Starting phenix.real_space_refine on Sun Jul 5 18:16:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0y_64676/07_2026/9v0y_64676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0y_64676/07_2026/9v0y_64676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v0y_64676/07_2026/9v0y_64676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0y_64676/07_2026/9v0y_64676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v0y_64676/07_2026/9v0y_64676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0y_64676/07_2026/9v0y_64676.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 18432 2.51 5 N 5136 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): 0.04s 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: 29096 Number of models: 1 Model: "" Number of chains: 32 Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1394 Classifications: {'peptide': 180} 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: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1394 Classifications: {'peptide': 180} 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: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1394 Classifications: {'peptide': 180} 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: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1394 Classifications: {'peptide': 180} 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: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1394 Classifications: {'peptide': 180} 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: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1394 Classifications: {'peptide': 180} 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: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1394 Classifications: {'peptide': 180} 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: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1394 Classifications: {'peptide': 180} 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: "g" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, 'Y43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "s" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.69, per 1000 atoms: 0.20 Number of scatterers: 29096 At special positions: 0 Unit cell: (172.25, 168.35, 119.6, 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 5136 7.00 C 18432 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 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 51.6% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 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: 3.786A pdb=" N VAL C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.754A 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: 3.766A 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: 3.658A 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: 3.714A pdb=" N ARG C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 22 removed outlier: 3.640A 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: 3.786A pdb=" N VAL F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 59 removed outlier: 3.755A 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: 3.659A 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: 3.658A 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: 3.786A 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: 4.858A 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: 3.557A 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: 3.766A 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: 3.714A 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: 3.556A pdb=" N GLU d 17 " --> pdb=" O GLU d 13 " (cutoff:3.500A) removed outlier: 3.786A 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: 3.607A 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: 3.573A 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: 3.517A 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: 4.047A 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: 3.551A 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: 3.523A 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: 3.732A 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: 3.552A 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: 4.155A 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: 4.047A 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: 3.609A 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: 4.155A 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 193 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: 3.785A 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: 3.658A 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: 4.858A pdb=" N THR o 173 " --> pdb=" O GLY o 169 " (cutoff:3.500A) removed outlier: 3.714A 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: 3.556A 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: 3.658A 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: 4.858A 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: 3.543A 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: 3.539A 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: 4.047A 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: 3.542A pdb=" N GLU t 99 " --> pdb=" O GLU t 95 " (cutoff:3.500A) removed outlier: 4.155A 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: 3.539A 