Starting phenix.real_space_refine on Sun Jul 5 18:20:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v57_64788/07_2026/9v57_64788.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v57_64788/07_2026/9v57_64788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v57_64788/07_2026/9v57_64788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v57_64788/07_2026/9v57_64788.map" model { file = "/net/cci-nas-00/data/ceres_data/9v57_64788/07_2026/9v57_64788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v57_64788/07_2026/9v57_64788.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 24 5.49 5 S 96 5.16 5 C 18384 2.51 5 N 5120 2.21 5 O 5400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 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: 29032 Number of models: 1 Model: "" Number of chains: 24 Chain: "C" 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: "F" 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: 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: "L" 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: "a" 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: "d" 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: "g" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "h" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "i" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "j" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} 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: "s" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "t" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "u" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "v" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "C" 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: "F" 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: 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: "L" 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: "a" 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: "d" 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} Time building chain proxies: 5.38, per 1000 atoms: 0.19 Number of scatterers: 29032 At special positions: 0 Unit cell: (151.71, 157.934, 119.034, 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 24 15.00 O 5400 8.00 N 5120 7.00 C 18384 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=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.0 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: 200 helices and 16 sheets defined 51.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.639A pdb=" N ARG C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.755A pdb=" N ILE C 52 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 81 Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.657A pdb=" N GLU C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 167 through 180 removed outlier: 4.858A pdb=" N THR C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 22 removed outlier: 3.639A pdb=" N ARG F 16 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 59 removed outlier: 3.754A pdb=" N ILE F 52 " --> pdb=" O ARG F 48 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 81 Processing helix chain 'F' and resid 82 through 89 removed outlier: 3.658A pdb=" N GLU F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 167 through 180 removed outlier: 4.858A pdb=" N THR F 173 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 22 removed outlier: 3.640A pdb=" N ARG I 16 " --> pdb=" O SER I 12 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU I 17 " --> pdb=" O GLU I 13 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 59 removed outlier: 3.754A pdb=" N ILE I 52 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 3.767A 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: 3.659A 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 167 through 180 removed outlier: 4.859A pdb=" N THR I 173 " --> pdb=" O GLY I 169 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 22 removed outlier: 3.640A pdb=" N ARG L 16 " --> pdb=" O SER L 12 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL L 21 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 59 removed outlier: 3.755A pdb=" N ILE L 52 " --> pdb=" O ARG L 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 81 Processing helix chain 'L' and resid 82 through 89 removed outlier: 3.658A pdb=" N GLU L 87 " --> pdb=" O LYS L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 95 Processing helix chain 'L' and resid 158 through 163 Processing helix chain 'L' and resid 167 through 180 removed outlier: 4.857A pdb=" N THR L 173 " --> pdb=" O GLY L 169 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG L 174 " --> pdb=" O ARG L 170 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 22 removed outlier: 3.639A pdb=" N ARG a 16 " --> pdb=" O SER a 12 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU a 17 " --> pdb=" O GLU a 13 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL a 21 " --> pdb=" O GLU a 17 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 59 removed outlier: 3.754A pdb=" N ILE a 52 " --> pdb=" O ARG a 48 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA a 53 " --> pdb=" O ALA a 49 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA a 57 " --> pdb=" O ALA a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 78 through 81 Processing helix chain 'a' and resid 82 through 89 removed outlier: 3.657A pdb=" N GLU a 87 " --> pdb=" O LYS a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 91 through 95 Processing helix chain 'a' and resid 158 through 163 Processing helix chain 'a' and resid 167 through 180 removed outlier: 4.858A pdb=" N THR a 173 " --> pdb=" O GLY a 169 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG a 174 " --> pdb=" O ARG a 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 22 removed outlier: 3.640A pdb=" N ARG d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU d 17 " --> pdb=" O GLU d 13 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL d 21 " --> pdb=" O GLU d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 59 removed outlier: 3.755A pdb=" N ILE d 52 " --> pdb=" O ARG d 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA d 53 " --> pdb=" O ALA d 49 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA d 57 " --> pdb=" O ALA d 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 81 Processing helix chain 'd' and resid 82 through 89 removed outlier: 3.658A pdb=" N GLU d 87 " --> pdb=" O LYS d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 95 Processing helix chain 'd' and resid 158 through 163 Processing helix chain 'd' and resid 167 through 180 removed outlier: 4.858A pdb=" N THR d 173 " --> pdb=" O GLY d 169 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG d 174 " --> pdb=" O ARG d 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 19 Proline residue: g 11 - end of helix removed outlier: 3.609A pdb=" N GLU g 16 " --> pdb=" O LEU g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 35 removed outlier: 3.574A pdb=" N LYS g 32 " --> pdb=" O GLY g 29 " (cutoff:3.500A) Proline residue: g 33 - end of helix Processing helix chain 'g' and resid 38 through 51 removed outlier: 4.149A pdb=" N ILE g 43 " --> pdb=" O GLY g 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS g 48 " --> pdb=" O ALA g 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 58 removed outlier: 3.638A pdb=" N ASP g 58 " --> pdb=" O PRO g 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 61 No H-bonds generated for 'chain 'g' and resid 59 through 61' Processing helix chain 'g' and resid 62 through 72 removed outlier: 3.524A pdb=" N ILE g 72 " --> pdb=" O GLU g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 90 removed outlier: 3.506A pdb=" N ARG g 80 " --> pdb=" O ASN g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 100 removed outlier: 3.542A pdb=" N GLU g 99 " --> pdb=" O GLU g 95 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS g 100 " --> pdb=" O ALA g 96 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 109 Processing helix chain 'g' and resid 124 through 131 removed outlier: 3.539A pdb=" N LEU g 128 " --> pdb=" O VAL g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 140 through 145 Processing helix chain 'g' and resid 164 through 168 removed outlier: 3.719A pdb=" N ILE g 168 " --> pdb=" O PRO g 165 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 178 Processing helix chain 'g' and resid 179 through 181 No H-bonds generated for 'chain 'g' and resid 179 through 181' Processing helix chain 'g' and resid 183 through 193 Processing helix chain 'g' and resid 209 through 224 removed outlier: 3.733A pdb=" N ASN g 218 " --> pdb=" O TRP g 214 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU g 220 " --> pdb=" O ARG g 216 " (cutoff:3.500A) Processing helix chain 'g' and resid 246 through 252 Processing helix chain 'g' and resid 265 through 278 removed outlier: 4.046A pdb=" N ALA g 278 " --> pdb=" O LEU g 274 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 19 Proline residue: h 11 - end of helix removed outlier: 3.609A pdb=" N GLU h 16 " --> pdb=" O LEU h 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 35 removed outlier: 3.574A pdb=" N LYS h 32 " --> pdb=" O GLY h 29 " (cutoff:3.500A) Proline residue: h 33 - end of helix Processing helix chain 'h' and resid 38 through 51 removed outlier: 4.149A pdb=" N ILE h 43 " --> pdb=" O GLY h 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS h 48 " --> pdb=" O ALA h 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 53 through 58 removed outlier: 3.638A pdb=" N ASP h 58 " --> pdb=" O PRO h 54 " (cutoff:3.500A) Processing helix chain 'h' and resid 59 through 61 No H-bonds generated for 'chain 'h' and resid 59 through 61' Processing helix chain 'h' and resid 62 through 72 removed outlier: 3.522A pdb=" N ILE h 72 " --> pdb=" O GLU h 68 " (cutoff:3.500A) Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.511A pdb=" N ARG h 80 " --> pdb=" O ASN h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 91 through 100 removed outlier: 3.542A pdb=" N GLU h 99 " --> pdb=" O GLU h 95 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS h 100 " --> pdb=" O ALA h 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 101 through 109 Processing helix chain 'h' and resid 124 through 131 removed outlier: 3.540A pdb=" N LEU h 128 " --> pdb=" O VAL h 124 " (cutoff:3.500A) Processing helix chain 'h' and resid 140 through 145 Processing helix chain 'h' and resid 164 through 168 removed outlier: 3.718A pdb=" N ILE h 168 " --> pdb=" O PRO h 165 " (cutoff:3.500A) Processing helix chain 'h' and resid 171 through 178 Processing helix chain 'h' and resid 179 through 181 No H-bonds generated for 'chain 'h' and resid 179 through 181' Processing helix chain 'h' and resid 183 through 193 Processing helix chain 'h' and resid 209 through 224 removed outlier: 3.733A pdb=" N ASN h 218 " --> pdb=" O TRP h 214 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU h 220 " --> pdb=" O ARG h 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 246 through 252 Processing helix chain 'h' and resid 265 through 278 removed outlier: 4.047A pdb=" N ALA h 278 " --> pdb=" O LEU h 274 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 19 Proline residue: i 11 - end of helix removed outlier: 3.608A pdb=" N GLU i 16 " --> pdb=" O LEU i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 35 removed outlier: 3.574A pdb=" N LYS i 32 " --> pdb=" O GLY i 29 " (cutoff:3.500A) Proline residue: i 33 - end of helix Processing helix chain 'i' and resid 38 through 51 removed outlier: 4.150A pdb=" N ILE i 43 " --> pdb=" O GLY i 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS i 48 " --> pdb=" O ALA i 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR i 49 " --> pdb=" O SER i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 53 through 58 removed outlier: 3.638A pdb=" N ASP i 58 " --> pdb=" O PRO i 54 " (cutoff:3.500A) Processing helix chain 'i' and resid 59 through 61 No H-bonds generated for 'chain 'i' and resid 59 through 61' Processing helix chain 'i' and resid 62 through 72 removed outlier: 3.524A pdb=" N ILE i 72 " --> pdb=" O GLU i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 90 removed outlier: 3.524A pdb=" N ARG i 80 " --> pdb=" O ASN i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 100 removed outlier: 3.542A pdb=" N GLU i 99 " --> pdb=" O GLU i 95 " (cutoff:3.500A) removed outlier: 4.156A 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: 3.539A pdb=" N LEU i 128 " --> pdb=" O VAL i 124 " (cutoff:3.500A) Processing helix chain 'i' and resid 140 through 145 Processing helix chain 'i' and resid 164 through 168 removed outlier: 3.718A 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 209 through 224 removed outlier: 3.733A pdb=" N ASN i 218 " --> pdb=" O TRP i 214 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU i 220 " --> pdb=" O ARG i 216 " (cutoff:3.500A) Processing helix chain 'i' and resid 246 through 252 Processing helix chain 'i' and resid 265 through 278 removed outlier: 4.046A 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: 3.608A pdb=" N GLU j 16 " --> pdb=" O LEU j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 35 removed outlier: 3.574A pdb=" N LYS j 32 " --> pdb=" O GLY j 29 " (cutoff:3.500A) Proline residue: j 33 - end of helix Processing helix chain 'j' and resid 38 through 51 removed outlier: 4.149A pdb=" N ILE j 43 " --> pdb=" O GLY j 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS j 48 " --> pdb=" O ALA j 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR j 49 " --> pdb=" O SER j 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 53 through 58 removed outlier: 3.637A pdb=" N ASP j 58 " --> pdb=" O PRO j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 59 through 61 No H-bonds generated for 'chain 'j' and resid 59 through 61' Processing helix chain 'j' and resid 62 through 72 removed outlier: 3.523A pdb=" N ILE j 72 " --> pdb=" O GLU j 68 " (cutoff:3.500A) Processing helix chain 'j' and resid 76 through 90 removed outlier: 3.517A pdb=" N ARG j 80 " --> pdb=" O ASN j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 91 through 100 removed outlier: 3.542A pdb=" N GLU j 99 " --> pdb=" O GLU j 95 " (cutoff:3.500A) removed outlier: 4.154A 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: 3.540A pdb=" N LEU j 128 " --> pdb=" O VAL j 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 140 through 145 Processing helix chain 'j' and resid 164 through 168 removed outlier: 3.718A 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 194 removed outlier: 3.578A pdb=" N LEU j 194 " --> pdb=" O ARG j 190 " (cutoff:3.500A) Processing helix chain 'j' and resid 209 through 224 removed outlier: 3.734A pdb=" N ASN j 218 " --> pdb=" O TRP j 214 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU j 220 " --> pdb=" O ARG j 216 " (cutoff:3.500A) Processing helix chain 'j' and resid 246 through 252 Processing helix chain 'j' and resid 265 through 278 removed outlier: 4.047A pdb=" N ALA j 278 " --> pdb=" O LEU j 274 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 22 removed outlier: 3.640A pdb=" N ARG o 16 " --> pdb=" O SER o 12 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU o 17 " --> pdb=" O GLU o 13 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL o 21 " --> pdb=" O GLU o 17 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 59 removed outlier: 3.753A pdb=" N ILE o 52 " --> pdb=" O ARG o 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA o 53 " --> pdb=" O ALA o 49 " (cutoff:3.500A) removed outlier: 3.766A 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: 3.659A 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 167 through 180 removed outlier: 4.859A pdb=" N THR o 173 " --> pdb=" O GLY o 169 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG o 174 " --> pdb=" O ARG o 170 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 22 removed outlier: 3.640A pdb=" N ARG r 16 " --> pdb=" O SER r 12 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU r 17 " --> pdb=" O GLU r 13 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL r 21 " --> pdb=" O GLU r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 59 removed outlier: 3.755A pdb=" N ILE r 52 " --> pdb=" O ARG r 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA r 53 " --> pdb=" O ALA r 49 " (cutoff:3.500A) removed outlier: 3.769A 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: 3.657A 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 167 through 180 removed outlier: 4.857A pdb=" N THR r 173 " --> pdb=" O GLY r 169 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG r 174 " --> pdb=" O ARG r 170 " (cutoff:3.500A) Processing helix chain 's' and resid 5 through 19 Proline residue: s 11 - end of helix removed outlier: 3.609A pdb=" N GLU s 16 " --> pdb=" O LEU s 12 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 35 removed outlier: 3.573A pdb=" N LYS s 32 " --> pdb=" O GLY s 29 " (cutoff:3.500A) Proline residue: s 33 - end of helix Processing helix chain 's' and resid 38 through 51 removed outlier: 4.148A pdb=" N ILE s 43 " --> pdb=" O GLY s 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR s 49 " --> pdb=" O SER s 45 " (cutoff:3.500A) Processing helix chain 's' and resid 53 through 58 removed outlier: 3.638A pdb=" N ASP s 58 " --> pdb=" O PRO s 54 " (cutoff:3.500A) Processing helix chain 's' and resid 59 through 61 No H-bonds generated for 'chain 's' and resid 59 through 61' Processing helix chain 's' and resid 62 through 72 removed outlier: 3.524A pdb=" N ILE s 72 " --> pdb=" O GLU s 68 " (cutoff:3.500A) Processing helix chain 's' and resid 76 through 90 removed outlier: 3.522A pdb=" N ARG s 80 " --> pdb=" O ASN s 76 " (cutoff:3.500A) Processing helix chain 's' and resid 91 through 100 removed outlier: 3.542A pdb=" N GLU s 99 " --> pdb=" O GLU s 95 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS s 100 " --> pdb=" O ALA s 96 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 109 Processing helix chain 's' and resid 124 through 131 removed outlier: 3.540A pdb=" N LEU s 128 " --> pdb=" O VAL s 124 " (cutoff:3.500A) Processing helix chain 's' and resid 140 through 145 Processing helix chain 's' and resid 164 through 168 removed outlier: 3.718A pdb=" N ILE s 168 " --> pdb=" O PRO s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 171 through 178 Processing helix chain 's' and resid 179 through 181 No H-bonds generated for 'chain 's' and resid 179 through 181' Processing helix chain 's' and resid 183 through 193 Processing helix chain 's' and resid 209 through 224 removed outlier: 3.734A pdb=" N ASN s 218 " --> pdb=" O TRP s 214 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU s 220 " --> pdb=" O ARG s 216 " (cutoff:3.500A) Processing helix chain 's' and resid 246 through 252 Processing helix chain 's' and resid 265 through 278 removed outlier: 4.048A pdb=" N ALA s 278 " --> pdb=" O LEU s 274 " (cutoff:3.500A) Processing helix chain 't' and resid 5 through 19 Proline residue: t 11 - end of helix removed outlier: 3.609A pdb=" N GLU t 16 " --> pdb=" O LEU t 12 " (cutoff:3.500A) Processing helix chain 't' and resid 28 through 35 removed outlier: 3.574A pdb=" N LYS t 32 " --> pdb=" O GLY t 29 " (cutoff:3.500A) Proline residue: t 33 - end of helix Processing helix chain 't' and resid 38 through 51 removed outlier: 4.149A pdb=" N ILE t 43 " --> pdb=" O GLY t 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS t 48 " --> pdb=" O ALA t 44 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR t 49 " --> pdb=" O SER t 45 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 58 removed outlier: 3.639A pdb=" N ASP t 58 " --> pdb=" O PRO t 54 " (cutoff:3.500A) Processing helix chain 't' and resid 59 through 61 No H-bonds generated for 'chain 't' and resid 59 through 61' Processing helix chain 't' and resid 62 through 72 removed outlier: 3.524A pdb=" N ILE t 72 " --> pdb=" O GLU t 68 " (cutoff:3.500A) Processing helix chain 't' and resid 76 through 90 removed outlier: 3.525A pdb=" N ARG t 80 " --> pdb=" O ASN t 76 " (cutoff:3.500A) Processing helix chain 't' and resid 91 through 100 removed outlier: 3.541A pdb=" N GLU t 99 " --> pdb=" O GLU t 95 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS t 100 " --> pdb=" O ALA t 96 " (cutoff:3.500A) Processing helix chain 't' and resid 101 through 109 Processing helix chain 't' and resid 124 through 131 removed outlier: 3.540A pdb=" N LEU t 128 " --> pdb=" O VAL t 124 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 145 Processing helix chain 't' and resid 164 through 168 removed outlier: 3.718A pdb=" N ILE t 168 " --> pdb=" O PRO t 165 " (cutoff:3.500A) Processing helix chain 't' and resid 171 through 178 Processing helix chain 't' and resid 179 through 181 No H-bonds generated for 'chain 't' and resid 179 through 181' Processing helix chain 't' and resid 183 through 193 Processing helix chain 't' and resid 209 through 224 removed outlier: 3.733A pdb=" N ASN t 218 " --> pdb=" O TRP t 214 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU t 220 " --> pdb=" O ARG t 216 " (cutoff:3.500A) Processing helix chain 't' and resid 246 through 252 Processing helix chain 't' and resid 265 through 278 removed outlier: 4.047A pdb=" N ALA t 278 " --> pdb=" O LEU t 274 " (cutoff:3.500A) Processing helix chain 'u' and resid 5 through 19 Proline residue: u 11 - end of helix removed outlier: 3.609A pdb=" N GLU u 16 " --> pdb=" O LEU u 12 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 35 removed outlier: 3.574A pdb=" N LYS u 32 " --> pdb=" O GLY u 29 " (cutoff:3.500A) Proline residue: u 33 - end of helix Processing helix chain 'u' and resid 38 through 51 removed outlier: 4.149A pdb=" N ILE u 43 " --> pdb=" O GLY u 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS u 48 " --> pdb=" O ALA u 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR u 49 " --> pdb=" O SER u 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 58 removed outlier: 3.638A pdb=" N ASP u 58 " --> pdb=" O PRO u 54 " (cutoff:3.500A) Processing helix chain 'u' and resid 59 through 61 No H-bonds generated for 'chain 'u' and resid 59 through 61' Processing helix chain 'u' and resid 62 through 72 removed outlier: 3.524A pdb=" N ILE u 72 " --> pdb=" O GLU u 68 " (cutoff:3.500A) Processing helix chain 'u' and resid 76 through 90 Processing helix chain 'u' and resid 91 through 100 removed outlier: 3.542A pdb=" N GLU u 99 " --> pdb=" O GLU u 95 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS u 100 " --> pdb=" O ALA u 96 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 109 Processing helix chain 'u' and resid 124 through 131 removed outlier: 3.539A pdb=" N LEU u 128 " --> pdb=" O VAL u 124 " (cutoff:3.500A) Processing helix chain 'u' and resid 140 through 145 Processing helix chain 'u' and resid 164 through 168 removed outlier: 3.719A pdb=" N ILE u 168 " --> pdb=" O PRO u 165 " (cutoff:3.500A) Processing helix chain 'u' and resid 171 through 178 Processing helix chain 'u' and resid 179 through 181 No H-bonds generated for 'chain 'u' and resid 179 through 181' Processing helix chain 'u' and resid 183 through 193 Processing helix chain 'u' and resid 209 through 224 removed outlier: 3.734A pdb=" N ASN u 218 " --> pdb=" O TRP u 214 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU u 220 " --> pdb=" O ARG u 216 " (cutoff:3.500A) Processing helix chain 'u' and resid 246 through 252 Processing helix chain 'u' and resid 265 through 278 removed outlier: 4.046A pdb=" N ALA u 278 " --> pdb=" O LEU u 274 " (cutoff:3.500A) Processing helix chain 'v' and resid 5 through 19 Proline residue: v 11 - end of helix removed outlier: 3.610A pdb=" N GLU v 16 " --> pdb=" O LEU v 12 " (cutoff:3.500A) Processing helix chain 'v' and resid 28 through 35 removed outlier: 3.573A pdb=" N LYS v 32 " --> pdb=" O GLY v 29 " (cutoff:3.500A) Proline residue: v 33 - end of helix Processing helix chain 'v' and resid 38 through 51 removed outlier: 4.149A pdb=" N ILE v 43 " --> pdb=" O GLY v 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS v 48 " --> pdb=" O ALA v 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR v 49 " --> pdb=" O SER v 45 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 58 removed outlier: 3.638A pdb=" N ASP v 58 " --> pdb=" O PRO v 54 " (cutoff:3.500A) Processing helix chain 'v' and resid 59 through 61 No H-bonds generated for 'chain 'v' and resid 59 through 61' Processing helix chain 'v' and resid 62 through 72 removed outlier: 3.524A pdb=" N ILE v 72 " --> pdb=" O GLU v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 90 removed outlier: 3.513A pdb=" N ARG v 80 " --> pdb=" O ASN v 76 " (cutoff:3.500A) Processing helix chain 'v' and resid 91 through 100 removed outlier: 3.542A pdb=" N GLU v 99 " --> pdb=" O GLU v 95 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS v 100 " --> pdb=" O ALA v 96 " (cutoff:3.500A) Processing helix chain 'v' and resid 101 through 109 Processing helix chain 'v' and resid 124 through 131 removed outlier: 3.539A pdb=" N LEU v 128 " --> pdb=" O VAL v 124 " (cutoff:3.500A) Processing helix chain 'v' and resid 140 through 145 Processing helix chain 'v' and resid 164 through 168 removed outlier: 3.717A pdb=" N ILE v 168 " --> pdb=" O PRO v 165 " (cutoff:3.500A) Processing helix chain 'v' and resid 171 through 178 Processing helix chain 'v' and resid 179 through 181 No H-bonds generated for 'chain 'v' and resid 179 through 181' Processing helix chain 'v' and resid 183 through 193 Processing helix chain 'v' and resid 209 through 224 removed outlier: 3.732A pdb=" N ASN v 218 " --> pdb=" O TRP v 214 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU v 220 " --> pdb=" O ARG v 216 " (cutoff:3.500A) Processing helix chain 'v' and resid 246 through 252 Processing helix chain 'v' and resid 265 through 278 removed outlier: 4.047A pdb=" N ALA v 278 " --> pdb=" O LEU v 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.474A pdb=" N TRP C 5 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU C 31 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR C 7 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE C 6 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU C 65 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN C 8 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N GLY C 67 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 28 through 31 removed outlier: 6.474A pdb=" N TRP F 5 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU F 31 " --> pdb=" O TRP F 5 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR F 7 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE F 6 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU F 65 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN F 8 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N GLY F 67 " --> pdb=" O ASN F 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 28 through 31 removed outlier: 6.474A pdb=" N TRP I 5 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU I 31 " --> pdb=" O TRP I 5 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR I 7 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE I 6 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU I 65 " --> pdb=" O PHE I 6 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN I 8 " --> pdb=" O GLU I 65 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N GLY I 67 " --> pdb=" O ASN I 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 28 through 31 removed outlier: 6.475A pdb=" N TRP L 5 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU L 31 " --> pdb=" O TRP L 5 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR L 7 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE L 6 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLU L 65 " --> pdb=" O PHE L 6 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN L 8 " --> pdb=" O GLU L 65 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N GLY L 67 " --> pdb=" O ASN L 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 28 through 31 removed outlier: 6.475A pdb=" N TRP a 5 " --> pdb=" O GLY a 29 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU a 31 " --> pdb=" O TRP a 5 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR a 7 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE a 6 " --> pdb=" O ILE a 63 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU a 65 " --> pdb=" O PHE a 6 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN a 8 " --> pdb=" O GLU a 65 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N GLY a 67 " --> pdb=" O ASN a 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 28 through 31 removed outlier: 6.475A pdb=" N TRP d 5 " --> pdb=" O GLY d 29 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU d 31 " --> pdb=" O TRP d 5 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR d 7 " --> pdb=" O LEU d 31 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE d 6 " --> pdb=" O ILE d 63 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU d 65 " --> pdb=" O PHE d 6 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN d 8 " --> pdb=" O GLU d 65 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N GLY d 67 " --> pdb=" O ASN d 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 135 through 138 removed outlier: 6.536A pdb=" N ILE g 115 " --> pdb=" O ILE g 156 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N THR g 114 " --> pdb=" O LEU g 22 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS g 236 " --> pdb=" O ASP g 257 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE g 259 " --> pdb=" O CYS g 236 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE g 238 " --> pdb=" O ILE g 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 135 through 138 removed outlier: 6.536A pdb=" N ILE h 115 " --> pdb=" O ILE h 156 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR h 114 " --> pdb=" O LEU h 22 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS h 236 " --> pdb=" O ASP h 257 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE h 259 " --> pdb=" O CYS h 236 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE h 238 " --> pdb=" O ILE h 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 135 through 138 removed outlier: 6.536A pdb=" N ILE i 115 " --> pdb=" O ILE i 156 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR i 114 " --> pdb=" O LEU i 22 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS i 236 " --> pdb=" O ASP i 257 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE i 259 " --> pdb=" O CYS i 236 " (cutoff:3.500A) removed outlier: 6.221A 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: 6.536A pdb=" N ILE j 115 " --> pdb=" O ILE j 156 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR j 114 " --> pdb=" O LEU j 22 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS j 236 " --> pdb=" O ASP j 257 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE j 259 " --> pdb=" O CYS j 236 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE j 238 " --> pdb=" O ILE j 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'o' and resid 28 through 31 removed outlier: 6.474A pdb=" N TRP o 5 " --> pdb=" O GLY o 29 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU o 31 " --> pdb=" O TRP o 5 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR o 7 " --> pdb=" O LEU o 31 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE o 6 " --> pdb=" O ILE o 63 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU o 65 " --> pdb=" O PHE o 6 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN o 8 " --> pdb=" O GLU o 65 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N GLY o 67 " --> pdb=" O ASN o 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'r' and resid 28 through 31 removed outlier: 6.474A pdb=" N TRP r 5 " --> pdb=" O GLY r 29 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU r 31 " --> pdb=" O TRP r 5 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR r 7 " --> pdb=" O LEU r 31 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE r 6 " --> pdb=" O ILE r 63 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU r 65 " --> pdb=" O PHE r 6 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN r 8 " --> pdb=" O GLU r 65 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N GLY r 67 " --> pdb=" O ASN r 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 's' and resid 135 through 138 removed outlier: 6.536A pdb=" N ILE s 115 " --> pdb=" O ILE s 156 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR s 114 " --> pdb=" O LEU s 22 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS s 236 " --> pdb=" O ASP s 257 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE s 259 " --> pdb=" O CYS s 236 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE s 238 " --> pdb=" O ILE s 259 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 't' and resid 135 through 138 removed outlier: 6.535A pdb=" N ILE t 115 " --> pdb=" O ILE t 156 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR t 114 " --> pdb=" O LEU t 22 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS t 236 " --> pdb=" O ASP t 257 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE t 259 " --> pdb=" O CYS t 236 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE t 238 " --> pdb=" O ILE t 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'u' and resid 135 through 138 removed outlier: 6.536A pdb=" N ILE u 115 " --> pdb=" O ILE u 156 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR u 114 " --> pdb=" O LEU u 22 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS u 236 " --> pdb=" O ASP u 257 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE u 259 " --> pdb=" O CYS u 236 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE u 238 " --> pdb=" O ILE u 