid 158 through 163 Processing helix chain 'V' and resid 164 through 166 No H-bonds generated for 'chain 'V' and resid 164 through 166' Processing helix chain 'V' and resid 167 through 180 removed outlier: 4.895A pdb=" N THR V 173 " --> pdb=" O GLY V 169 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG V 174 " --> pdb=" O ARG V 170 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 22 removed outlier: 3.582A pdb=" N ARG X 16 " --> pdb=" O SER X 12 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL X 21 " --> pdb=" O GLU X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 59 removed outlier: 3.804A pdb=" N ILE X 52 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA X 53 " --> pdb=" O ALA X 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 81 Processing helix chain 'X' and resid 82 through 89 removed outlier: 3.610A pdb=" N GLU X 87 " --> pdb=" O LYS X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 95 Processing helix chain 'X' and resid 158 through 163 Processing helix chain 'X' and resid 164 through 166 No H-bonds generated for 'chain 'X' and resid 164 through 166' Processing helix chain 'X' and resid 167 through 180 removed outlier: 4.894A pdb=" N THR X 173 " --> pdb=" O GLY X 169 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG X 174 " --> pdb=" O ARG X 170 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 19 Proline residue: i 11 - end of helix removed outlier: 3.694A pdb=" N GLU i 16 " --> pdb=" O LEU i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 35 Proline residue: i 33 - end of helix Processing helix chain 'i' and resid 38 through 51 removed outlier: 4.078A pdb=" N ILE i 43 " --> pdb=" O GLY i 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS i 48 " --> pdb=" O ALA i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 53 through 58 removed outlier: 3.552A pdb=" N ASP i 58 " --> pdb=" O PRO i 54 " (cutoff:3.500A) Processing helix chain 'i' and resid 62 through 72 removed outlier: 3.543A pdb=" N ILE i 72 " --> pdb=" O GLU i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 90 removed outlier: 3.608A pdb=" N ARG i 80 " --> pdb=" O ASN i 76 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP i 90 " --> pdb=" O SER i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 100 removed outlier: 3.598A pdb=" N ARG i 98 " --> pdb=" O ALA i 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU i 99 " --> pdb=" O GLU i 95 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS i 100 " --> pdb=" O ALA i 96 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 109 Processing helix chain 'i' and resid 124 through 131 removed outlier: 3.557A pdb=" N LEU i 128 " --> pdb=" O VAL i 124 " (cutoff:3.500A) Processing helix chain 'i' and resid 140 through 146 removed outlier: 3.516A pdb=" N PHE i 144 " --> pdb=" O SER i 140 " (cutoff:3.500A) Processing helix chain 'i' and resid 164 through 168 removed outlier: 3.738A pdb=" N ILE i 168 " --> pdb=" O PRO i 165 " (cutoff:3.500A) Processing helix chain 'i' and resid 171 through 178 Processing helix chain 'i' and resid 179 through 181 No H-bonds generated for 'chain 'i' and resid 179 through 181' Processing helix chain 'i' and resid 183 through 193 Processing helix chain 'i' and resid 207 through 224 removed outlier: 3.520A pdb=" N ARG i 211 " --> pdb=" O ASP i 207 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE i 213 " --> pdb=" O ASN i 209 " (cutoff:3.500A) Processing helix chain 'i' and resid 246 through 251 Processing helix chain 'i' and resid 265 through 278 removed outlier: 3.717A pdb=" N VAL i 270 " --> pdb=" O LYS i 266 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA i 278 " --> pdb=" O LEU i 274 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 19 Proline residue: j 11 - end of helix removed outlier: 3.694A pdb=" N GLU j 16 " --> pdb=" O LEU j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 35 Proline residue: j 33 - end of helix Processing helix chain 'j' and resid 38 through 51 removed outlier: 4.079A pdb=" N ILE j 43 " --> pdb=" O GLY j 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS j 48 " --> pdb=" O ALA j 44 " (cutoff:3.500A) Processing helix chain 'j' and resid 53 through 58 removed outlier: 3.552A pdb=" N ASP j 58 " --> pdb=" O PRO j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 72 removed outlier: 3.542A pdb=" N ILE j 72 " --> pdb=" O GLU j 68 " (cutoff:3.500A) Processing helix chain 'j' and resid 76 through 90 removed outlier: 3.634A pdb=" N ARG j 80 " --> pdb=" O ASN j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 91 through 100 removed outlier: 3.598A pdb=" N ARG j 98 " --> pdb=" O ALA j 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU j 99 " --> pdb=" O GLU j 95 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS j 100 " --> pdb=" O ALA j 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 101 through 109 Processing helix chain 'j' and resid 124 through 131 removed outlier: 3.557A pdb=" N LEU j 128 " --> pdb=" O VAL j 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 140 through 146 removed outlier: 3.517A pdb=" N PHE j 144 " --> pdb=" O SER j 140 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 168 removed outlier: 3.739A pdb=" N ILE j 168 " --> pdb=" O PRO j 165 " (cutoff:3.500A) Processing helix chain 'j' and resid 171 through 178 Processing helix chain 'j' and resid 179 through 181 No H-bonds generated for 'chain 'j' and resid 179 through 181' Processing helix chain 'j' and resid 183 through 193 Processing helix chain 'j' and resid 207 through 224 removed outlier: 3.530A pdb=" N ARG j 211 " --> pdb=" O ASP j 207 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE j 213 " --> pdb=" O ASN j 209 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU j 220 " --> pdb=" O ARG j 216 " (cutoff:3.500A) Processing helix chain 'j' and resid 246 through 251 Processing helix chain 'j' and resid 265 through 278 removed outlier: 3.716A pdb=" N VAL j 270 " --> pdb=" O LYS j 266 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA j 278 " --> pdb=" O LEU j 274 " (cutoff:3.500A) Processing helix chain 'k' and resid 5 through 19 Proline residue: k 11 - end of helix removed outlier: 3.694A pdb=" N GLU k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 35 Proline residue: k 33 - end of helix Processing helix chain 'k' and resid 38 through 51 removed outlier: 4.079A pdb=" N ILE k 43 " --> pdb=" O GLY k 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS k 48 " --> pdb=" O ALA k 44 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 3.637A pdb=" N ASP k 58 " --> pdb=" O PRO k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 61 No H-bonds generated for 'chain 'k' and resid 59 through 61' Processing helix chain 'k' and resid 62 through 72 removed outlier: 3.543A pdb=" N ILE k 72 " --> pdb=" O GLU k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 90 removed outlier: 3.615A pdb=" N ARG k 80 " --> pdb=" O ASN k 76 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 100 removed outlier: 3.598A pdb=" N ARG k 98 " --> pdb=" O ALA k 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU k 99 " --> pdb=" O GLU k 95 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS k 100 " --> pdb=" O ALA k 96 " (cutoff:3.500A) Processing helix chain 'k' and resid 101 through 109 Processing helix chain 'k' and resid 124 through 131 removed outlier: 3.556A pdb=" N LEU k 128 " --> pdb=" O VAL k 124 " (cutoff:3.500A) Processing helix chain 'k' and resid 140 through 146 removed outlier: 3.517A pdb=" N PHE k 144 " --> pdb=" O SER k 140 " (cutoff:3.500A) Processing helix chain 'k' and resid 164 through 168 removed outlier: 3.740A pdb=" N ILE k 168 " --> pdb=" O PRO k 165 " (cutoff:3.500A) Processing helix chain 'k' and resid 171 through 178 Processing helix chain 'k' and resid 179 through 181 No H-bonds generated for 'chain 'k' and resid 179 through 181' Processing helix chain 'k' and resid 183 through 193 Processing helix chain 'k' and resid 207 through 224 removed outlier: 3.502A pdb=" N ARG k 211 " --> pdb=" O ASP k 207 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE k 213 " --> pdb=" O ASN k 209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU k 220 " --> pdb=" O ARG k 216 " (cutoff:3.500A) Processing helix chain 'k' and resid 246 through 251 Processing helix chain 'k' and resid 265 through 278 removed outlier: 3.717A pdb=" N VAL k 270 " --> pdb=" O LYS k 266 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA k 278 " --> pdb=" O LEU k 274 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 19 Proline residue: l 11 - end of helix removed outlier: 3.694A pdb=" N GLU l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 35 Proline residue: l 33 - end of helix Processing helix chain 'l' and resid 38 through 51 removed outlier: 4.079A pdb=" N ILE l 43 " --> pdb=" O GLY l 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS l 48 " --> pdb=" O ALA l 44 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 58 removed outlier: 3.559A pdb=" N ASP l 58 " --> pdb=" O PRO l 54 " (cutoff:3.500A) Processing helix chain 'l' and resid 62 through 72 removed outlier: 3.543A pdb=" N ILE l 72 " --> pdb=" O GLU l 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 90 removed outlier: 3.661A pdb=" N ARG l 80 " --> pdb=" O ASN l 76 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 100 removed outlier: 3.598A pdb=" N ARG l 98 " --> pdb=" O ALA l 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU l 99 " --> pdb=" O GLU l 95 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS l 100 " --> pdb=" O ALA l 96 " (cutoff:3.500A) Processing helix chain 'l' and resid 101 through 109 Processing helix chain 'l' and resid 124 through 131 removed outlier: 3.556A pdb=" N LEU l 128 " --> pdb=" O VAL l 124 " (cutoff:3.500A) Processing helix chain 'l' and resid 140 through 146 removed outlier: 3.517A pdb=" N PHE l 144 " --> pdb=" O SER l 140 " (cutoff:3.500A) Processing helix chain 'l' and resid 164 through 168 removed outlier: 3.739A pdb=" N ILE l 168 " --> pdb=" O PRO l 165 " (cutoff:3.500A) Processing helix chain 'l' and resid 171 through 178 Processing helix chain 'l' and resid 179 through 181 No H-bonds generated for 'chain 'l' and resid 179 through 181' Processing helix chain 'l' and resid 183 through 193 Processing helix chain 'l' and resid 207 through 224 removed outlier: 3.504A pdb=" N ARG l 211 " --> pdb=" O ASP l 207 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE l 213 " --> pdb=" O ASN l 209 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU l 220 " --> pdb=" O ARG l 216 " (cutoff:3.500A) Processing helix chain 'l' and resid 246 through 251 Processing helix chain 'l' and resid 265 through 278 removed outlier: 3.717A pdb=" N VAL l 270 " --> pdb=" O LYS l 266 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA l 278 " --> pdb=" O LEU l 274 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 19 Proline residue: m 11 - end of helix removed outlier: 3.694A pdb=" N GLU m 16 " --> pdb=" O LEU m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 35 Proline residue: m 33 - end of helix Processing helix chain 'm' and resid 38 through 51 removed outlier: 4.079A pdb=" N ILE m 43 " --> pdb=" O GLY m 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS m 48 " --> pdb=" O ALA m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 53 through 58 removed outlier: 3.560A pdb=" N ASP m 58 " --> pdb=" O PRO m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 removed outlier: 3.543A pdb=" N ILE m 72 " --> pdb=" O GLU m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 90 removed outlier: 3.511A pdb=" N ARG m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP m 90 " --> pdb=" O SER m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 91 through 100 removed outlier: 3.597A pdb=" N ARG m 98 " --> pdb=" O ALA m 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU m 99 " --> pdb=" O GLU m 95 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS m 100 " --> pdb=" O ALA m 96 " (cutoff:3.500A) Processing helix chain 'm' and resid 101 through 109 Processing helix chain 'm' and resid 124 through 131 removed outlier: 3.556A pdb=" N LEU m 128 " --> pdb=" O VAL m 124 " (cutoff:3.500A) Processing helix chain 'm' and resid 140 through 146 removed outlier: 3.517A pdb=" N PHE m 144 " --> pdb=" O SER m 140 " (cutoff:3.500A) Processing helix chain 'm' and resid 164 through 168 removed outlier: 3.739A pdb=" N ILE m 168 " --> pdb=" O PRO m 165 " (cutoff:3.500A) Processing helix chain 'm' and resid 171 through 178 Processing helix chain 'm' and resid 179 through 181 No H-bonds generated for 'chain 'm' and resid 179 through 181' Processing helix chain 'm' and resid 183 through 193 Processing helix chain 'm' and resid 207 through 224 removed outlier: 3.515A pdb=" N ARG m 211 " --> pdb=" O ASP m 207 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE m 213 " --> pdb=" O ASN m 209 " (cutoff:3.500A) Processing helix chain 'm' and resid 246 through 251 Processing helix chain 'm' and resid 265 through 278 removed outlier: 3.717A pdb=" N VAL m 270 " --> pdb=" O LYS m 266 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA m 278 " --> pdb=" O LEU m 274 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 19 Proline residue: n 11 - end of helix removed outlier: 3.694A pdb=" N GLU n 16 " --> pdb=" O LEU n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 28 through 35 Proline residue: n 33 - end of helix Processing helix chain 'n' and resid 38 through 51 removed outlier: 4.079A pdb=" N ILE n 43 " --> pdb=" O GLY n 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 58 removed outlier: 3.561A pdb=" N ASP n 58 " --> pdb=" O PRO n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 62 through 72 removed outlier: 3.543A pdb=" N ILE n 72 " --> pdb=" O GLU n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 76 through 90 removed outlier: 3.504A pdb=" N ARG n 80 " --> pdb=" O ASN n 76 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP n 90 " --> pdb=" O SER n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 91 through 100 removed outlier: 3.598A pdb=" N ARG n 98 " --> pdb=" O ALA n 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU n 99 " --> pdb=" O GLU n 95 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS n 100 " --> pdb=" O ALA n 96 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 109 Processing helix chain 'n' and resid 124 through 131 removed outlier: 3.556A pdb=" N LEU n 128 " --> pdb=" O VAL n 124 " (cutoff:3.500A) Processing helix chain 'n' and resid 140 through 146 removed outlier: 3.517A pdb=" N PHE n 144 " --> pdb=" O SER n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 164 through 168 removed outlier: 3.739A pdb=" N ILE n 168 " --> pdb=" O PRO n 165 " (cutoff:3.500A) Processing helix chain 'n' and resid 171 through 178 Processing helix chain 'n' and resid 179 through 181 No H-bonds generated for 'chain 'n' and resid 179 through 181' Processing helix chain 'n' and resid 183 through 193 Processing helix chain 'n' and resid 207 through 224 removed outlier: 3.513A pdb=" N ARG n 211 " --> pdb=" O ASP n 207 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE n 213 " --> pdb=" O ASN n 209 " (cutoff:3.500A) Processing helix chain 'n' and resid 246 through 251 Processing helix chain 'n' and resid 265 through 278 removed outlier: 3.717A pdb=" N VAL n 270 " --> pdb=" O LYS n 266 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA n 278 " --> pdb=" O LEU n 274 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 19 Proline residue: o 11 - end of helix removed outlier: 3.694A pdb=" N GLU o 16 " --> pdb=" O LEU o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 35 Proline residue: o 33 - end of helix Processing helix chain 'o' and resid 38 through 51 removed outlier: 4.079A pdb=" N ILE o 43 " --> pdb=" O GLY o 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS o 48 " --> pdb=" O ALA o 44 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 59 removed outlier: 3.665A pdb=" N ASP o 58 " --> pdb=" O PRO o 54 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET o 59 " --> pdb=" O GLU o 55 " (cutoff:3.500A) Processing helix chain 'o' and resid 62 through 72 removed outlier: 3.544A pdb=" N ILE o 72 " --> pdb=" O GLU o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 76 through 90 removed outlier: 3.613A pdb=" N ARG o 80 " --> pdb=" O ASN o 76 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 100 removed outlier: 3.597A pdb=" N ARG o 98 " --> pdb=" O ALA o 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU o 99 " --> pdb=" O GLU o 95 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS o 100 " --> pdb=" O ALA o 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 109 Processing helix chain 'o' and resid 124 through 131 removed outlier: 3.556A pdb=" N LEU o 128 " --> pdb=" O VAL o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 140 through 146 removed outlier: 3.517A pdb=" N PHE o 144 " --> pdb=" O SER o 140 " (cutoff:3.500A) Processing helix chain 'o' and resid 164 through 168 removed outlier: 3.739A pdb=" N ILE o 168 " --> pdb=" O PRO o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 171 through 178 Processing helix chain 'o' and resid 179 through 181 No H-bonds generated for 'chain 'o' and resid 179 through 181' Processing helix chain 'o' and resid 183 through 193 Processing helix chain 'o' and resid 207 through 224 removed outlier: 3.511A pdb=" N ARG o 211 " --> pdb=" O ASP o 207 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE o 213 " --> pdb=" O ASN o 209 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU o 220 " --> pdb=" O ARG o 216 " (cutoff:3.500A) Processing helix chain 'o' and resid 246 through 251 Processing helix chain 'o' and resid 265 through 278 removed outlier: 3.717A pdb=" N VAL o 270 " --> pdb=" O LYS o 266 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA o 278 " --> pdb=" O LEU o 274 " (cutoff:3.500A) Processing helix chain 'p' and resid 5 through 19 Proline residue: p 11 - end of helix removed outlier: 3.694A pdb=" N GLU p 16 " --> pdb=" O LEU p 12 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 35 Proline residue: p 33 - end of helix Processing helix chain 'p' and resid 38 through 51 removed outlier: 4.078A pdb=" N ILE p 43 " --> pdb=" O GLY p 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS p 48 " --> pdb=" O ALA p 44 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 58 removed outlier: 3.603A pdb=" N ASP p 58 " --> pdb=" O PRO p 54 " (cutoff:3.500A) Processing helix chain 'p' and resid 59 through 61 No H-bonds generated for 'chain 'p' and resid 59 through 61' Processing helix chain 'p' and resid 62 through 72 removed outlier: 3.543A pdb=" N ILE p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 90 removed outlier: 3.511A pdb=" N ARG p 80 " --> pdb=" O ASN p 76 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP p 90 " --> pdb=" O SER p 86 " (cutoff:3.500A) Processing helix chain 'p' and resid 91 through 100 removed outlier: 3.599A pdb=" N ARG p 98 " --> pdb=" O ALA p 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU p 99 " --> pdb=" O GLU p 95 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS p 100 " --> pdb=" O ALA p 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 109 Processing helix chain 'p' and resid 124 through 131 removed outlier: 3.556A pdb=" N LEU p 128 " --> pdb=" O VAL p 124 " (cutoff:3.500A) Processing helix chain 'p' and resid 140 through 146 removed outlier: 3.516A pdb=" N PHE p 144 " --> pdb=" O SER p 140 " (cutoff:3.500A) Processing helix chain 'p' and resid 164 through 168 removed outlier: 3.739A pdb=" N ILE p 168 " --> pdb=" O PRO p 165 " (cutoff:3.500A) Processing helix chain 'p' and resid 171 through 178 Processing helix chain 'p' and resid 179 through 181 No H-bonds generated for 'chain 'p' and resid 179 through 181' Processing helix chain 'p' and resid 183 through 193 Processing helix chain 'p' and resid 207 through 224 removed outlier: 3.519A pdb=" N ARG p 211 " --> pdb=" O ASP p 207 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE p 213 " --> pdb=" O ASN p 209 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU p 220 " --> pdb=" O ARG p 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 246 through 251 Processing helix chain 'p' and resid 265 through 278 removed outlier: 3.717A pdb=" N VAL p 270 " --> pdb=" O LYS p 266 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA p 278 " --> pdb=" O LEU p 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 28 through 31 removed outlier: 6.442A pdb=" N TRP I 5 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU I 31 " --> pdb=" O TRP I 5 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR I 7 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE I 6 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLU I 65 " --> pdb=" O PHE I 6 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN I 8 " --> pdb=" O GLU I 65 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N GLY I 67 " --> pdb=" O ASN I 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 28 through 31 removed outlier: 6.442A pdb=" N TRP K 5 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU K 31 " --> pdb=" O TRP K 5 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR K 7 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE K 6 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLU K 65 " --> pdb=" O PHE K 6 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN K 8 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N GLY K 67 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.442A pdb=" N TRP M 5 " --> pdb=" O GLY M 29 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU M 31 " --> pdb=" O TRP M 5 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR M 7 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE M 6 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLU M 65 " --> pdb=" O PHE M 6 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASN M 8 " --> pdb=" O GLU M 65 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N GLY M 67 " --> pdb=" O ASN M 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 28 through 31 removed outlier: 6.443A pdb=" N TRP O 5 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU O 31 " --> pdb=" O TRP O 5 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR O 7 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE O 6 " --> pdb=" O ILE O 63 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLU O 65 " --> pdb=" O PHE O 6 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN O 8 " --> pdb=" O GLU O 65 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N GLY O 67 " --> pdb=" O ASN O 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 28 through 31 removed outlier: 6.442A pdb=" N TRP R 5 " --> pdb=" O GLY R 29 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU R 31 " --> pdb=" O TRP R 5 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR R 7 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE R 6 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLU R 65 " --> pdb=" O PHE R 6 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN R 8 " --> pdb=" O GLU R 65 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N GLY R 67 " --> pdb=" O ASN R 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 28 through 31 removed outlier: 6.443A pdb=" N TRP T 5 " --> pdb=" O GLY T 29 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU T 31 " --> pdb=" O TRP T 5 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR T 7 " --> pdb=" O LEU T 31 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE T 6 " --> pdb=" O ILE T 63 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLU T 65 " --> pdb=" O PHE T 6 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN T 8 " --> pdb=" O GLU T 65 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N GLY T 67 " --> pdb=" O ASN T 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 28 through 31 removed outlier: 6.441A pdb=" N TRP V 5 " --> pdb=" O GLY V 29 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU V 31 " --> pdb=" O TRP V 5 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR V 7 " --> pdb=" O LEU V 31 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE V 6 " --> pdb=" O ILE V 63 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLU V 65 " --> pdb=" O PHE V 6 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASN V 8 " --> pdb=" O GLU V 65 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N GLY V 67 " --> pdb=" O ASN V 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 28 through 31 removed outlier: 6.442A pdb=" N TRP X 5 " --> pdb=" O GLY X 29 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU X 31 " --> pdb=" O TRP X 5 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR X 7 " --> pdb=" O LEU X 31 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE X 6 " --> pdb=" O ILE X 63 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLU X 65 " --> pdb=" O PHE X 6 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN X 8 " --> pdb=" O GLU X 65 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N GLY X 67 " --> pdb=" O ASN X 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 135 through 138 removed outlier: 6.422A pdb=" N ILE i 115 " --> pdb=" O ILE i 156 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR i 114 " --> pdb=" O LEU i 22 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N CYS i 236 " --> pdb=" O ASP i 257 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE i 259 " --> pdb=" O CYS i 236 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE i 238 " --> pdb=" O ILE i 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 135 through 138 removed outlier: 6.422A pdb=" N ILE j 115 " --> pdb=" O ILE j 156 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR j 114 " --> pdb=" O LEU j 22 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N CYS j 236 " --> pdb=" O ASP j 257 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE j 259 " --> pdb=" O CYS j 236 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE j 238 " --> pdb=" O ILE j 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'k' and resid 135 through 138 removed outlier: 6.422A pdb=" N ILE k 115 " --> pdb=" O ILE k 156 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR k 114 " --> pdb=" O LEU k 22 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N CYS k 236 " --> pdb=" O ASP k 257 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE k 259 " --> pdb=" O CYS k 236 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE k 238 " --> pdb=" O ILE k 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 135 through 138 removed outlier: 6.421A pdb=" N ILE l 115 " --> pdb=" O ILE l 156 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR l 114 " --> pdb=" O LEU l 22 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N CYS l 236 " --> pdb=" O ASP l 257 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE l 259 " --> pdb=" O CYS l 236 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE l 238 " --> pdb=" O ILE l 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 135 through 138 removed outlier: 6.422A pdb=" N ILE m 115 " --> pdb=" O ILE m 156 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR m 114 " --> pdb=" O LEU m 22 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N CYS m 236 " --> pdb=" O ASP m 257 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE m 259 " --> pdb=" O CYS m 236 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE m 238 " --> pdb=" O ILE m 259 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 135 through 138 removed outlier: 6.422A pdb=" N ILE n 115 " --> pdb=" O ILE n 156 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR n 114 " --> pdb=" O LEU n 22 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N CYS n 236 " --> pdb=" O ASP n 257 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE n 259 " --> pdb=" O CYS n 236 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE n 238 " --> pdb=" O ILE n 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'o' and resid 135 through 138 removed outlier: 6.422A pdb=" N ILE o 115 " --> pdb=" O ILE o 156 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR o 114 " --> pdb=" O LEU o 22 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N CYS o 236 " --> pdb=" O ASP o 257 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE o 259 " --> pdb=" O CYS o 236 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE o 238 " --> pdb=" O ILE o 259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'p' and resid 135 through 138 removed outlier: 6.422A pdb=" N ILE p 115 " --> pdb=" O ILE p 156 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR p 114 " --> pdb=" O LEU p 22 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS p 236 " --> pdb=" O ASP p 257 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE p 259 " --> pdb=" O CYS p 236 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE p 238 " --> pdb=" O ILE p 259 " (cutoff:3.500A) 1183 hydrogen bonds defined for protein. 3381 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: 5.23 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4824 1.29 - 1.42: 7720 1.42 - 1.55: 17152 1.55 - 1.68: 134 1.68 - 1.81: 146 Bond restraints: 29976 Sorted by residual: bond pdb=" C2B NAD k 301 " pdb=" C3B NAD k 301 " ideal model delta sigma weight residual 1.524 1.236 0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C2B NAD j 301 " pdb=" C3B NAD j 301 " ideal model delta sigma weight residual 1.524 1.237 0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C2B NAD i 301 " pdb=" C3B NAD i 301 " ideal model delta sigma weight residual 1.524 1.237 0.287 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C2B NAD m 301 " pdb=" C3B NAD m 301 " ideal model delta sigma weight residual 1.524 1.237 0.287 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C2B NAD l 301 " pdb=" C3B NAD l 301 " ideal model delta sigma weight residual 1.524 1.238 0.286 2.00e-02 2.50e+03 2.05e+02 ... (remaining 29971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 39604 2.85 - 5.70: 871 5.70 - 8.56: 212 8.56 - 11.41: 36 11.41 - 14.26: 13 Bond angle restraints: 40736 Sorted by residual: angle pdb=" N MET k 217 " pdb=" CA MET k 217 " pdb=" C MET k 217 " ideal model delta sigma weight residual 112.90 105.37 7.53 1.31e+00 5.83e-01 3.31e+01 angle pdb=" N MET j 217 " pdb=" CA MET j 217 " pdb=" C MET j 217 " ideal model delta sigma weight residual 112.90 105.55 7.35 1.31e+00 5.83e-01 3.15e+01 angle pdb=" N MET p 217 " pdb=" CA MET p 217 " pdb=" C MET p 217 " ideal model delta sigma weight residual 112.90 105.71 7.19 1.31e+00 5.83e-01 3.01e+01 angle pdb=" N MET o 217 " pdb=" CA MET o 217 " pdb=" C MET o 217 " ideal model delta sigma weight residual 112.90 105.71 7.19 1.31e+00 5.83e-01 3.01e+01 angle pdb=" N MET l 217 " pdb=" CA MET l 217 " pdb=" C MET l 217 " ideal model delta sigma weight residual 112.90 105.76 7.14 1.31e+00 5.83e-01 2.97e+01 ... (remaining 40731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.12: 17855 34.12 - 68.23: 420 68.23 - 102.35: 113 102.35 - 136.47: 0 136.47 - 170.58: 20 Dihedral angle restraints: 18408 sinusoidal: 7848 harmonic: 10560 Sorted by residual: dihedral pdb=" CD ARG i 216 " pdb=" NE ARG i 216 " pdb=" CZ ARG i 216 " pdb=" NH1 ARG i 216 " ideal model delta sinusoidal sigma weight residual 0.00 87.98 -87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CD ARG n 216 " pdb=" NE ARG n 216 " pdb=" CZ ARG n 216 " pdb=" NH1 ARG n 216 " ideal model delta sinusoidal sigma weight residual 0.00 86.67 -86.67 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CD ARG m 216 " pdb=" NE ARG m 216 " pdb=" CZ ARG m 216 " pdb=" NH1 ARG m 216 " ideal model delta sinusoidal sigma weight residual 0.00 86.54 -86.54 1 1.00e+01 1.00e-02 9.02e+01 ... (remaining 18405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3514 0.067 - 0.134: 833 0.134 - 0.200: 132 0.200 - 0.267: 33 0.267 - 0.334: 16 Chirality restraints: 4528 Sorted by residual: chirality pdb=" C3D NAD m 301 " pdb=" C2D NAD m 301 " pdb=" C4D NAD m 301 " pdb=" O3D NAD m 301 " both_signs ideal model delta sigma weight residual False -2.73 -2.39 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C3D NAD k 301 " pdb=" C2D NAD k 301 " pdb=" C4D NAD k 301 " pdb=" O3D NAD k 301 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C3D NAD o 301 " pdb=" C2D NAD o 301 " pdb=" C4D NAD o 301 " pdb=" O3D NAD o 301 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 4525 not shown) Planarity restraints: 5216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG i 216 " 1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG i 216 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG i 216 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG i 216 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG i 216 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG m 216 " -1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG m 216 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG m 216 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG m 216 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG m 216 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG n 216 " 1.099 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG n 216 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG n 216 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG n 216 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG n 216 " 0.016 2.00e-02 2.50e+03 ... (remaining 5213 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 532 2.67 - 3.23: 26311 3.23 - 3.79: 45523 3.79 - 4.34: 65214 4.34 - 4.90: 107150 Nonbonded interactions: 244730 Sorted by model distance: nonbonded pdb=" OE2 GLU O 37 " pdb="ZN ZN O 201 " model vdw 2.118 2.230 nonbonded pdb=" OE2 GLU T 37 " pdb="ZN ZN T 201 " model vdw 2.118 2.230 nonbonded pdb=" OE2 GLU K 37 " pdb="ZN ZN K 201 " model vdw 2.118 2.230 nonbonded pdb=" OE2 GLU X 37 " pdb="ZN ZN X 201 " model vdw 2.118 2.230 nonbonded pdb="ZN ZN X 201 " pdb=" OAO Y43 X 202 " model vdw 2.145 2.230 ... (remaining 244725 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 'I' and resid 2 through 181) selection = (chain 'K' and resid 2 through 181) selection = (chain 'M' and resid 2 through 181) selection = (chain 'O' and resid 2 through 181) selection = (chain 'R' and resid 2 through 181) selection = (chain 'T' and resid 2 through 181) selection = (chain 'V' and resid 2 through 181) selection = (chain 'X' and resid 2 through 181) } ncs_group { reference = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } 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: 5.830 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: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.380 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.019 0.779 29984 Z= 1.398 Angle : 1.106 14.259 40736 Z= 0.581 Chirality : 0.062 0.334 4528 Planarity : 0.027 0.493 5216 Dihedral : 15.471 170.585 11576 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -4.87 (0.11), residues: 3624 helix: -4.18 (0.06), residues: 1704 sheet: -1.29 (0.21), residues: 544 loop : -2.44 (0.14), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG k 216 TYR 0.018 0.003 TYR R 112 PHE 0.053 0.003 PHE T 139 TRP 0.026 0.004 TRP o 214 HIS 0.011 0.002 HIS O 172 Details of bonding type rmsd/Z covalent geometry : bond 0.01521 / 0.75 (29976) covalent geometry : angle 1.10617 / 0.58 (40736) hydrogen bonds : bond 0.30731 / 20.98 ( 1183) hydrogen bonds : angle 8.92970 / 6.21 ( 3381) Misc. bond : bond 0.72231 / 46.64 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 805 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 172 HIS cc_start: 0.5350 (m90) cc_final: 0.4885 (m90) REVERT: X 172 HIS cc_start: 0.5380 (m90) cc_final: 0.4946 (m90) REVERT: i 19 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8114 (mt-10) REVERT: j 2 THR cc_start: 0.8042 (p) cc_final: 0.7822 (t) REVERT: j 19 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8128 (mt-10) REVERT: j 229 LYS cc_start: 0.9207 (tttp) cc_final: 0.8998 (ttmt) REVERT: k 99 GLU cc_start: 0.7806 (mp0) cc_final: 0.7535 (mp0) REVERT: m 95 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7918 (mt-10) REVERT: m 203 TYR cc_start: 0.8672 (t80) cc_final: 0.6097 (t80) REVERT: m 249 ASP cc_start: 0.8340 (m-30) cc_final: 0.8065 (m-30) REVERT: n 2 THR cc_start: 0.8320 (p) cc_final: 0.8109 (t) REVERT: n 15 LYS cc_start: 0.8908 (tttt) cc_final: 0.8703 (tttp) REVERT: n 19 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8225 (mt-10) REVERT: n 229 LYS cc_start: 0.9204 (tttp) cc_final: 0.8985 (ttpt) REVERT: o 95 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7946 (mt-10) REVERT: o 203 TYR cc_start: 0.8639 (t80) cc_final: 0.6324 (t80) REVERT: o 249 ASP cc_start: 0.8313 (m-30) cc_final: 0.8041 (m-30) REVERT: p 2 THR cc_start: 0.8286 (p) cc_final: 0.8077 (t) REVERT: p 229 LYS cc_start: 0.9214 (tttp) cc_final: 0.9002 (ttpt) outliers start: 0 outliers final: 0 residues processed: 805 average time/residue: 0.7264 time to fit residues: 668.2641 Evaluate side-chains 413 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 140 HIS ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** M 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 ASN ** V 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 HIS i 223 GLN ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 223 GLN j 252 GLN ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 223 GLN ** k 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 209 ASN ** m 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 209 ASN ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 209 ASN ** o 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 209 ASN ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.121699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.077968 restraints weight = 45354.765| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.44 r_work: 0.2881 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29984 Z= 0.123 Angle : 0.600 7.847 40736 Z= 0.305 Chirality : 0.043 0.224 4528 Planarity : 0.006 0.061 5216 Dihedral : 13.041 140.954 4760 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.20 % Allowed : 11.20 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.78 (0.12), residues: 3624 helix: -1.99 (0.11), residues: 1760 sheet: -0.83 (0.22), residues: 528 loop : -1.78 (0.15), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 92 TYR 0.015 0.002 TYR o 83 PHE 0.041 0.002 PHE O 139 TRP 0.022 0.002 TRP R 141 HIS 0.014 0.001 HIS O 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (29976) covalent geometry : angle 0.60036 / 0.31 (40736) hydrogen bonds : bond 0.03931 / 2.67 ( 1183) hydrogen bonds : angle 5.14955 / 3.59 ( 3381) Misc. bond : bond 0.00337 / 0.22 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 517 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: I 90 ASP cc_start: 0.8697 (t70) cc_final: 0.8384 (t0) REVERT: I 92 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8470 (ttp80) REVERT: I 146 ILE cc_start: 0.7124 (mp) cc_final: 0.6859 (mm) REVERT: K 72 ASP cc_start: 0.9001 (m-30) cc_final: 0.8627 (m-30) REVERT: M 92 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8438 (ttp80) REVERT: M 146 ILE cc_start: 0.7106 (mp) cc_final: 0.6851 (mm) REVERT: O 65 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7161 (tp30) REVERT: O 72 ASP cc_start: 0.9044 (m-30) cc_final: 0.8703 (m-30) REVERT: O 86 TRP cc_start: 0.7898 (t-100) cc_final: 0.7250 (t-100) REVERT: R 21 VAL cc_start: 0.8362 (m) cc_final: 0.7839 (p) REVERT: R 86 TRP cc_start: 0.8169 (t-100) cc_final: 0.7868 (t-100) REVERT: T 34 LYS cc_start: 0.9060 (tptp) cc_final: 0.8844 (tptp) REVERT: T 72 ASP cc_start: 0.8584 (m-30) cc_final: 0.7919 (m-30) REVERT: T 101 GLN cc_start: 0.8174 (pt0) cc_final: 0.7909 (tp-100) REVERT: V 21 VAL cc_start: 0.8421 (m) cc_final: 0.7962 (p) REVERT: V 86 TRP cc_start: 0.8178 (t-100) cc_final: 0.7802 (t-100) REVERT: X 27 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7985 (mtmt) REVERT: X 72 ASP cc_start: 0.8523 (m-30) cc_final: 0.7815 (m-30) REVERT: X 101 GLN cc_start: 0.8186 (pt0) cc_final: 0.7811 (tp-100) REVERT: i 19 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8726 (mt-10) REVERT: i 48 LYS cc_start: 0.9241 (mtpp) cc_final: 0.8985 (ttmm) REVERT: i 105 ARG cc_start: 0.8793 (mtt90) cc_final: 0.8569 (mmt90) REVERT: j 2 THR cc_start: 0.8086 (p) cc_final: 0.7783 (t) REVERT: j 8 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8858 (mt-10) REVERT: j 19 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8711 (mt-10) REVERT: j 229 LYS cc_start: 0.9361 (tttp) cc_final: 0.8976 (ttmt) REVERT: k 48 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8991 (ttmm) REVERT: l 2 THR cc_start: 0.8075 (p) cc_final: 0.7805 (t) REVERT: l 8 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8768 (mt-10) REVERT: m 84 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8681 (mt-10) REVERT: m 186 ASP cc_start: 0.8965 (m-30) cc_final: 0.8679 (m-30) REVERT: m 249 ASP cc_start: 0.8868 (m-30) cc_final: 0.8556 (m-30) REVERT: n 2 THR cc_start: 0.8344 (p) cc_final: 0.8043 (t) REVERT: n 15 LYS cc_start: 0.8941 (tttt) cc_final: 0.8695 (tttm) REVERT: n 48 LYS cc_start: 0.9220 (mtpm) cc_final: 0.8973 (tppp) REVERT: n 113 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8356 (mtm-85) REVERT: n 229 LYS cc_start: 0.9376 (tttp) cc_final: 0.9019 (ttpt) REVERT: o 186 ASP cc_start: 0.8917 (m-30) cc_final: 0.8668 (m-30) REVERT: o 249 ASP cc_start: 0.8857 (m-30) cc_final: 0.8545 (m-30) REVERT: p 2 THR cc_start: 0.8332 (p) cc_final: 0.8023 (t) REVERT: p 105 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8743 (mmt90) REVERT: p 113 ARG cc_start: 0.8584 (mtm180) cc_final: 0.8370 (mtm-85) REVERT: p 229 LYS cc_start: 0.9390 (tttp) cc_final: 0.9043 (ttpt) outliers start: 66 outliers final: 20 residues processed: 556 average time/residue: 0.6172 time to fit residues: 399.2704 Evaluate side-chains 428 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 406 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 92 ARG Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 97 ILE Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 163 ASP Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 120 TYR Chi-restraints excluded: chain l residue 64 GLU Chi-restraints excluded: chain n residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 133 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 346 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 259 optimal weight: 0.0030 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 20 HIS M 20 HIS R 75 ASN R 172 HIS ** T 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN V 172 HIS X 75 ASN ** X 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 253 GLN l 253 GLN m 253 GLN ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 253 GLN p 253 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.117069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071947 restraints weight = 44510.151| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.47 r_work: 0.2747 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29984 Z= 0.163 Angle : 0.583 7.150 40736 Z= 0.295 Chirality : 0.043 0.235 4528 Planarity : 0.005 0.036 5216 Dihedral : 11.005 140.503 4760 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.83 % Allowed : 13.23 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.13), residues: 3624 helix: -0.81 (0.12), residues: 1776 sheet: -0.55 (0.22), residues: 528 loop : -1.42 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG k 77 TYR 0.018 0.002 TYR X 112 PHE 0.041 0.002 PHE T 139 TRP 0.022 0.002 TRP T 141 HIS 0.007 0.001 HIS M 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (29976) covalent geometry : angle 0.58310 / 0.29 (40736) hydrogen bonds : bond 0.03750 / 2.57 ( 1183) hydrogen bonds : angle 4.60567 / 3.24 ( 