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: 3.606A 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: 3.573A 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: 3.518A 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: 3.538A 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: 3.733A 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: 4.047A 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: 3.609A 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: 3.639A 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: 4.154A 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: 3.718A 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: 7.345A 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: 8.377A 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: 8.436A 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: 10.789A 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: 6.474A 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: 8.437A 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: 10.788A 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: 6.474A 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: 10.790A 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: 6.474A 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: 8.377A 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: 5.991A 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: 7.269A pdb=" N ILE h 259 " --> pdb=" O CYS h 236 " (cutoff:3.500A) removed outlier: 6.221A 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: 6.290A pdb=" N CYS i 236 " --> pdb=" O ASP i 257 " (cutoff:3.500A) removed outlier: 7.268A 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: 6.290A 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: 8.376A pdb=" N ASN o 8 " --> pdb=" O GLU o 65 " (cutoff:3.500A) removed outlier: 10.789A 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: 7.345A 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: 6.535A 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: 6.536A 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: 6.221A 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: 5.35 Time building geometry restraints manager: 3.14 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: 7688 1.42 - 1.55: 17032 1.55 - 1.68: 64 1.68 - 1.81: 144 Bond restraints: 29728 Sorted by residual: bond pdb=" CAD Y43 I 201 " pdb=" OAE Y43 I 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 r 201 " pdb=" OAE Y43 r 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 a 201 " pdb=" OAE Y43 a 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 1.16e+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 ... (remaining 29723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 39060 2.51 - 5.02: 1025 5.02 - 7.54: 191 7.54 - 10.05: 28 10.05 - 12.56: 16 Bond angle restraints: 40320 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 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 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 angle pdb=" OAJ Y43 d 201 " pdb=" PAI Y43 d 201 " pdb=" OAK Y43 d 201 " ideal model delta sigma weight residual 121.66 109.14 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" OAJ Y43 o 201 " pdb=" PAI Y43 o 201 " pdb=" OAK Y43 o 201 " ideal model delta sigma weight residual 121.66 109.14 12.52 3.00e+00 1.11e-01 1.74e+01 ... (remaining 40315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 17557 33.88 - 67.77: 354 67.77 - 101.65: 69 101.65 - 135.53: 16 135.53 - 169.41: 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 52.70 -52.70 1 1.00e+01 1.00e-02 3.78e+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 50.78 -50.78 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 50.37 -50.37 1 1.00e+01 1.00e-02 3.48e+01 ... (remaining 17997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2945 0.051 - 0.101: 1103 0.101 - 0.152: 369 0.152 - 0.203: 38 0.203 - 0.254: 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 2.26 0.25 2.00e-01 2.50e+01 1.61e+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 1.60e+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 1.60e+00 ... (remaining 4461 not shown) Planarity restraints: 5216 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 9.13e+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 3.76e-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 5213 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 169 2.53 - 3.12: 20193 3.12 - 3.71: 44555 3.71 - 4.31: 66999 4.31 - 4.90: 111626 Nonbonded interactions: 243542 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 2.049 2.230 nonbonded pdb=" OAO Y43 d 201 " pdb="ZN ZN d 202 " model vdw 2.052 2.230 nonbonded pdb=" OAN Y43 a 201 " pdb="ZN ZN a 202 " model vdw 2.066 2.230 ... (remaining 243537 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: 0.10 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.090 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 0.215 29728 Z= 0.541 Angle : 1.008 12.562 40320 Z= 0.540 Chirality : 0.059 0.254 4464 Planarity : 0.016 0.388 5216 Dihedral : 13.977 169.415 11168 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.85 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 g 216 TYR 0.021 0.003 TYR u 212 PHE 0.053 0.004 PHE o 139 TRP 0.028 0.004 