259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'v' and resid 135 through 138 removed outlier: 6.536A pdb=" N ILE v 115 " --> pdb=" O ILE v 156 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR v 114 " --> pdb=" O LEU v 22 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS v 236 " --> pdb=" O ASP v 257 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE v 259 " --> pdb=" O CYS v 236 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE v 238 " --> pdb=" O ILE v 259 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3387 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: 2.36 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: 4800 1.29 - 1.42: 7640 1.42 - 1.55: 17016 1.55 - 1.68: 64 1.68 - 1.81: 144 Bond restraints: 29664 Sorted by residual: bond pdb=" CAD Y43 r 201 " pdb=" OAE Y43 r 201 " ideal model delta sigma weight residual 1.391 1.607 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" CAD Y43 I 201 " pdb=" OAE Y43 I 201 " ideal model delta sigma weight residual 1.391 1.607 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" CAD Y43 o 201 " pdb=" OAE Y43 o 201 " ideal model delta sigma weight residual 1.391 1.606 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CAD Y43 C 201 " pdb=" OAE Y43 C 201 " ideal model delta sigma weight residual 1.391 1.606 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CAD Y43 d 201 " pdb=" OAE Y43 d 201 " ideal model delta sigma weight residual 1.391 1.606 -0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 29659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 39022 2.51 - 5.02: 992 5.02 - 7.53: 190 7.53 - 10.04: 28 10.04 - 12.56: 16 Bond angle restraints: 40248 Sorted by residual: angle pdb=" OAJ Y43 F 201 " pdb=" PAI Y43 F 201 " pdb=" OAK Y43 F 201 " ideal model delta sigma weight residual 121.66 109.10 12.56 3.00e+00 1.11e-01 1.75e+01 angle pdb=" OAJ Y43 o 201 " pdb=" PAI Y43 o 201 " pdb=" OAK Y43 o 201 " ideal model delta sigma weight residual 121.66 109.13 12.53 3.00e+00 1.11e-01 1.75e+01 angle pdb=" OAJ Y43 L 201 " pdb=" PAI Y43 L 201 " pdb=" OAK Y43 L 201 " ideal model delta sigma weight residual 121.66 109.13 12.53 3.00e+00 1.11e-01 1.75e+01 angle pdb=" OAJ Y43 d 201 " pdb=" PAI Y43 d 201 " pdb=" OAK Y43 d 201 " ideal model delta sigma weight residual 121.66 109.13 12.53 3.00e+00 1.11e-01 1.74e+01 angle pdb=" OAJ Y43 r 201 " pdb=" PAI Y43 r 201 " pdb=" OAK Y43 r 201 " ideal model delta sigma weight residual 121.66 109.13 12.53 3.00e+00 1.11e-01 1.74e+01 ... (remaining 40243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 17565 33.88 - 67.75: 346 67.75 - 101.63: 69 101.63 - 135.51: 16 135.51 - 169.38: 4 Dihedral angle restraints: 18000 sinusoidal: 7440 harmonic: 10560 Sorted by residual: dihedral pdb=" CD ARG u 80 " pdb=" NE ARG u 80 " pdb=" CZ ARG u 80 " pdb=" NH1 ARG u 80 " ideal model delta sinusoidal sigma weight residual 0.00 52.74 -52.74 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CD ARG j 80 " pdb=" NE ARG j 80 " pdb=" CZ ARG j 80 " pdb=" NH1 ARG j 80 " ideal model delta sinusoidal sigma weight residual 0.00 50.79 -50.79 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CD ARG h 80 " pdb=" NE ARG h 80 " pdb=" CZ ARG h 80 " pdb=" NH1 ARG h 80 " ideal model delta sinusoidal sigma weight residual 0.00 50.34 -50.34 1 1.00e+01 1.00e-02 3.47e+01 ... (remaining 17997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2970 0.051 - 0.102: 1085 0.102 - 0.154: 365 0.154 - 0.205: 35 0.205 - 0.256: 9 Chirality restraints: 4464 Sorted by residual: chirality pdb=" CA TRP C 141 " pdb=" N TRP C 141 " pdb=" C TRP C 141 " pdb=" CB TRP C 141 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA TRP L 141 " pdb=" N TRP L 141 " pdb=" C TRP L 141 " pdb=" CB TRP L 141 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA TRP I 141 " pdb=" N TRP I 141 " pdb=" C TRP I 141 " pdb=" CB TRP I 141 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 4461 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG u 80 " 0.865 9.50e-02 1.11e+02 3.88e-01 9.12e+01 pdb=" NE ARG u 80 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG u 80 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG u 80 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG u 80 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG j 80 " -0.844 9.50e-02 1.11e+02 3.78e-01 8.69e+01 pdb=" NE ARG j 80 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG j 80 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG j 80 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG j 80 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG h 80 " 0.840 9.50e-02 1.11e+02 3.77e-01 8.61e+01 pdb=" NE ARG h 80 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG h 80 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG h 80 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG h 80 " 0.024 2.00e-02 2.50e+03 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 169 2.53 - 3.12: 20141 3.12 - 3.71: 44441 3.71 - 4.31: 66684 4.31 - 4.90: 111151 Nonbonded interactions: 242586 Sorted by model distance: nonbonded pdb=" OAN Y43 I 201 " pdb="ZN ZN I 202 " model vdw 1.935 2.230 nonbonded pdb=" OAO Y43 r 201 " pdb="ZN ZN r 202 " model vdw 1.987 2.230 nonbonded pdb=" OAO Y43 F 201 " pdb="ZN ZN F 202 " model vdw 2.050 2.230 nonbonded pdb=" OAO Y43 d 201 " pdb="ZN ZN d 202 " model vdw 2.052 2.230 nonbonded pdb=" OAN Y43 C 201 " pdb="ZN ZN C 202 " model vdw 2.066 2.230 ... (remaining 242581 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: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'a' selection = chain 'd' selection = chain 'o' selection = chain 'r' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.012 0.216 29664 Z= 0.531 Angle : 1.002 12.555 40248 Z= 0.539 Chirality : 0.059 0.256 4464 Planarity : 0.016 0.388 5208 Dihedral : 13.916 169.382 11168 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -4.80 (0.11), residues: 3624 helix: -4.03 (0.07), residues: 1728 sheet: -1.70 (0.18), residues: 656 loop : -2.28 (0.15), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG s 216 TYR 0.021 0.003 TYR v 212 PHE 0.053 0.004 PHE I 139 TRP 0.028 0.004 TRP j 214 HIS 0.012 0.003 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.01152 / 0.53 (29664) covalent geometry : angle 1.00190 / 0.54 (40248) hydrogen bonds : bond 0.30407 / 20.75 ( 1177) hydrogen bonds : angle 8.99194 / 6.25 ( 3387) *********************** 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 685 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 157 MET cc_start: 0.3387 (mtm) cc_final: 0.3039 (ptm) REVERT: h 182 ASP cc_start: 0.7645 (t70) cc_final: 0.7328 (t0) REVERT: i 79 GLN cc_start: 0.8630 (mp10) cc_final: 0.8393 (mp10) REVERT: j 182 ASP cc_start: 0.7749 (t70) cc_final: 0.7412 (t0) REVERT: o 157 MET cc_start: 0.3470 (mtm) cc_final: 0.3149 (ptm) outliers start: 0 outliers final: 0 residues processed: 685 average time/residue: 0.2136 time to fit residues: 222.4017 Evaluate side-chains 297 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 8 ASN C 11 ASN C 75 ASN F 11 ASN F 75 ASN I 8 ASN I 11 ASN I 75 ASN L 11 ASN a 8 ASN a 11 ASN a 75 ASN ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 11 ASN d 75 ASN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 145 GLN g 223 GLN ** g 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 145 GLN h 223 GLN ** h 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 145 GLN i 223 GLN ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 145 GLN j 223 GLN ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 8 ASN o 11 ASN o 75 ASN r 11 ASN r 75 ASN s 145 GLN s 218 ASN ** s 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 145 GLN ** t 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 145 GLN u 218 ASN ** u 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 145 GLN v 223 GLN ** v 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.086773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.057315 restraints weight = 94659.146| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.66 r_work: 0.2821 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29664 Z= 0.151 Angle : 0.622 6.714 40248 Z= 0.325 Chirality : 0.045 0.188 4464 Planarity : 0.006 0.042 5208 Dihedral : 9.485 133.079 4320 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.76 % Allowed : 9.15 % Favored : 89.09 % 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: -1.87 (0.10), residues: 1760 sheet: -1.14 (0.21), residues: 544 loop : -1.83 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG u 272 TYR 0.017 0.002 TYR d 112 PHE 0.020 0.002 PHE L 139 TRP 0.020 0.002 TRP L 141 HIS 0.016 0.001 HIS I 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (29664) covalent geometry : angle 0.62245 / 0.32 (40248) hydrogen bonds : bond 0.04297 / 2.95 ( 1177) hydrogen bonds : angle 5.15258 / 3.67 ( 3387) *********************** 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 388 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8413 (mmmt) cc_final: 0.7958 (mmmt) REVERT: C 66 HIS cc_start: 0.8326 (t-90) cc_final: 0.8055 (t-90) REVERT: C 70 CYS cc_start: 0.7894 (m) cc_final: 0.7472 (p) REVERT: C 157 MET cc_start: 0.4978 (mtt) cc_final: 0.4702 (mpp) REVERT: F 70 CYS cc_start: 0.7870 (m) cc_final: 0.7457 (p) REVERT: I 66 HIS cc_start: 0.8516 (t-90) cc_final: 0.8249 (t-90) REVERT: I 70 CYS cc_start: 0.7909 (m) cc_final: 0.7474 (p) REVERT: I 157 MET cc_start: 0.4961 (mtt) cc_final: 0.4692 (mpp) REVERT: L 70 CYS cc_start: 0.7930 (m) cc_final: 0.7502 (p) REVERT: a 74 LEU cc_start: 0.7693 (mt) cc_final: 0.7399 (mm) REVERT: d 30 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: d 66 HIS cc_start: 0.8469 (t-90) cc_final: 0.8240 (t-90) REVERT: g 186 ASP cc_start: 0.9231 (m-30) cc_final: 0.9031 (m-30) REVERT: h 182 ASP cc_start: 0.8824 (t70) cc_final: 0.8551 (t0) REVERT: i 79 GLN cc_start: 0.9359 (mp10) cc_final: 0.9028 (mp10) REVERT: i 186 ASP cc_start: 0.9455 (m-30) cc_final: 0.9201 (m-30) REVERT: j 182 ASP cc_start: 0.8876 (t70) cc_final: 0.8602 (t0) REVERT: o 74 LEU cc_start: 0.7694 (mt) cc_final: 0.7360 (mm) REVERT: r 30 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: r 157 MET cc_start: 0.5592 (ptm) cc_final: 0.4185 (mtt) REVERT: v 79 GLN cc_start: 0.9264 (mp10) cc_final: 0.9027 (mp10) outliers start: 53 outliers final: 39 residues processed: 372 average time/residue: 0.1809 time to fit residues: 109.1593 Evaluate side-chains 315 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 30 TYR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 30 TYR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 62 VAL Chi-restraints excluded: chain d residue 113 CYS Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain o residue 122 ILE Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 30 TYR Chi-restraints excluded: chain r residue 35 VAL Chi-restraints excluded: chain r residue 62 VAL Chi-restraints excluded: chain r residue 113 CYS Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 169 VAL Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 169 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 25 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 351 optimal weight: 0.7980 chunk 321 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 142 optimal weight: 0.0970 chunk 259 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 