3381) Misc. bond : bond 0.00450 / 0.30 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 444 time to evaluate : 1.067 Fit side-chains REVERT: I 90 ASP cc_start: 0.8741 (t70) cc_final: 0.8472 (t0) REVERT: I 146 ILE cc_start: 0.7008 (mp) cc_final: 0.6700 (mm) REVERT: K 72 ASP cc_start: 0.9048 (m-30) cc_final: 0.8762 (m-30) REVERT: M 146 ILE cc_start: 0.7016 (mp) cc_final: 0.6707 (mm) REVERT: O 72 ASP cc_start: 0.9070 (m-30) cc_final: 0.8775 (m-30) REVERT: O 86 TRP cc_start: 0.8086 (t-100) cc_final: 0.7884 (t-100) REVERT: O 144 ILE cc_start: 0.8857 (pt) cc_final: 0.8650 (mm) REVERT: R 86 TRP cc_start: 0.8192 (t-100) cc_final: 0.7896 (t-100) REVERT: T 34 LYS cc_start: 0.9162 (tptp) cc_final: 0.8957 (tptp) REVERT: T 72 ASP cc_start: 0.8688 (m-30) cc_final: 0.8365 (m-30) REVERT: T 86 TRP cc_start: 0.8182 (t-100) cc_final: 0.7879 (t-100) REVERT: T 164 SER cc_start: 0.9228 (m) cc_final: 0.8859 (p) REVERT: V 86 TRP cc_start: 0.8177 (t-100) cc_final: 0.7920 (t-100) REVERT: X 72 ASP cc_start: 0.8585 (m-30) cc_final: 0.8269 (m-30) REVERT: X 86 TRP cc_start: 0.8262 (t-100) cc_final: 0.8022 (t-100) REVERT: X 164 SER cc_start: 0.9300 (m) cc_final: 0.8964 (p) REVERT: i 19 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8704 (mt-10) REVERT: i 186 ASP cc_start: 0.9044 (m-30) cc_final: 0.8801 (m-30) REVERT: j 2 THR cc_start: 0.8111 (p) cc_final: 0.7794 (t) REVERT: j 8 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8837 (mt-10) REVERT: j 15 LYS cc_start: 0.8975 (ttpp) cc_final: 0.8708 (tttp) REVERT: j 64 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8526 (pm20) REVERT: j 105 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8309 (mtt90) REVERT: j 161 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8681 (p) REVERT: k 2 THR cc_start: 0.8111 (p) cc_final: 0.7800 (t) REVERT: k 99 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: k 105 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8107 (mtt90) REVERT: l 2 THR cc_start: 0.8099 (p) cc_final: 0.7814 (t) REVERT: l 8 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8777 (mt-10) REVERT: l 64 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: l 161 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8744 (p) REVERT: m 105 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8398 (mtt90) REVERT: m 161 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8727 (p) REVERT: n 2 THR cc_start: 0.8388 (p) cc_final: 0.8055 (t) REVERT: n 15 LYS cc_start: 0.8868 (tttt) cc_final: 0.8652 (tttm) REVERT: n 113 ARG cc_start: 0.8644 (mtm180) cc_final: 0.8402 (mtm-85) REVERT: n 229 LYS cc_start: 0.9394 (tttp) cc_final: 0.9046 (ttpt) REVERT: o 161 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8767 (p) REVERT: p 2 THR cc_start: 0.8349 (p) cc_final: 0.8002 (t) REVERT: p 64 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: p 95 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8105 (mm-30) REVERT: p 113 ARG cc_start: 0.8600 (mtm180) cc_final: 0.8347 (mtm-85) REVERT: p 122 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7966 (pptt) REVERT: p 229 LYS cc_start: 0.9386 (tttp) cc_final: 0.9038 (ttpt) outliers start: 85 outliers final: 22 residues processed: 498 average time/residue: 0.6337 time to fit residues: 366.8647 Evaluate side-chains 423 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 389 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain X residue 157 MET Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 99 GLU Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain k residue 120 TYR Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 64 GLU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 161 THR Chi-restraints excluded: chain m residue 105 ARG Chi-restraints excluded: chain m residue 161 THR Chi-restraints excluded: chain m residue 163 ASP Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 120 TYR Chi-restraints excluded: chain n residue 161 THR Chi-restraints excluded: chain o residue 151 ASP Chi-restraints excluded: chain o residue 161 THR Chi-restraints excluded: chain p residue 64 GLU Chi-restraints excluded: chain p residue 122 LYS Chi-restraints excluded: chain p residue 161 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 97 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 310 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 20 HIS M 20 HIS R 75 ASN R 101 GLN T 8 ASN V 101 GLN ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 223 GLN l 223 GLN ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.069295 restraints weight = 43816.186| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.42 r_work: 0.2700 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 29984 Z= 0.204 Angle : 0.597 6.891 40736 Z= 0.302 Chirality : 0.045 0.227 4528 Planarity : 0.005 0.038 5216 Dihedral : 10.747 142.353 4760 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.80 % Allowed : 15.33 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.97 (0.13), residues: 3624 helix: -0.19 (0.12), residues: 1768 sheet: -0.36 (0.21), residues: 528 loop : -1.20 (0.15), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 105 TYR 0.019 0.002 TYR V 112 PHE 0.028 0.002 PHE l 198 TRP 0.030 0.002 TRP K 86 HIS 0.008 0.001 HIS I 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.20 (29976) covalent geometry : angle 0.59696 / 0.30 (40736) hydrogen bonds : bond 0.03901 / 2.67 ( 1183) hydrogen bonds : angle 4.50050 / 3.17 ( 3381) Misc. bond : bond 0.00361 / 0.24 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 400 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 65 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7618 (tm-30) REVERT: I 83 LYS cc_start: 0.8551 (tppp) cc_final: 0.8291 (tptp) REVERT: K 65 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7321 (tp30) REVERT: M 92 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8596 (ttp80) REVERT: O 65 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7343 (tp30) REVERT: R 87 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8718 (mm-30) REVERT: T 72 ASP cc_start: 0.8636 (m-30) cc_final: 0.8320 (m-30) REVERT: T 86 TRP cc_start: 0.8286 (t-100) cc_final: 0.8040 (t-100) REVERT: T 164 SER cc_start: 0.9254 (m) cc_final: 0.8930 (p) REVERT: V 71 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8168 (mp) REVERT: X 72 ASP cc_start: 0.8596 (m-30) cc_final: 0.8270 (m-30) REVERT: X 86 TRP cc_start: 0.8344 (t-100) cc_final: 0.8097 (t-100) REVERT: X 164 SER cc_start: 0.9292 (m) cc_final: 0.8987 (p) REVERT: i 2 THR cc_start: 0.8122 (p) cc_final: 0.7755 (t) REVERT: i 19 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8708 (mt-10) REVERT: i 99 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: i 105 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8155 (mtt90) REVERT: j 2 THR cc_start: 0.8134 (p) cc_final: 0.7829 (t) REVERT: j 64 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8557 (pm20) REVERT: j 105 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8039 (mtt90) REVERT: k 2 THR cc_start: 0.8126 (p) cc_final: 0.7783 (t) REVERT: k 99 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: k 105 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8194 (mtt90) REVERT: l 2 THR cc_start: 0.8116 (p) cc_final: 0.7809 (t) REVERT: l 64 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: l 105 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8116 (mtt90) REVERT: m 105 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8418 (mtt90) REVERT: n 2 THR cc_start: 0.8428 (p) cc_final: 0.8080 (t) REVERT: n 15 LYS cc_start: 0.8874 (tttt) cc_final: 0.8652 (tttp) REVERT: n 105 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8512 (mtt90) REVERT: n 229 LYS cc_start: 0.9385 (tttp) cc_final: 0.9016 (ttpt) REVERT: o 62 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8418 (mtm-85) REVERT: o 99 GLU cc_start: 0.8354 (mp0) cc_final: 0.7663 (mp0) REVERT: o 186 ASP cc_start: 0.8892 (m-30) cc_final: 0.8678 (m-30) REVERT: p 2 THR cc_start: 0.8401 (p) cc_final: 0.8034 (t) REVERT: p 64 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8565 (pm20) REVERT: p 229 LYS cc_start: 0.9390 (tttp) cc_final: 0.9021 (ttpt) outliers start: 84 outliers final: 25 residues processed: 455 average time/residue: 0.6474 time to fit residues: 342.7828 Evaluate side-chains 418 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 379 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 92 ARG Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain i residue 99 GLU Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 182 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain k residue 99 GLU Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain k residue 120 TYR Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 64 GLU Chi-restraints excluded: chain l residue 105 ARG Chi-restraints excluded: chain l residue 161 THR Chi-restraints excluded: chain m residue 105 ARG Chi-restraints excluded: chain m residue 161 THR Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 105 ARG Chi-restraints excluded: chain n residue 120 TYR Chi-restraints excluded: chain n residue 161 THR Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 151 ASP Chi-restraints excluded: chain o residue 161 THR Chi-restraints excluded: chain p residue 64 GLU Chi-restraints excluded: chain p residue 120 TYR Chi-restraints excluded: chain p residue 161 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 131 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 205 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 241 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 318 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 20 HIS K 172 HIS M 20 HIS M 172 HIS O 172 HIS R 75 ASN T 172 HIS X 101 GLN ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.116862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.071917 restraints weight = 44107.369| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.44 r_work: 0.2742 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29984 Z= 0.110 Angle : 0.524 6.908 40736 Z= 0.267 Chirality : 0.042 0.230 4528 Planarity : 0.004 0.035 5216 Dihedral : 10.049 145.253 4760 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.37 % Allowed : 16.23 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.14), residues: 3624 helix: 0.25 (0.13), residues: 1760 sheet: -0.21 (0.22), residues: 528 loop : -1.02 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG p 105 TYR 0.015 0.001 TYR o 83 PHE 0.021 0.001 PHE M 139 TRP 0.029 0.002 TRP O 86 HIS 0.008 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (29976) covalent geometry : angle 0.52427 / 0.27 (40736) hydrogen bonds : bond 0.02882 / 1.96 ( 1183) hydrogen bonds : angle 4.26619 / 3.00 ( 3381) Misc. bond : bond 0.00289 / 0.20 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 459 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 19 GLN cc_start: 0.8919 (mt0) cc_final: 0.8597 (mt0) REVERT: R 71 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8192 (mp) REVERT: R 72 ASP cc_start: 0.9202 (m-30) cc_final: 0.8980 (m-30) REVERT: R 83 LYS cc_start: 0.8488 (tppp) cc_final: 0.7876 (tppp) REVERT: T 72 ASP cc_start: 0.8536 (m-30) cc_final: 0.8191 (m-30) REVERT: T 86 TRP cc_start: 0.8200 (t-100) cc_final: 0.7974 (t-100) REVERT: T 164 SER cc_start: 0.9257 (m) cc_final: 0.8930 (p) REVERT: X 72 ASP cc_start: 0.8535 (m-30) cc_final: 0.8185 (m-30) REVERT: X 164 SER cc_start: 0.9285 (m) cc_final: 0.8973 (p) REVERT: i 2 THR cc_start: 0.8140 (p) cc_final: 0.7783 (t) REVERT: i 19 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8624 (mt-10) REVERT: i 105 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8130 (mtt90) REVERT: i 186 ASP cc_start: 0.8986 (m-30) cc_final: 0.8766 (m-30) REVERT: j 2 THR cc_start: 0.8166 (p) cc_final: 0.7893 (t) REVERT: j 64 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8503 (pm20) REVERT: j 161 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8619 (p) REVERT: k 2 THR cc_start: 0.8118 (p) cc_final: 0.7790 (t) REVERT: k 105 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8115 (mtt90) REVERT: l 2 THR cc_start: 0.8112 (p) cc_final: 0.7844 (t) REVERT: l 64 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8535 (pm20) REVERT: l 105 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8071 (mtt90) REVERT: l 161 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8645 (p) REVERT: m 161 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8668 (p) REVERT: n 2 THR cc_start: 0.8417 (p) cc_final: 0.8069 (t) REVERT: n 15 LYS cc_start: 0.8867 (tttt) cc_final: 0.8644 (tttp) REVERT: n 64 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: n 229 LYS cc_start: 0.9356 (tttp) cc_final: 0.9033 (ttpt) REVERT: o 161 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8638 (p) REVERT: p 2 THR cc_start: 0.8424 (p) cc_final: 0.8061 (t) REVERT: p 64 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: p 68 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8702 (tp30) REVERT: p 229 LYS cc_start: 0.9365 (tttp) cc_final: 0.9042 (ttpt) outliers start: 71 outliers final: 19 residues processed: 503 average time/residue: 0.6167 time to fit residues: 364.0663 Evaluate side-chains 465 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 433 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 182 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain k residue 120 TYR Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain l residue 64 GLU Chi-restraints excluded: chain l residue 105 ARG Chi-restraints excluded: chain l residue 120 TYR Chi-restraints excluded: chain l residue 161 THR Chi-restraints excluded: chain m residue 120 TYR Chi-restraints excluded: chain m residue 161 THR Chi-restraints excluded: chain m residue 163 ASP Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 120 TYR Chi-restraints excluded: chain o residue 120 TYR Chi-restraints excluded: chain o residue 161 THR Chi-restraints excluded: chain o residue 163 ASP Chi-restraints excluded: chain o residue 182 ASP Chi-restraints excluded: chain p residue 64 GLU Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 120 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 175 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 174 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 121 optimal weight: 40.0000 chunk 214 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 20 HIS M 20 HIS R 75 ASN ** V 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 223 GLN ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 223 GLN ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.069366 restraints weight = 44110.696| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.41 r_work: 0.2701 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 29984 Z= 0.188 Angle : 0.573 6.975 40736 Z= 0.292 Chirality : 0.044 0.230 4528 Planarity : 0.004 0.036 5216 Dihedral : 10.129 147.637 4760 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.23 % Allowed : 17.73 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.39 (0.14), residues: 3624 helix: 0.36 (0.13), residues: 1768 sheet: -0.11 (0.22), residues: 528 loop : -1.04 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 92 TYR 0.020 0.002 TYR R 112 PHE 0.037 0.002 PHE T 139 TRP 0.021 0.002 TRP T 141 HIS 0.008 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (29976) covalent geometry : angle 0.57300 / 0.29 (40736) hydrogen bonds : bond 0.03674 / 2.51 ( 1183) hydrogen bonds : angle 4.31196 / 3.03 ( 3381) Misc. bond : bond 0.00382 / 0.25 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 390 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 65 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7249 (tp30) REVERT: K 86 TRP cc_start: 0.8135 (t-100) cc_final: 0.7928 (t-100) REVERT: M 144 ILE cc_start: 0.8703 (pt) cc_final: 0.8500 (mm) REVERT: O 65 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7237 (tp30) REVERT: O 86 TRP cc_start: 0.8118 (t-100) cc_final: 0.7907 (t-100) REVERT: R 71 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8150 (mp) REVERT: R 72 ASP cc_start: 0.9166 (m-30) cc_final: 0.8928 (m-30) REVERT: T 72 ASP cc_start: 0.8560 (m-30) cc_final: 0.8195 (m-30) REVERT: T 86 TRP cc_start: 0.8266 (t-100) cc_final: 0.7961 (t-100) REVERT: T 164 SER cc_start: 0.9278 (m) cc_final: 0.8958 (p) REVERT: V 87 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8810 (mm-30) REVERT: X 65 GLU cc_start: 0.7270 (tp30) cc_final: 0.6953 (tp30) REVERT: X 72 ASP cc_start: 0.8518 (m-30) cc_final: 0.8158 (m-30) REVERT: X 164 SER cc_start: 0.9304 (m) cc_final: 0.9003 (p) REVERT: i 2 THR cc_start: 0.8149 (p) cc_final: 0.7789 (t) REVERT: i 19 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8671 (mt-10) REVERT: i 41 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8306 (mp10) REVERT: i 105 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8189 (mtt90) REVERT: i 186 ASP cc_start: 0.9023 (m-30) cc_final: 0.8804 (m-30) REVERT: j 2 THR cc_start: 0.8157 (p) cc_final: 0.7870 (t) REVERT: j 64 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8579 (pm20) REVERT: j 105 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8101 (mtt90) REVERT: k 2 THR cc_start: 0.8118 (p) cc_final: 0.7790 (t) REVERT: k 41 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8306 (mp10) REVERT: k 105 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8210 (mtt90) REVERT: l 2 THR cc_start: 0.8120 (p) cc_final: 0.7761 (t) REVERT: l 64 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: l 68 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: l 105 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8136 (mtt90) REVERT: m 105 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8435 (mtt90) REVERT: n 2 THR cc_start: 0.8437 (p) cc_final: 0.8086 (t) REVERT: n 15 LYS cc_start: 0.8920 (tttt) cc_final: 0.8704 (tttp) REVERT: n 68 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8791 (tp30) REVERT: n 105 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8522 (mtt90) REVERT: n 122 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8366 (pptt) REVERT: n 229 LYS cc_start: 0.9368 (tttp) cc_final: 0.9028 (ttpt) REVERT: o 62 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8439 (mtm-85) REVERT: p 2 THR cc_start: 0.8428 (p) cc_final: 0.8074 (t) REVERT: p 64 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8603 (pm20) REVERT: p 68 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8777 (tp30) REVERT: p 229 LYS cc_start: 0.9374 (tttp) cc_final: 0.9031 (ttpt) outliers start: 67 outliers final: 30 residues processed: 427 average time/residue: 0.6031 time to fit residues: 300.9770 Evaluate side-chains 417 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 370 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 MET Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 162 LYS Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 164 SER Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 41 GLN Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 182 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 41 GLN Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain k residue 120 TYR Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 64 GLU Chi-restraints excluded: chain l residue 68 GLU Chi-restraints excluded: chain l residue 105 ARG Chi-restraints excluded: chain l residue 120 TYR Chi-restraints excluded: chain l residue 161 THR Chi-restraints excluded: chain m residue 105 ARG Chi-restraints excluded: chain m residue 120 TYR Chi-restraints excluded: chain m residue 151 ASP Chi-restraints excluded: chain m residue 161 THR Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 68 GLU Chi-restraints excluded: chain n residue 105 ARG Chi-restraints excluded: chain n residue 120 TYR Chi-restraints excluded: chain n residue 122 LYS Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 120 TYR Chi-restraints excluded: chain o residue 151 ASP Chi-restraints excluded: chain o residue 161 THR Chi-restraints excluded: chain p residue 64 GLU Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 120 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 195 optimal weight: 0.8980 chunk 312 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 121 optimal weight: 40.0000 chunk 245 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.115405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.070495 restraints weight = 44156.396| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.43 r_work: 0.2723 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29984 Z= 0.141 Angle : 0.541 7.098 40736 Z= 0.277 Chirality : 0.043 0.233 4528 Planarity : 0.004 0.035 5216 Dihedral : 9.987 149.320 4760 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.33 % Allowed : 17.90 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.15 (0.14), residues: 3624 helix: 0.58 (0.13), residues: 1760 sheet: -0.08 (0.22), residues: 528 loop : -0.92 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG p 105 TYR 0.014 0.002 TYR o 83 PHE 0.027 0.001 PHE T 139 TRP 0.022 0.002 TRP T 141 HIS 0.008 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (29976) covalent geometry : angle 0.54060 / 0.28 (40736) hydrogen bonds : bond 0.03185 / 2.17 ( 1183) hydrogen bonds : angle 4.20536 / 2.96 ( 3381) Misc. bond : bond 0.00337 / 0.22 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 418 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 65 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7257 (tp30) REVERT: K 86 TRP cc_start: 0.8104 (t-100) cc_final: 0.7900 (t-100) REVERT: M 92 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8494 (ttp80) REVERT: O 65 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7280 (tp30) REVERT: R 71 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8130 (mp) REVERT: R 72 ASP cc_start: 0.9134 (m-30) cc_final: 0.8861 (m-30) REVERT: T 72 ASP cc_start: 0.8517 (m-30) cc_final: 0.8147 (m-30) REVERT: T 164 SER cc_start: 0.9296 (m) cc_final: 0.9001 (p) REVERT: V 87 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8822 (mm-30) REVERT: X 65 GLU cc_start: 0.7237 (tp30) cc_final: 0.6979 (tp30) REVERT: X 72 ASP cc_start: 0.8443 (m-30) cc_final: 0.8067 (m-30) REVERT: X 164 SER cc_start: 0.9323 (m) cc_final: 0.9032 (p) REVERT: i 2 THR cc_start: 0.8134 (p) cc_final: 0.7789 (t) REVERT: i 19 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8640 (mt-10) REVERT: i 41 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8288 (mp10) REVERT: i 105 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8152 (mtt90) REVERT: i 186 ASP cc_start: 0.9027 (m-30) cc_final: 0.8805 (m-30) REVERT: j 2 THR cc_start: 0.8163 (p) cc_final: 0.7894 (t) REVERT: j 64 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: j 105 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8069 (mtt90) REVERT: k 2 THR cc_start: 0.8127 (p) cc_final: 0.7809 (t) REVERT: k 41 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8280 (mp10) REVERT: k 93 GLU cc_start: 0.8895 (pt0) cc_final: 0.8659 (pm20) REVERT: k 105 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8166 (mtt90) REVERT: l 2 THR cc_start: 0.8112 (p) cc_final: 0.7771 (t) REVERT: l 64 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8557 (pm20) REVERT: l 68 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: l 105 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8129 (mtt90) REVERT: m 62 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8448 (mtm-85) REVERT: m 105 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8422 (mtt90) REVERT: n 2 THR cc_start: 0.8461 (p) cc_final: 0.8107 (t) REVERT: n 15 LYS cc_start: 0.8902 (tttt) cc_final: 0.8684 (tttp) REVERT: n 64 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8522 (pm20) REVERT: n 68 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8741 (tp30) REVERT: n 105 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8503 (mtt90) REVERT: n 229 LYS cc_start: 0.9340 (tttp) cc_final: 0.9007 (ttpt) REVERT: p 2 THR cc_start: 0.8442 (p) cc_final: 0.8085 (t) REVERT: p 64 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: p 68 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8775 (tp30) REVERT: p 229 LYS cc_start: 0.9334 (tttp) cc_final: 0.9001 (ttpt) outliers start: 70 outliers final: 33 residues processed: 458 average time/residue: 0.6250 time to fit residues: 336.5273 Evaluate side-chains 459 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 408 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 157 MET Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 92 ARG Chi-restraints excluded: chain M residue 162 LYS Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 41 GLN Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 182 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 41 GLN Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain k residue 120 TYR Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 64 GLU Chi-restraints excluded: chain l residue 68 GLU Chi-restraints excluded: chain l residue 105 ARG Chi-restraints excluded: chain l residue 120 TYR Chi-restraints excluded: chain l residue 161 THR Chi-restraints excluded: chain m residue 62 ARG Chi-restraints excluded: chain m residue 105 ARG Chi-restraints excluded: chain m residue 120 TYR Chi-restraints excluded: chain m residue 151 ASP Chi-restraints excluded: chain m residue 161 THR Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 68 GLU Chi-restraints excluded: chain n residue 105 ARG Chi-restraints excluded: chain n residue 120 TYR Chi-restraints excluded: chain o residue 120 TYR Chi-restraints excluded: chain o residue 151 ASP Chi-restraints excluded: chain o residue 161 THR Chi-restraints excluded: chain p residue 64 GLU Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 120 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 151 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 349 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 309 optimal weight: 0.0070 chunk 1 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.071317 restraints weight = 44462.464| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.42 r_work: 0.2726 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29984 Z= 0.124 Angle : 0.536 7.119 40736 Z= 0.274 Chirality : 0.042 0.233 4528 Planarity : 0.004 0.039 5216 Dihedral : 9.882 151.024 4760 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.03 % Allowed : 18.43 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3624 helix: 0.71 (0.13), residues: 1760 sheet: -0.01 (0.22), residues: 528 loop : -0.89 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG p 105 TYR 0.021 0.002 TYR R 112 PHE 0.022 0.001 PHE X 139 TRP 0.026 0.002 TRP O 141 HIS 0.008 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (29976) covalent geometry : angle 0.53566 / 0.27 (40736) hydrogen bonds : bond 0.03039 / 2.07 ( 1183) hydrogen bonds : angle 4.12918 / 2.91 ( 3381) Misc. bond : bond 0.00303 / 0.20 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 429 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 65 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7286 (tp30) REVERT: M 92 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8498 (ttp80) REVERT: M 144 ILE cc_start: 0.8926 (mm) cc_final: 0.8341 (pt) REVERT: O 65 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7273 (tp30) REVERT: R 11 ASN cc_start: 0.7467 (t0) cc_final: 0.7073 (t0) REVERT: R 71 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8160 (mp) REVERT: R 72 ASP cc_start: 0.9125 (m-30) cc_final: 0.8841 (m-30) REVERT: T 72 ASP cc_start: 0.8491 (m-30) cc_final: 0.8129 (m-30) REVERT: T 86 TRP cc_start: 0.8161 (t-100) cc_final: 0.7793 (t-100) REVERT: T 164 SER cc_start: 0.9355 (m) cc_final: 0.9044 (p) REVERT: X 72 ASP cc_start: 0.8380 (m-30) cc_final: 0.8026 (m-30) REVERT: X 157 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8374 (ptm) REVERT: X 164 SER cc_start: 0.9348 (m) cc_final: 0.9078 (p) REVERT: i 2 THR cc_start: 0.8160 (p) cc_final: 0.7819 (t) REVERT: i 19 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8623 (mt-10) REVERT: i 105 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8161 (mtt90) REVERT: i 186 ASP cc_start: 0.9037 (m-30) cc_final: 0.8822 (m-30) REVERT: j 2 THR cc_start: 0.8173 (p) cc_final: 0.7918 (t) REVERT: j 64 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: j 68 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8292 (tp30) REVERT: j 105 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8052 (mtt90) REVERT: k 2 THR cc_start: 0.8128 (p) cc_final: 0.7808 (t) REVERT: k 93 GLU cc_start: 0.8859 (pt0) cc_final: 0.8623 (pm20) REVERT: k 105 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8159 (mtt90) REVERT: l 2 THR cc_start: 0.8119 (p) cc_final: 0.7795 (t) REVERT: l 64 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: l 68 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8359 (tp30) REVERT: l 105 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8124 (mtt90) REVERT: l 161 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8669 (p) REVERT: m 62 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8455 (mtm-85) REVERT: m 105 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8426 (mtt90) REVERT: m 161 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8668 (p) REVERT: n 2 THR cc_start: 0.8462 (p) cc_final: 0.8109 (t) REVERT: n 15 LYS cc_start: 0.8913 (tttt) cc_final: 0.8693 (tttp) REVERT: n 105 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8553 (mtt90) REVERT: n 122 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8301 (pptt) REVERT: n 229 LYS cc_start: 0.9318 (tttp) cc_final: 0.8997 (ttpt) REVERT: p 2 THR cc_start: 0.8455 (p) cc_final: 0.8103 (t) REVERT: p 64 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: p 68 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8750 (tp30) REVERT: p 229 LYS cc_start: 0.9314 (tttp) cc_final: 0.8992 (ttpt) outliers start: 61 outliers final: 33 residues processed: 461 average time/residue: 0.6240 time to fit residues: 338.8526 Evaluate side-chains 446 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 394 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain K residue 157 MET Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 92 ARG Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 164 SER Chi-restraints excluded: chain X residue 157 MET Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 182 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain k residue 120 TYR Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 64 GLU Chi-restraints excluded: chain l residue 68 GLU Chi-restraints excluded: chain l residue 105 ARG Chi-restraints excluded: chain l residue 120 TYR Chi-restraints excluded: chain l residue 161 THR Chi-restraints excluded: chain m residue 62 ARG Chi-restraints excluded: chain m residue 105 ARG Chi-restraints excluded: chain m residue 120 TYR Chi-restraints excluded: chain m residue 151 ASP Chi-restraints excluded: chain m residue 161 THR Chi-restraints excluded: chain n residue 105 ARG Chi-restraints excluded: chain n residue 120 TYR Chi-restraints excluded: chain n residue 122 LYS Chi-restraints excluded: chain o residue 120 TYR Chi-restraints excluded: chain o residue 151 ASP Chi-restraints excluded: chain o residue 161 THR Chi-restraints excluded: chain p residue 64 GLU Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 120 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 110 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 223 GLN ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.068387 restraints weight = 44384.252| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.41 r_work: 0.2657 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29984 Z= 0.216 Angle : 0.594 7.097 40736 Z= 0.304 Chirality : 0.045 0.234 4528 Planarity : 0.005 0.043 5216 Dihedral : 10.148 152.425 4760 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.10 % Allowed : 18.73 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.14 (0.14), residues: 3624 helix: 0.64 (0.13), residues: 1760 sheet: -0.27 (0.21), residues: 560 loop : -0.90 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG p 105 TYR 0.015 0.002 TYR l 120 PHE 0.027 0.002 PHE j 198 TRP 0.043 0.002 TRP R 86 HIS 0.007 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (29976) covalent geometry : angle 0.59441 / 0.30 (40736) hydrogen bonds : bond 0.03858 / 2.64 ( 1183) hydrogen bonds : angle 4.26939 / 3.01 ( 3381) Misc. bond : bond 0.00365 / 0.23 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 373 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 65 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7348 (tp30) REVERT: K 86 TRP cc_start: 0.8008 (t-100) cc_final: 0.7733 (t-100) REVERT: M 144 ILE cc_start: 0.8956 (mm) cc_final: 0.8392 (pt) REVERT: O 65 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7346 (tp30) REVERT: R 11 ASN cc_start: 0.7342 (t0) cc_final: 0.7065 (t0) REVERT: R 71 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8148 (mp) REVERT: R 72 ASP cc_start: 