chunk 115 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 GLN ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN a 8 ASN ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 ASN d 140 HIS ** g 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 8 ASN ** o 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 8 ASN s 76 ASN s 223 GLN ** s 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 223 GLN ** t 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 223 GLN ** v 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.084091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055007 restraints weight = 94585.103| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.61 r_work: 0.2761 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29664 Z= 0.137 Angle : 0.544 8.020 40248 Z= 0.280 Chirality : 0.043 0.179 4464 Planarity : 0.005 0.072 5208 Dihedral : 8.866 147.037 4320 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.45 % Allowed : 10.25 % Favored : 87.30 % 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: -1.57 (0.13), residues: 3624 helix: -0.61 (0.12), residues: 1704 sheet: -0.95 (0.21), residues: 544 loop : -1.46 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 16 TYR 0.017 0.001 TYR F 112 PHE 0.021 0.001 PHE L 139 TRP 0.018 0.002 TRP L 141 HIS 0.007 0.001 HIS r 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (29664) covalent geometry : angle 0.54377 / 0.28 (40248) hydrogen bonds : bond 0.03472 / 2.37 ( 1177) hydrogen bonds : angle 4.56852 / 3.25 ( 3387) *********************** 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 359 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 285 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8110 (mmmt) REVERT: C 157 MET cc_start: 0.5241 (mtt) cc_final: 0.4742 (mpp) REVERT: F 34 LYS cc_start: 0.9266 (tmtm) cc_final: 0.8764 (tptp) REVERT: I 27 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8330 (mmmt) REVERT: I 157 MET cc_start: 0.5191 (mtt) cc_final: 0.4639 (mpp) REVERT: L 34 LYS cc_start: 0.9294 (tmtm) cc_final: 0.8793 (tptp) REVERT: a 27 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8568 (mmmt) REVERT: a 74 LEU cc_start: 0.7500 (mt) cc_final: 0.7202 (mm) REVERT: a 157 MET cc_start: 0.5987 (ptp) cc_final: 0.5474 (ptp) REVERT: d 30 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: d 66 HIS cc_start: 0.8462 (t-90) cc_final: 0.8216 (t70) REVERT: h 266 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8257 (mmmm) REVERT: i 79 GLN cc_start: 0.9388 (mp10) cc_final: 0.9057 (mp10) REVERT: i 186 ASP cc_start: 0.9470 (m-30) cc_final: 0.9230 (m-30) REVERT: j 266 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8257 (mmmm) REVERT: o 27 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8552 (mmmt) REVERT: o 34 LYS cc_start: 0.9118 (tptm) cc_final: 0.8744 (tptp) REVERT: o 74 LEU cc_start: 0.7514 (mt) cc_final: 0.7184 (mm) REVERT: r 30 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: r 157 MET cc_start: 0.5659 (ptm) cc_final: 0.5132 (ptm) REVERT: t 68 GLU cc_start: 0.9514 (tp30) cc_final: 0.9053 (tp30) REVERT: t 186 ASP cc_start: 0.9403 (m-30) cc_final: 0.9130 (m-30) REVERT: t 266 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8283 (mmmm) REVERT: u 79 GLN cc_start: 0.9064 (mp10) cc_final: 0.8676 (mp10) REVERT: v 68 GLU cc_start: 0.9477 (tp30) cc_final: 0.9252 (tp30) REVERT: v 79 GLN cc_start: 0.9326 (mp10) cc_final: 0.8997 (mp10) REVERT: v 266 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8348 (mmmm) outliers start: 74 outliers final: 41 residues processed: 331 average time/residue: 0.1837 time to fit residues: 99.1028 Evaluate side-chains 299 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 30 TYR Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 266 LYS Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 169 VAL Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 266 LYS Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 122 ILE Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 30 TYR Chi-restraints excluded: chain r residue 35 VAL Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 169 VAL Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 266 LYS Chi-restraints excluded: chain t residue 277 ILE Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 169 VAL Chi-restraints excluded: chain v residue 169 VAL Chi-restraints excluded: chain v residue 266 LYS Chi-restraints excluded: chain v residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 224 optimal weight: 8.9990 chunk 258 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 294 optimal weight: 8.9990 chunk 330 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 338 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 chunk 241 optimal weight: 0.5980 chunk 214 optimal weight: 0.4980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 GLN ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN I 19 GLN ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 HIS a 8 ASN ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 ASN g 223 GLN ** g 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 8 ASN ** o 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 8 ASN ** s 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 60 HIS ** v 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.083798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.054792 restraints weight = 93980.821| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.60 r_work: 0.2754 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29664 Z= 0.114 Angle : 0.516 9.220 40248 Z= 0.265 Chirality : 0.042 0.191 4464 Planarity : 0.004 0.032 5208 Dihedral : 8.779 148.776 4320 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.16 % Allowed : 10.84 % Favored : 87.00 % 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: -1.00 (0.13), residues: 3624 helix: 0.01 (0.12), residues: 1704 sheet: -0.82 (0.22), residues: 544 loop : -1.31 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG v 113 TYR 0.016 0.001 TYR F 112 PHE 0.018 0.001 PHE L 139 TRP 0.017 0.001 TRP d 141 HIS 0.017 0.001 HIS d 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (29664) covalent geometry : angle 0.51607 / 0.27 (40248) hydrogen bonds : bond 0.02994 / 2.04 ( 1177) hydrogen bonds : angle 4.38108 / 3.12 ( 3387) *********************** 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 336 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8089 (mmmt) REVERT: C 157 MET cc_start: 0.5148 (mtt) cc_final: 0.4501 (mpp) REVERT: F 34 LYS cc_start: 0.9314 (tmtm) cc_final: 0.8822 (tptp) REVERT: I 27 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8278 (mmmt) REVERT: I 66 HIS cc_start: 0.8328 (t-90) cc_final: 0.7833 (t-90) REVERT: I 157 MET cc_start: 0.5332 (mtt) cc_final: 0.4665 (mpp) REVERT: L 34 LYS cc_start: 0.9328 (tmtm) cc_final: 0.8851 (tptp) REVERT: a 27 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8536 (mmmt) REVERT: a 74 LEU cc_start: 0.7482 (mt) cc_final: 0.7201 (mm) REVERT: a 93 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4904 (pp) REVERT: a 157 MET cc_start: 0.6024 (ptp) cc_final: 0.5589 (ptp) REVERT: d 8 ASN cc_start: 0.8185 (t0) cc_final: 0.7887 (t0) REVERT: d 30 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: d 32 THR cc_start: 0.8970 (p) cc_final: 0.8767 (t) REVERT: d 157 MET cc_start: 0.4889 (ttp) cc_final: 0.4211 (mtp) REVERT: d 162 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7784 (mppt) REVERT: h 266 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8264 (mmmm) REVERT: i 68 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.8906 (tp30) REVERT: i 79 GLN cc_start: 0.9392 (mp10) cc_final: 0.9061 (mp10) REVERT: i 186 ASP cc_start: 0.9482 (m-30) cc_final: 0.9234 (m-30) REVERT: j 266 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8271 (mmmm) REVERT: o 27 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8540 (mmmt) REVERT: o 74 LEU cc_start: 0.7470 (mt) cc_final: 0.7166 (mm) REVERT: o 157 MET cc_start: 0.5783 (ptp) cc_final: 0.5087 (ptp) REVERT: r 8 ASN cc_start: 0.8160 (t0) cc_final: 0.7901 (t0) REVERT: r 30 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: s 68 GLU cc_start: 0.9449 (tp30) cc_final: 0.9007 (tp30) REVERT: t 68 GLU cc_start: 0.9494 (tp30) cc_final: 0.9118 (tp30) REVERT: t 186 ASP cc_start: 0.9417 (m-30) cc_final: 0.9137 (m-30) REVERT: t 266 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8222 (mmmm) REVERT: u 68 GLU cc_start: 0.9468 (tp30) cc_final: 0.9034 (tp30) REVERT: u 79 GLN cc_start: 0.9111 (mp10) cc_final: 0.8720 (mp10) REVERT: v 68 GLU cc_start: 0.9462 (tp30) cc_final: 0.9176 (tp30) REVERT: v 79 GLN cc_start: 0.9347 (mp10) cc_final: 0.8989 (mp10) REVERT: v 266 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8223 (mmmm) outliers start: 65 outliers final: 34 residues processed: 313 average time/residue: 0.1850 time to fit residues: 94.8696 Evaluate side-chains 288 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 30 TYR Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 266 LYS Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 169 VAL Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 266 LYS Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 122 ILE Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 30 TYR Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 169 VAL Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 266 LYS Chi-restraints excluded: chain t residue 277 ILE Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 169 VAL Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 169 VAL Chi-restraints excluded: chain v residue 266 LYS Chi-restraints excluded: chain v residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 354 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 347 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 8 ASN C 11 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN I 8 ASN ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN a 11 ASN ** a 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 75 ASN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 223 GLN ** g 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN ** h 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 41 GLN i 223 GLN ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 GLN j 145 GLN ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 8 ASN o 11 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 75 ASN ** r 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 41 GLN ** s 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 223 GLN ** t 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 41 GLN u 223 GLN v 60 HIS ** v 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.078470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.049786 restraints weight = 93142.530| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.51 r_work: 0.2629 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29664 Z= 0.272 Angle : 0.642 9.096 40248 Z= 0.327 Chirality : 0.046 0.180 4464 Planarity : 0.005 0.038 5208 Dihedral : 9.384 159.078 4320 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.88 % Allowed : 10.51 % 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: -0.63 (0.14), residues: 3624 helix: 0.34 (0.13), residues: 1744 sheet: -0.88 (0.21), residues: 544 loop : -1.08 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG j 62 TYR 0.018 0.002 TYR a 112 PHE 0.028 0.002 PHE C 139 TRP 0.024 0.002 TRP d 86 HIS 0.009 0.001 HIS r 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.27 (29664) covalent geometry : angle 0.64238 / 0.33 (40248) hydrogen bonds : bond 0.03955 / 2.69 ( 1177) hydrogen bonds : angle 4.64873 / 3.32 ( 3387) *********************** 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 328 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 241 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8159 (mmmt) REVERT: C 34 LYS cc_start: 0.9298 (tmtm) cc_final: 0.9013 (tptm) REVERT: F 34 LYS cc_start: 0.9394 (tmtm) cc_final: 0.8963 (tptp) REVERT: F 157 MET cc_start: 0.6421 (ptm) cc_final: 0.5342 (ttp) REVERT: I 27 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8331 (mmmt) REVERT: I 34 LYS cc_start: 0.9278 (tmtm) cc_final: 0.8973 (tptm) REVERT: L 34 LYS cc_start: 0.9394 (tmtm) cc_final: 0.8991 (tptp) REVERT: L 157 MET cc_start: 0.6403 (ptm) cc_final: 0.5318 (ttp) REVERT: a 8 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7740 (t0) REVERT: d 11 ASN cc_start: 0.4115 (OUTLIER) cc_final: 0.3385 (m110) REVERT: d 34 LYS cc_start: 0.9259 (tmtm) cc_final: 0.8924 (tppt) REVERT: d 157 MET cc_start: 0.5423 (ttp) cc_final: 0.4289 (mtt) REVERT: d 162 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7861 (mtpt) REVERT: h 266 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8621 (mmmm) REVERT: i 68 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.8852 (tp30) REVERT: i 79 GLN cc_start: 0.9388 (mp10) cc_final: 0.9073 (mp10) REVERT: i 186 ASP cc_start: 0.9429 (m-30) cc_final: 0.9198 (m-30) REVERT: j 266 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8585 (mmmm) REVERT: o 8 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7750 (t0) REVERT: o 34 LYS cc_start: 0.9309 (tptm) cc_final: 0.9038 (tptp) REVERT: o 157 MET cc_start: 0.6645 (ptp) cc_final: 0.6313 (ptp) REVERT: r 11 ASN cc_start: 0.4183 (OUTLIER) cc_final: 0.3494 (m110) REVERT: r 34 LYS cc_start: 0.9253 (tmtm) cc_final: 0.8918 (tppt) REVERT: t 186 ASP cc_start: 0.9345 (m-30) cc_final: 0.9026 (m-30) REVERT: t 266 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8388 (mmmm) REVERT: u 79 GLN cc_start: 0.9169 (mp10) cc_final: 0.8740 (mp10) REVERT: v 266 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8373 (mmmm) outliers start: 87 outliers final: 63 residues processed: 299 average time/residue: 0.1873 time to fit residues: 90.2773 Evaluate side-chains 295 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 223 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain d residue 11 ASN Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 38 ILE Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 181 LEU Chi-restraints excluded: chain g residue 120 TYR Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain g residue 277 ILE Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 266 LYS Chi-restraints excluded: chain h residue 277 ILE Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 169 VAL Chi-restraints excluded: chain i residue 277 ILE Chi-restraints excluded: chain j residue 59 MET Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 266 LYS Chi-restraints excluded: chain j residue 277 ILE Chi-restraints excluded: chain o residue 8 ASN Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain o residue 38 ILE Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 122 ILE Chi-restraints excluded: chain r residue 11 ASN Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 35 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 181 LEU Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 169 VAL Chi-restraints excluded: chain t residue 85 MET Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 266 LYS Chi-restraints excluded: chain t residue 277 ILE Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 169 VAL Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 169 VAL Chi-restraints excluded: chain v residue 266 LYS Chi-restraints excluded: chain v residue 277 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 82 optimal weight: 30.0000 chunk 186 optimal weight: 0.0070 chunk 66 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 300 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 351 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN a 75 ASN ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 ASN ** g 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 145 GLN ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 8 ASN o 75 ASN ** o 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 140 HIS t 60 HIS ** t 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 60 HIS ** v 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.080472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.051679 restraints weight = 92817.168| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.48 r_work: 0.2704 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29664 Z= 0.108 Angle : 0.526 8.697 40248 Z= 0.267 Chirality : 0.042 0.188 4464 Planarity : 0.004 0.034 5208 Dihedral : 9.033 156.722 4320 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.19 % Allowed : 11.24 % Favored : 86.57 % 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: -0.35 (0.14), residues: 3624 helix: 0.68 (0.13), residues: 1752 sheet: -0.91 (0.21), residues: 544 loop : -1.04 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 118 TYR 0.016 0.001 TYR a 112 PHE 0.034 0.001 PHE a 154 TRP 0.014 0.001 TRP L 141 HIS 0.011 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (29664) covalent geometry : angle 0.52573 / 0.27 (40248) hydrogen bonds : bond 0.02966 / 2.01 ( 1177) hydrogen bonds : angle 4.30002 / 3.07 ( 3387) *********************** 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 347 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 281 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8108 (mmmt) REVERT: C 34 LYS cc_start: 0.9325 (tmtm) cc_final: 0.9041 (tptm) REVERT: F 34 LYS cc_start: 0.9421 (tmtm) cc_final: 0.9006 (tptp) REVERT: I 27 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8278 (mmmt) REVERT: I 157 MET cc_start: 0.4781 (mtt) cc_final: 0.4122 (mpp) REVERT: L 34 LYS cc_start: 0.9416 (tmtm) cc_final: 0.9015 (tptp) REVERT: L 157 MET cc_start: 0.6432 (ptm) cc_final: 0.5461 (ttp) REVERT: a 34 LYS cc_start: 0.9349 (tptm) cc_final: 0.8976 (tptp) REVERT: a 74 LEU cc_start: 0.7448 (mt) cc_final: 0.7126 (mm) REVERT: d 11 ASN cc_start: 0.3700 (OUTLIER) cc_final: 0.2986 (m110) REVERT: d 27 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8327 (mmmt) REVERT: d 32 THR cc_start: 0.9036 (p) cc_final: 0.8728 (t) REVERT: d 34 LYS cc_start: 0.9257 (tmtm) cc_final: 0.8898 (tppt) REVERT: d 157 MET cc_start: 0.5424 (ttp) cc_final: 0.4607 (mtt) REVERT: d 162 LYS cc_start: 0.8445 (mtpt) cc_final: 0.7892 (mtmm) REVERT: h 68 GLU cc_start: 0.9476 (tp30) cc_final: 0.9179 (tp30) REVERT: h 93 GLU cc_start: 0.9195 (mp0) cc_final: 0.8933 (pm20) REVERT: h 266 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8526 (mmmm) REVERT: i 68 GLU cc_start: 0.9407 (OUTLIER) cc_final: 0.8852 (tp30) REVERT: i 79 GLN cc_start: 0.9386 (mp10) cc_final: 0.9085 (mp10) REVERT: i 186 ASP cc_start: 0.9455 (m-30) cc_final: 0.9230 (m-30) REVERT: j 266 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8520 (mmmm) REVERT: o 34 LYS cc_start: 0.9303 (tptm) cc_final: 0.9030 (tptp) REVERT: o 157 MET cc_start: 0.6573 (ptp) cc_final: 0.6262 (ptp) REVERT: r 11 ASN cc_start: 0.3705 (OUTLIER) cc_final: 0.2929 (m110) REVERT: r 27 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8310 (mmmt) REVERT: r 32 THR cc_start: 0.9009 (p) cc_final: 0.8707 (t) REVERT: r 34 LYS cc_start: 0.9262 (tmtm) cc_final: 0.8924 (tppt) REVERT: s 68 GLU cc_start: 0.9483 (tp30) cc_final: 0.9045 (tp30) REVERT: s 143 ASP cc_start: 0.9125 (m-30) cc_final: 0.8682 (m-30) REVERT: t 68 GLU cc_start: 0.9475 (tp30) cc_final: 0.9065 (tp30) REVERT: t 113 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8434 (mtm-85) REVERT: t 186 ASP cc_start: 0.9427 (m-30) cc_final: 0.9153 (m-30) REVERT: t 266 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8220 (mmmm) REVERT: u 68 GLU cc_start: 0.9483 (tp30) cc_final: 0.9044 (tp30) REVERT: u 79 GLN cc_start: 0.9190 (mp10) cc_final: 0.8758 (mp10) REVERT: u 143 ASP cc_start: 0.9130 (m-30) cc_final: 0.8697 (m-30) REVERT: v 68 GLU cc_start: 0.9450 (tp30) cc_final: 0.9247 (tp30) REVERT: v 266 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8213 (mmmm) outliers start: 66 outliers final: 47 residues processed: 326 average time/residue: 0.1922 time to fit residues: 101.4772 Evaluate side-chains 309 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain a residue 38 ILE Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain a residue 129 ILE Chi-restraints excluded: chain d residue 11 ASN Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 181 LEU Chi-restraints excluded: chain g residue 120 TYR Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 266 LYS Chi-restraints excluded: chain h residue 277 ILE Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 169 VAL Chi-restraints excluded: chain i residue 277 ILE Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 266 LYS Chi-restraints excluded: chain j residue 277 ILE Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 122 ILE Chi-restraints excluded: chain r residue 11 ASN Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 140 HIS Chi-restraints excluded: chain r residue 157 MET Chi-restraints excluded: chain r residue 181 LEU Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 169 VAL Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 266 LYS Chi-restraints excluded: chain t residue 277 ILE Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 169 VAL Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 169 VAL Chi-restraints excluded: chain v residue 266 LYS Chi-restraints excluded: chain v residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 27 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 346 optimal weight: 10.0000 chunk 279 optimal weight: 0.0970 chunk 228 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 ASN a 8 ASN g 76 ASN ** h 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 8 ASN ** o 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 140 HIS t 223 GLN v 223 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.080358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.051761 restraints weight = 93247.137| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.48 r_work: 0.2702 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29664 Z= 0.120 Angle : 0.526 8.356 40248 Z= 0.266 Chirality : 0.042 0.182 4464 Planarity : 0.004 0.034 5208 Dihedral : 8.906 163.059 4320 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.12 % Allowed : 11.51 % Favored : 86.37 % 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: 0.87 (0.13), residues: 1752 sheet: -0.83 (0.21), residues: 544 loop : -1.00 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 152 TYR 0.015 0.001 TYR a 112 PHE 0.026 0.001 PHE r 139 TRP 0.017 0.001 TRP r 86 HIS 0.019 0.001 HIS r 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (29664) covalent