0.9137 (m-30) cc_final: 0.8824 (m-30) REVERT: R 86 TRP cc_start: 0.7636 (t-100) cc_final: 0.7308 (t-100) REVERT: T 72 ASP cc_start: 0.8457 (m-30) cc_final: 0.8124 (m-30) REVERT: T 164 SER cc_start: 0.9344 (m) cc_final: 0.9052 (p) REVERT: X 65 GLU cc_start: 0.7345 (tp30) cc_final: 0.6998 (tp30) REVERT: X 72 ASP cc_start: 0.8419 (m-30) cc_final: 0.8097 (m-30) REVERT: X 86 TRP cc_start: 0.8064 (t-100) cc_final: 0.7632 (t-100) REVERT: X 157 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8404 (ptm) REVERT: X 164 SER cc_start: 0.9347 (m) cc_final: 0.9075 (p) REVERT: i 2 THR cc_start: 0.8086 (p) cc_final: 0.7730 (t) REVERT: i 19 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8672 (mt-10) REVERT: i 105 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8173 (mtt90) REVERT: i 186 ASP cc_start: 0.9008 (m-30) cc_final: 0.8783 (m-30) REVERT: j 2 THR cc_start: 0.8116 (p) cc_final: 0.7841 (t) REVERT: j 64 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: j 68 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: j 105 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8112 (mtt90) REVERT: k 2 THR cc_start: 0.8065 (p) cc_final: 0.7732 (t) REVERT: k 99 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: k 105 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8209 (mtt90) REVERT: l 2 THR cc_start: 0.8107 (p) cc_final: 0.7744 (t) REVERT: l 64 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8550 (pm20) REVERT: l 68 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: l 105 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8157 (mtt90) REVERT: m 62 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8428 (mtm-85) REVERT: m 105 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8408 (mtt90) REVERT: n 2 THR cc_start: 0.8455 (p) cc_final: 0.8104 (t) REVERT: n 15 LYS cc_start: 0.8896 (tttt) cc_final: 0.8684 (tttp) REVERT: n 105 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8490 (mtt90) REVERT: n 229 LYS cc_start: 0.9333 (tttp) cc_final: 0.8995 (ttpt) REVERT: o 62 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8398 (mtm-85) REVERT: p 2 THR cc_start: 0.8412 (p) cc_final: 0.8063 (t) REVERT: p 64 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: p 68 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8765 (tp30) REVERT: p 229 LYS cc_start: 0.9329 (tttp) cc_final: 0.8991 (ttpt) outliers start: 63 outliers final: 34 residues processed: 411 average time/residue: 0.6730 time to fit residues: 323.8646 Evaluate side-chains 414 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 157 MET Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 162 LYS Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 164 SER Chi-restraints excluded: chain X residue 157 MET Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 182 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 99 GLU Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain k residue 120 TYR Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 64 GLU Chi-restraints excluded: chain l residue 68 GLU Chi-restraints excluded: chain l residue 105 ARG Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 120 TYR Chi-restraints excluded: chain l residue 161 THR Chi-restraints excluded: chain m residue 62 ARG Chi-restraints excluded: chain m residue 105 ARG Chi-restraints excluded: chain m residue 120 TYR Chi-restraints excluded: chain m residue 151 ASP Chi-restraints excluded: chain m residue 161 THR Chi-restraints excluded: chain n residue 105 ARG Chi-restraints excluded: chain n residue 120 TYR Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 120 TYR Chi-restraints excluded: chain o residue 151 ASP Chi-restraints excluded: chain o residue 161 THR Chi-restraints excluded: chain p residue 64 GLU Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 120 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 59 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 249 optimal weight: 0.0980 chunk 107 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 201 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 75 ASN ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.073437 restraints weight = 44169.723| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.42 r_work: 0.2766 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29984 Z= 0.095 Angle : 0.521 7.129 40736 Z= 0.268 Chirality : 0.041 0.231 4528 Planarity : 0.004 0.044 5216 Dihedral : 9.748 151.550 4760 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.33 % Allowed : 19.47 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.09 (0.14), residues: 3624 helix: 0.82 (0.13), residues: 1768 sheet: 0.01 (0.22), residues: 528 loop : -0.85 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG p 216 TYR 0.020 0.001 TYR R 112 PHE 0.017 0.001 PHE T 139 TRP 0.044 0.002 TRP R 86 HIS 0.009 0.001 HIS V 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.09 (29976) covalent geometry : angle 0.52102 / 0.27 (40736) hydrogen bonds : bond 0.02552 / 1.73 ( 1183) hydrogen bonds : angle 4.05023 / 2.85 ( 3381) Misc. bond : bond 0.00265 / 0.17 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 428 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 65 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7197 (tp30) REVERT: K 86 TRP cc_start: 0.7942 (t-100) cc_final: 0.7662 (t-100) REVERT: M 144 ILE cc_start: 0.8869 (mm) cc_final: 0.8271 (pt) REVERT: O 65 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7200 (tp30) REVERT: R 17 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8787 (mt-10) REVERT: R 71 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8142 (mp) REVERT: R 72 ASP cc_start: 0.9103 (m-30) cc_final: 0.8796 (m-30) REVERT: R 86 TRP cc_start: 0.7378 (t-100) cc_final: 0.7043 (t-100) REVERT: T 72 ASP cc_start: 0.8372 (m-30) cc_final: 0.8018 (m-30) REVERT: T 86 TRP cc_start: 0.8086 (t-100) cc_final: 0.7630 (t-100) REVERT: T 164 SER cc_start: 0.9344 (m) cc_final: 0.9045 (p) REVERT: V 11 ASN cc_start: 0.7333 (t0) cc_final: 0.7035 (t0) REVERT: V 86 TRP cc_start: 0.7277 (t-100) cc_final: 0.6962 (t-100) REVERT: X 65 GLU cc_start: 0.7191 (tp30) cc_final: 0.6874 (tp30) REVERT: X 72 ASP cc_start: 0.8314 (m-30) cc_final: 0.7984 (m-30) REVERT: X 86 TRP cc_start: 0.8009 (t-100) cc_final: 0.7586 (t-100) REVERT: X 164 SER cc_start: 0.9376 (m) cc_final: 0.9105 (p) REVERT: i 2 THR cc_start: 0.8162 (p) cc_final: 0.7837 (t) REVERT: i 19 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8562 (mt-10) REVERT: i 105 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8094 (mtt90) REVERT: i 166 ASP cc_start: 0.9143 (m-30) cc_final: 0.8911 (p0) REVERT: i 186 ASP cc_start: 0.9020 (m-30) cc_final: 0.8787 (m-30) REVERT: j 2 THR cc_start: 0.8161 (p) cc_final: 0.7917 (t) REVERT: j 64 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: j 68 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8281 (tp30) REVERT: j 105 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7980 (mtt90) REVERT: j 113 ARG cc_start: 0.8460 (mtm180) cc_final: 0.8172 (mtp180) REVERT: j 161 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8621 (p) REVERT: k 2 THR cc_start: 0.8159 (p) cc_final: 0.7835 (t) REVERT: k 19 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8635 (mt-10) REVERT: k 93 GLU cc_start: 0.8847 (pt0) cc_final: 0.8601 (pm20) REVERT: k 105 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8103 (mtt90) REVERT: l 2 THR cc_start: 0.8114 (p) cc_final: 0.7792 (t) REVERT: l 64 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: l 68 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: l 105 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8101 (mtt90) REVERT: l 113 ARG cc_start: 0.8518 (mtm180) cc_final: 0.8224 (mtp180) REVERT: l 161 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8661 (p) REVERT: m 161 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8606 (p) REVERT: n 2 THR cc_start: 0.8465 (p) cc_final: 0.8108 (t) REVERT: n 15 LYS cc_start: 0.8885 (tttt) cc_final: 0.8665 (tttp) REVERT: n 48 LYS cc_start: 0.9254 (mtpp) cc_final: 0.9010 (tppp) REVERT: n 229 LYS cc_start: 0.9282 (tttp) cc_final: 0.8971 (ttpt) REVERT: o 58 ASP cc_start: 0.8989 (t70) cc_final: 0.8713 (t0) REVERT: o 161 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8571 (p) REVERT: p 2 THR cc_start: 0.8443 (p) cc_final: 0.8091 (t) REVERT: p 48 LYS cc_start: 0.9257 (mtpp) cc_final: 0.9010 (tppp) REVERT: p 64 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: p 68 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8656 (tp30) REVERT: p 229 LYS cc_start: 0.9295 (tttp) cc_final: 0.8983 (ttpt) outliers start: 40 outliers final: 15 residues processed: 454 average time/residue: 0.6102 time to fit residues: 326.2184 Evaluate side-chains 434 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 404 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 64 GLU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain k residue 120 TYR Chi-restraints excluded: chain l residue 64 GLU Chi-restraints excluded: chain l residue 68 GLU Chi-restraints excluded: chain l residue 105 ARG Chi-restraints excluded: chain l residue 120 TYR Chi-restraints excluded: chain l residue 161 THR Chi-restraints excluded: chain m residue 120 TYR Chi-restraints excluded: chain m residue 151 ASP Chi-restraints excluded: chain m residue 161 THR Chi-restraints excluded: chain n residue 120 TYR Chi-restraints excluded: chain o residue 120 TYR Chi-restraints excluded: chain o residue 151 ASP Chi-restraints excluded: chain o residue 161 THR Chi-restraints excluded: chain p residue 64 GLU Chi-restraints excluded: chain p residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 193 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 284 optimal weight: 0.0470 chunk 329 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 223 GLN ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 223 GLN ** n 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.070103 restraints weight = 44520.746| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.36 r_work: 0.2698 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29984 Z= 0.171 Angle : 0.567 7.110 40736 Z= 0.290 Chirality : 0.044 0.225 4528 Planarity : 0.004 0.043 5216 Dihedral : 9.914 154.554 4760 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.30 % Allowed : 19.70 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.07 (0.14), residues: 3624 helix: 0.83 (0.13), residues: 1760 sheet: -0.17 (0.21), residues: 560 loop : -0.82 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG p 77 TYR 0.020 0.002 TYR V 112 PHE 0.040 0.001 PHE K 139 TRP 0.040 0.002 TRP R 86 HIS 0.007 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (29976) covalent geometry : angle 0.56695 / 0.29 (40736) hydrogen bonds : bond 0.03410 / 2.32 ( 1183) hydrogen bonds : angle 4.10759 / 2.90 ( 3381) Misc. bond : bond 0.00339 / 0.22 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11747.96 seconds wall clock time: 200 minutes 3.13 seconds (12003.13 seconds total)