geometry : angle 0.52589 / 0.27 (40248) hydrogen bonds : bond 0.02907 / 1.97 ( 1177) hydrogen bonds : angle 4.20449 / 3.01 ( 3387) *********************** 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 334 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8086 (mmmt) REVERT: C 34 LYS cc_start: 0.9323 (tmtm) cc_final: 0.9046 (tptm) REVERT: F 34 LYS cc_start: 0.9429 (tmtm) cc_final: 0.9013 (tptp) REVERT: F 157 MET cc_start: 0.5636 (ptm) cc_final: 0.4588 (ttp) REVERT: I 27 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8330 (mmmt) REVERT: I 34 LYS cc_start: 0.9365 (tptm) cc_final: 0.8980 (tptp) REVERT: I 157 MET cc_start: 0.4763 (mtt) cc_final: 0.4231 (mpp) REVERT: L 34 LYS cc_start: 0.9410 (tmtm) cc_final: 0.8989 (tptp) REVERT: a 19 GLN cc_start: 0.8937 (pt0) cc_final: 0.8725 (pp30) REVERT: a 34 LYS cc_start: 0.9373 (tptm) cc_final: 0.9038 (tptp) REVERT: d 11 ASN cc_start: 0.3459 (OUTLIER) cc_final: 0.2487 (m110) REVERT: d 27 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8232 (mmmt) REVERT: d 32 THR cc_start: 0.9055 (p) cc_final: 0.8709 (t) REVERT: d 34 LYS cc_start: 0.9264 (tmtm) cc_final: 0.8909 (tppt) REVERT: d 157 MET cc_start: 0.5660 (ttp) cc_final: 0.4833 (mtt) REVERT: d 162 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8271 (mtpt) REVERT: h 68 GLU cc_start: 0.9455 (tp30) cc_final: 0.9155 (tp30) REVERT: h 266 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8508 (mmmm) REVERT: i 68 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.8830 (tp30) REVERT: i 79 GLN cc_start: 0.9400 (mp10) cc_final: 0.9091 (mp10) REVERT: i 186 ASP cc_start: 0.9449 (m-30) cc_final: 0.9218 (m-30) REVERT: j 266 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8503 (mmmm) REVERT: o 19 GLN cc_start: 0.8957 (pt0) cc_final: 0.8733 (pp30) REVERT: o 34 LYS cc_start: 0.9271 (tptm) cc_final: 0.8936 (tptp) REVERT: o 157 MET cc_start: 0.6637 (ptp) cc_final: 0.6428 (ptp) REVERT: r 27 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8266 (mmmt) REVERT: r 32 THR cc_start: 0.9016 (p) cc_final: 0.8671 (t) REVERT: r 34 LYS cc_start: 0.9271 (tmtm) cc_final: 0.8914 (tppt) REVERT: s 68 GLU cc_start: 0.9461 (tp30) cc_final: 0.9063 (tt0) REVERT: s 113 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8407 (mmp80) REVERT: t 68 GLU cc_start: 0.9465 (tp30) cc_final: 0.9024 (tp30) REVERT: t 113 ARG cc_start: 0.8663 (mtm-85) cc_final: 0.8447 (mtm-85) REVERT: t 186 ASP cc_start: 0.9430 (m-30) cc_final: 0.9146 (m-30) REVERT: t 266 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8183 (mmmm) REVERT: u 68 GLU cc_start: 0.9462 (tp30) cc_final: 0.9066 (tt0) REVERT: u 79 GLN cc_start: 0.9199 (mp10) cc_final: 0.8753 (mp10) REVERT: v 68 GLU cc_start: 0.9439 (tp30) cc_final: 0.9205 (tp30) REVERT: v 266 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8194 (mmmm) outliers start: 64 outliers final: 54 residues processed: 317 average time/residue: 0.1987 time to fit residues: 101.7069 Evaluate side-chains 315 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain d residue 11 ASN Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 38 ILE Chi-restraints excluded: chain d residue 181 LEU Chi-restraints excluded: chain g residue 120 TYR Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 266 LYS Chi-restraints excluded: chain h residue 277 ILE Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 169 VAL Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 266 LYS Chi-restraints excluded: chain j residue 277 ILE Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 122 ILE Chi-restraints excluded: chain r residue 11 ASN Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 140 HIS Chi-restraints excluded: chain r residue 157 MET Chi-restraints excluded: chain r residue 181 LEU Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 166 ASP Chi-restraints excluded: chain s residue 169 VAL Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 266 LYS Chi-restraints excluded: chain t residue 277 ILE Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 169 VAL Chi-restraints excluded: chain v residue 59 MET Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 169 VAL Chi-restraints excluded: chain v residue 266 LYS Chi-restraints excluded: chain v residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 331 optimal weight: 5.9990 chunk 359 optimal weight: 1.9990 chunk 255 optimal weight: 0.0970 chunk 87 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 333 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 303 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 ASN g 76 ASN ** h 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 223 GLN v 223 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.081362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.052808 restraints weight = 93626.600| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.51 r_work: 0.2724 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 29664 Z= 0.099 Angle : 0.524 9.459 40248 Z= 0.264 Chirality : 0.042 0.176 4464 Planarity : 0.004 0.032 5208 Dihedral : 8.813 166.126 4320 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.72 % Allowed : 12.23 % Favored : 86.04 % 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: 1.12 (0.13), residues: 1688 sheet: -0.70 (0.21), residues: 544 loop : -0.89 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG t 113 TYR 0.015 0.001 TYR a 112 PHE 0.025 0.001 PHE C 154 TRP 0.014 0.001 TRP L 141 HIS 0.008 0.001 HIS r 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (29664) covalent geometry : angle 0.52438 / 0.26 (40248) hydrogen bonds : bond 0.02680 / 1.80 ( 1177) hydrogen bonds : angle 4.10267 / 2.92 ( 3387) *********************** 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 323 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8120 (mmmt) REVERT: C 34 LYS cc_start: 0.9313 (tmtm) cc_final: 0.9040 (tptm) REVERT: F 8 ASN cc_start: 0.8159 (t0) cc_final: 0.7905 (t0) REVERT: F 34 LYS cc_start: 0.9433 (tmtm) cc_final: 0.9002 (tptp) REVERT: I 27 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8316 (mmmt) REVERT: I 34 LYS cc_start: 0.9355 (tptm) cc_final: 0.8953 (tptp) REVERT: I 157 MET cc_start: 0.4893 (mtt) cc_final: 0.3025 (ptt) REVERT: L 8 ASN cc_start: 0.8223 (t0) cc_final: 0.8008 (t0) REVERT: L 34 LYS cc_start: 0.9418 (tmtm) cc_final: 0.9000 (tptp) REVERT: a 34 LYS cc_start: 0.9384 (tptm) cc_final: 0.9067 (tptp) REVERT: d 11 ASN cc_start: 0.3550 (OUTLIER) cc_final: 0.2590 (m110) REVERT: d 32 THR cc_start: 0.8985 (p) cc_final: 0.8699 (t) REVERT: d 34 LYS cc_start: 0.9325 (tmtm) cc_final: 0.8959 (tppt) REVERT: d 157 MET cc_start: 0.5087 (ttp) cc_final: 0.4527 (mtt) REVERT: d 162 LYS cc_start: 0.8582 (mtpt) cc_final: 0.7977 (mtpt) REVERT: h 68 GLU cc_start: 0.9444 (tp30) cc_final: 0.9179 (tp30) REVERT: h 266 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8527 (mmmm) REVERT: i 68 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.8881 (tp30) REVERT: i 79 GLN cc_start: 0.9402 (mp10) cc_final: 0.9090 (mp10) REVERT: i 186 ASP cc_start: 0.9460 (m-30) cc_final: 0.9232 (m-30) REVERT: j 266 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8525 (mmmm) REVERT: o 34 LYS cc_start: 0.9257 (tptm) cc_final: 0.8936 (tptp) REVERT: o 39 LEU cc_start: 0.6103 (mt) cc_final: 0.5567 (pp) REVERT: o 50 LYS cc_start: 0.8934 (tmtt) cc_final: 0.8660 (ptmm) REVERT: r 11 ASN cc_start: 0.3424 (OUTLIER) cc_final: 0.2482 (m110) REVERT: r 27 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8233 (mmmt) REVERT: r 32 THR cc_start: 0.8955 (p) cc_final: 0.8680 (t) REVERT: r 34 LYS cc_start: 0.9270 (tmtm) cc_final: 0.8918 (tppt) REVERT: r 157 MET cc_start: 0.5345 (OUTLIER) cc_final: 0.5041 (ptp) REVERT: s 68 GLU cc_start: 0.9440 (tp30) cc_final: 0.9104 (tt0) REVERT: s 143 ASP cc_start: 0.9198 (m-30) cc_final: 0.8750 (m-30) REVERT: t 68 GLU cc_start: 0.9452 (tp30) cc_final: 0.9020 (tp30) REVERT: t 186 ASP cc_start: 0.9428 (m-30) cc_final: 0.9175 (m-30) REVERT: t 266 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8162 (mmmm) REVERT: u 68 GLU cc_start: 0.9438 (tp30) cc_final: 0.9079 (tt0) REVERT: u 79 GLN cc_start: 0.9226 (mp10) cc_final: 0.8757 (mp10) REVERT: u 143 ASP cc_start: 0.9193 (m-30) cc_final: 0.8747 (m-30) REVERT: v 68 GLU cc_start: 0.9422 (tp30) cc_final: 0.9196 (tp30) REVERT: v 266 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8164 (mmmm) outliers start: 52 outliers final: 33 residues processed: 315 average time/residue: 0.2017 time to fit residues: 101.9513 Evaluate side-chains 300 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 259 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain d residue 11 ASN Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 181 LEU Chi-restraints excluded: chain g residue 120 TYR Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 266 LYS Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 169 VAL Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 266 LYS Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 122 ILE Chi-restraints excluded: chain r residue 11 ASN Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 157 MET Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 169 VAL Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 266 LYS Chi-restraints excluded: chain t residue 277 ILE Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 169 VAL Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 169 VAL Chi-restraints excluded: chain v residue 266 LYS Chi-restraints excluded: chain v residue 277 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 127 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 198 optimal weight: 0.1980 chunk 249 optimal weight: 0.0970 chunk 69 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 ASN ** h 253 GLN ** 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** r 140 HIS t 223 GLN ** t 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 223 GLN v 223 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.081350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.052936 restraints weight = 93297.636| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.50 r_work: 0.2726 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29664 Z= 0.104 Angle : 0.522 9.428 40248 Z= 0.263 Chirality : 0.042 0.175 4464 Planarity : 0.004 0.032 5208 Dihedral : 8.763 170.870 4320 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.59 % Allowed : 12.33 % Favored : 86.07 % 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: 0.21 (0.14), residues: 3624 helix: 1.24 (0.13), residues: 1688 sheet: -0.61 (0.21), residues: 544 loop : -0.83 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 118 TYR 0.015 0.001 TYR a 112 PHE 0.016 0.001 PHE a 139 TRP 0.014 0.001 TRP L 141 HIS 0.005 0.001 HIS r 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (29664) covalent geometry : angle 0.52192 / 0.26 (40248) hydrogen bonds : bond 0.02671 / 1.80 ( 1177) hydrogen bonds : angle 4.07207 / 2.89 ( 3387) *********************** 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 323 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 LYS cc_start: 0.9311 (tmtm) cc_final: 0.9045 (tptm) REVERT: F 8 ASN cc_start: 0.8166 (t0) cc_final: 0.7933 (t0) REVERT: F 34 LYS cc_start: 0.9429 (tmtm) cc_final: 0.8999 (tptp) REVERT: I 34 LYS cc_start: 0.9352 (tptm) cc_final: 0.8939 (tptp) REVERT: I 157 MET cc_start: 0.4869 (mtt) cc_final: 0.3212 (ptp) REVERT: L 8 ASN cc_start: 0.8152 (t0) cc_final: 0.7940 (t0) REVERT: L 34 LYS cc_start: 0.9416 (tmtm) cc_final: 0.8995 (tptp) REVERT: L 50 LYS cc_start: 0.8945 (tmtt) cc_final: 0.8718 (ptmm) REVERT: a 19 GLN cc_start: 0.9390 (tt0) cc_final: 0.8980 (pt0) REVERT: a 34 LYS cc_start: 0.9418 (tptm) cc_final: 0.9076 (tptp) REVERT: a 39 LEU cc_start: 0.6364 (mt) cc_final: 0.5718 (pp) REVERT: d 11 ASN cc_start: 0.3512 (OUTLIER) cc_final: 0.2524 (m110) REVERT: d 32 THR cc_start: 0.9001 (p) cc_final: 0.8704 (t) REVERT: d 34 LYS cc_start: 0.9308 (tmtm) cc_final: 0.8941 (tppt) REVERT: d 157 MET cc_start: 0.5241 (ttp) cc_final: 0.4676 (mtt) REVERT: d 162 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8018 (mtpt) REVERT: h 68 GLU cc_start: 0.9439 (tp30) cc_final: 0.9180 (tp30) REVERT: h 266 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8564 (mmmm) REVERT: i 68 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.8892 (tp30) REVERT: i 79 GLN cc_start: 0.9405 (mp10) cc_final: 0.9097 (mp10) REVERT: i 186 ASP cc_start: 0.9454 (m-30) cc_final: 0.9227 (m-30) REVERT: j 266 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8533 (mmmm) REVERT: o 19 GLN cc_start: 0.9421 (tt0) cc_final: 0.9021 (pt0) REVERT: o 39 LEU cc_start: 0.6180 (mt) cc_final: 0.5714 (pt) REVERT: o 50 LYS cc_start: 0.8952 (tmtt) cc_final: 0.8597 (ptmm) REVERT: r 11 ASN cc_start: 0.3510 (OUTLIER) cc_final: 0.2424 (m110) REVERT: r 27 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8206 (mmmt) REVERT: r 32 THR cc_start: 0.9003 (p) cc_final: 0.8714 (t) REVERT: r 34 LYS cc_start: 0.9266 (tmtm) cc_final: 0.8935 (tppt) REVERT: r 157 MET cc_start: 0.5334 (OUTLIER) cc_final: 0.4537 (ptt) REVERT: s 68 GLU cc_start: 0.9435 (tp30) cc_final: 0.9116 (tt0) REVERT: s 113 ARG cc_start: 0.8668 (mmp80) cc_final: 0.8406 (mmp80) REVERT: s 143 ASP cc_start: 0.9197 (m-30) cc_final: 0.8746 (m-30) REVERT: t 68 GLU cc_start: 0.9454 (tp30) cc_final: 0.9009 (tp30) REVERT: t 186 ASP cc_start: 0.9433 (m-30) cc_final: 0.9185 (m-30) REVERT: t 196 ASN cc_start: 0.9620 (m-40) cc_final: 0.9289 (m-40) REVERT: t 266 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8169 (mmmm) REVERT: u 68 GLU cc_start: 0.9439 (tp30) cc_final: 0.9126 (tt0) REVERT: u 79 GLN cc_start: 0.9247 (mp10) cc_final: 0.8768 (mp10) REVERT: u 143 ASP cc_start: 0.9198 (m-30) cc_final: 0.8750 (m-30) REVERT: v 68 GLU cc_start: 0.9421 (tp30) cc_final: 0.9187 (tp30) REVERT: v 196 ASN cc_start: 0.9621 (m-40) cc_final: 0.9276 (m-40) REVERT: v 266 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8146 (mmmm) outliers start: 48 outliers final: 38 residues processed: 314 average time/residue: 0.1929 time to fit residues: 98.5434 Evaluate side-chains 305 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain d residue 11 ASN Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 181 LEU Chi-restraints excluded: chain g residue 120 TYR Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 266 LYS Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 169 VAL Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 166 ASP Chi-restraints excluded: chain j residue 266 LYS Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 122 ILE Chi-restraints excluded: chain r residue 11 ASN Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 140 HIS Chi-restraints excluded: chain r residue 157 MET Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 166 ASP Chi-restraints excluded: chain s residue 169 VAL Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 266 LYS Chi-restraints excluded: chain t residue 277 ILE Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 169 VAL Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 169 VAL Chi-restraints excluded: chain v residue 266 LYS Chi-restraints excluded: chain v residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 27 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 294 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 HIS g 76 ASN h 223 GLN ** h 253 GLN ** 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** ** r 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 223 GLN ** t 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 223 GLN v 223 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.081518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.053116 restraints weight = 93092.847| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.53 r_work: 0.2727 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29664 Z= 0.104 Angle : 0.530 11.188 40248 Z= 0.269 Chirality : 0.042 0.211 4464 Planarity : 0.004 0.032 5208 Dihedral : 8.735 173.910 4320 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.49 % Allowed : 12.70 % Favored : 85.81 % 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: 0.32 (0.14), residues: 3624 helix: 1.33 (0.13), residues: 1688 sheet: -0.53 (0.21), residues: 544 loop : -0.81 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 16 TYR 0.014 0.001 TYR a 112 PHE 0.022 0.001 PHE r 139 TRP 0.017 0.001 TRP r 86 HIS 0.005 0.001 HIS d 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (29664) covalent geometry : angle 0.53037 / 0.27 (40248) hydrogen bonds : bond 0.02627 / 1.77 ( 1177) hydrogen bonds : angle 4.05324 / 2.87 ( 3387) ********************** 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 313 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8475 (mmmt) REVERT: C 34 LYS cc_start: 0.9308 (tmtm) cc_final: 0.9051 (tptm) REVERT: C 50 LYS cc_start: 0.9067 (ptmt) cc_final: 0.8857 (ptmm) REVERT: C 175 LEU cc_start: 0.9059 (tt) cc_final: 0.8770 (mm) REVERT: F 8 ASN cc_start: 0.8142 (t0) cc_final: 0.7929 (t0) REVERT: F 34 LYS cc_start: 0.9428 (tmtm) cc_final: 0.9012 (tptp) REVERT: I 34 LYS cc_start: 0.9312 (tptm) cc_final: 0.9059 (tptm) REVERT: L 8 ASN cc_start: 0.8139 (t0) cc_final: 0.7937 (t0) REVERT: L 34 LYS cc_start: 0.9421 (tmtm) cc_final: 0.9008 (tptp) REVERT: L 50 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8754 (ptmm) REVERT: a 19 GLN cc_start: 0.9413 (tt0) cc_final: 0.8973 (pt0) REVERT: a 34 LYS cc_start: 0.9436 (tptm) cc_final: 0.9097 (tptp) REVERT: d 11 ASN cc_start: 0.3429 (OUTLIER) cc_final: 0.2474 (m110) REVERT: d 32 THR cc_start: 0.9016 (p) cc_final: 0.8708 (t) REVERT: d 34 LYS cc_start: 0.9345 (tmtm) cc_final: 0.8930 (tppt) REVERT: d 157 MET cc_start: 0.5421 (ttp) cc_final: 0.5002 (mtp) REVERT: d 162 LYS cc_start: 0.8526 (mtpt) cc_final: 0.7975 (mtpt) REVERT: h 68 GLU cc_start: 0.9423 (tp30) cc_final: 0.9174 (tp30) REVERT: h 266 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8584 (mmmm) REVERT: i 68 GLU cc_start: 0.9406 (OUTLIER) cc_final: 0.8908 (tp30) REVERT: i 79 GLN cc_start: 0.9412 (mp10) cc_final: 0.9104 (mp10) REVERT: i 186 ASP cc_start: 0.9451 (m-30) cc_final: 0.9228 (m-30) REVERT: j 143 ASP cc_start: 0.9175 (m-30) cc_final: 0.8669 (m-30) REVERT: j 266 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8540 (mmmm) REVERT: o 19 GLN cc_start: 0.9442 (tt0) cc_final: 0.8994 (pt0) REVERT: o 34 LYS cc_start: 0.9398 (tptm) cc_final: 0.9043 (tptp) REVERT: o 39 LEU cc_start: 0.5971 (mt) cc_final: 0.5688 (pt) REVERT: o 157 MET cc_start: 0.6020 (ptp) cc_final: 0.5571 (ptp) REVERT: r 11 ASN cc_start: 0.3469 (OUTLIER) cc_final: 0.2418 (m110) REVERT: r 27 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8138 (mmmt) REVERT: r 32 THR cc_start: 0.9020 (p) cc_final: 0.8732 (t) REVERT: r 34 LYS cc_start: 0.9258 (tmtm) cc_final: 0.8938 (tppt) REVERT: r 50 LYS cc_start: 0.9075 (ptmt) cc_final: 0.8859 (ptmm) REVERT: r 157 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.4579 (ptt) REVERT: s 68 GLU cc_start: 0.9440 (tp30) cc_final: 0.9130 (tt0) REVERT: s 113 ARG cc_start: 0.8665 (mmp80) cc_final: 0.8450 (mmp80) REVERT: s 143 ASP cc_start: 0.9207 (m-30) cc_final: 0.8761 (m-30) REVERT: t 68 GLU cc_start: 0.9454 (tp30) cc_final: 0.9109 (tp30) REVERT: t 186 ASP cc_start: 0.9433 (m-30) cc_final: 0.9198 (m-30) REVERT: t 266 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8173 (mmmm) REVERT: u 68 GLU cc_start: 0.9439 (tp30) cc_final: 0.9138 (tt0) REVERT: u 79 GLN cc_start: 0.9261 (mp10) cc_final: 0.8781 (mp10) REVERT: u 143 ASP cc_start: 0.9204 (m-30) cc_final: 0.8761 (m-30) REVERT: v 68 GLU cc_start: 0.9420 (tp30) cc_final: 0.9190 (tp30) REVERT: v 196 ASN cc_start: 0.9623 (m-40) cc_final: 0.9294 (m-40) REVERT: v 266 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8168 (mmmm) outliers start: 45 outliers final: 36 residues processed: 306 average time/residue: 0.1932 time to fit residues: 96.1512 Evaluate side-chains 302 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain d residue 11 ASN Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 181 LEU Chi-restraints excluded: chain g residue 120 TYR Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 266 LYS Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 169 VAL Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 266 LYS Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 122 ILE Chi-restraints excluded: chain r residue 11 ASN Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 157 MET Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 169 VAL Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 266 LYS Chi-restraints excluded: chain t residue 277 ILE Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 169 VAL Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 169 VAL Chi-restraints excluded: chain v residue 266 LYS Chi-restraints excluded: chain v residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 261 optimal weight: 0.9990 chunk 341 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 258 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 318 optimal weight: 8.9990 chunk 264 optimal weight: 0.7980 chunk 356 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 192 optimal weight: 0.1980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 ASN h 223 GLN ** h 253 GLN ** 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** r 140 HIS t 223 GLN ** t 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 223 GLN v 223 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.080548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052276 restraints weight = 93797.023| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.49 r_work: 0.2702 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29664 Z= 0.126 Angle : 0.542 9.190 40248 Z= 0.273 Chirality : 0.042 0.177 4464 Planarity : 0.004 0.033 5208 Dihedral : 8.784 177.238 4320 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.86 % Allowed : 12.50 % Favored : 85.64 % 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: 0.40 (0.14), residues: 3624 helix: 1.41 (0.13), residues: 1688 sheet: -0.50 (0.21), residues: 544 loop : -0.77 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG h 62 TYR 0.015 0.001 TYR a 112 PHE 0.023 0.001 PHE d 139 TRP 0.018 0.001 TRP d 86 HIS 0.007 0.001 HIS r 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (29664) covalent geometry : angle 0.54151 / 0.27 (40248) hydrogen bonds : bond 0.02775 / 1.88 ( 1177) hydrogen bonds : angle 4.10513 / 2.92 ( 3387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7326.20 seconds wall clock time: 126 minutes 25.08 seconds (7585.08 seconds total)