TRP j 214 HIS 0.012 0.003 HIS r 172 Details of bonding type rmsd/Z covalent geometry : bond 0.01171 / 0.54 (29728) covalent geometry : angle 1.00801 / 0.54 (40320) hydrogen bonds : bond 0.30406 / 20.75 ( 1177) hydrogen bonds : angle 8.99210 / 6.28 ( 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 586 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 1.187 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: C 139 PHE cc_start: 0.2708 (p90) cc_final: 0.2441 (p90) REVERT: C 172 HIS cc_start: 0.3911 (m90) cc_final: 0.3017 (m90) REVERT: F 139 PHE cc_start: 0.2339 (p90) cc_final: 0.2026 (p90) REVERT: I 139 PHE cc_start: 0.2692 (p90) cc_final: 0.2275 (p90) REVERT: I 172 HIS cc_start: 0.3893 (m90) cc_final: 0.2993 (m90) REVERT: L 139 PHE cc_start: 0.2397 (p90) cc_final: 0.2036 (p90) REVERT: a 139 PHE cc_start: 0.2758 (p90) cc_final: 0.2476 (p90) REVERT: d 139 PHE cc_start: 0.2522 (p90) cc_final: 0.2131 (p90) REVERT: g 229 LYS cc_start: 0.9269 (tttp) cc_final: 0.8963 (ttmt) REVERT: h 8 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8655 (mt-10) REVERT: h 229 LYS cc_start: 0.9216 (tttp) cc_final: 0.8952 (ttmt) REVERT: i 229 LYS cc_start: 0.9273 (tttp) cc_final: 0.8980 (ttmt) REVERT: j 8 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8663 (mt-10) REVERT: j 229 LYS cc_start: 0.9211 (tttp) cc_final: 0.8949 (ttmt) REVERT: o 32 THR cc_start: 0.6522 (p) cc_final: 0.6293 (t) REVERT: r 32 THR cc_start: 0.6467 (p) cc_final: 0.6247 (t) REVERT: r 139 PHE cc_start: 0.2524 (p90) cc_final: 0.2058 (p90) REVERT: v 229 LYS cc_start: 0.9192 (tttp) cc_final: 0.8982 (ttmt) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.8131 time to fit residues: 541.4009 Evaluate side-chains 307 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN C 75 ASN F 75 ASN F 101 GLN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN I 101 GLN L 11 ASN L 75 ASN L 101 GLN a 11 ASN a 75 ASN d 11 ASN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 145 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 j 145 GLN j 223 GLN ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN o 75 ASN o 101 GLN r 11 ASN ** r 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 145 GLN ** s 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 145 GLN ** t 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 255 ASN u 145 GLN ** u 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 145 GLN ** v 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 255 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083509 restraints weight = 45292.436| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.52 r_work: 0.2947 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29728 Z= 0.132 Angle : 0.578 7.368 40320 Z= 0.300 Chirality : 0.043 0.184 4464 Planarity : 0.006 0.050 5216 Dihedral : 9.523 133.953 4320 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.19 % Allowed : 11.07 % Favored : 86.74 % 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: -2.82 (0.12), residues: 3624 helix: -2.01 (0.10), residues: 1760 sheet: -1.29 (0.20), residues: 616 loop : -1.58 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 107 TYR 0.017 0.002 TYR d 112 PHE 0.026 0.002 PHE a 139 TRP 0.018 0.002 TRP a 86 HIS 0.009 0.001 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (29728) covalent geometry : angle 0.57821 / 0.30 (40320) hydrogen bonds : bond 0.04252 / 2.93 ( 1177) hydrogen bonds : angle 5.25642 / 3.70 ( 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 457 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 391 time to evaluate : 0.797 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 LYS cc_start: 0.6628 (mttt) cc_final: 0.5923 (mmtm) REVERT: I 14 LYS cc_start: 0.6561 (mttt) cc_final: 0.5826 (mmtm) REVERT: a 139 PHE cc_start: 0.2914 (p90) cc_final: 0.2633 (p90) REVERT: d 14 LYS cc_start: 0.6687 (mttt) cc_final: 0.6123 (mmtm) REVERT: g 64 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: g 229 LYS cc_start: 0.9235 (tttp) cc_final: 0.8848 (ttmt) REVERT: h 2 THR cc_start: 0.7928 (p) cc_final: 0.7611 (t) REVERT: h 8 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8548 (mt-10) REVERT: h 62 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8139 (mtm-85) REVERT: h 113 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8093 (mtp85) REVERT: h 217 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8533 (tpp) REVERT: h 229 LYS cc_start: 0.9121 (tttp) cc_final: 0.8779 (ttmt) REVERT: i 186 ASP cc_start: 0.9086 (m-30) cc_final: 0.8780 (m-30) REVERT: i 229 LYS cc_start: 0.9248 (tttp) cc_final: 0.8866 (ttmt) REVERT: j 2 THR cc_start: 0.7921 (p) cc_final: 0.7600 (t) REVERT: j 8 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8546 (mt-10) REVERT: j 113 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8088 (mtp85) REVERT: j 217 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8534 (tpp) REVERT: j 229 LYS cc_start: 0.9128 (tttp) cc_final: 0.8786 (ttmt) REVERT: r 14 LYS cc_start: 0.6614 (mttt) cc_final: 0.5965 (mmtm) REVERT: s 68 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8295 (tp30) REVERT: t 2 THR cc_start: 0.8209 (p) cc_final: 0.7970 (t) REVERT: t 105 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8058 (mtt90) REVERT: u 2 THR cc_start: 0.8091 (p) cc_final: 0.7836 (t) REVERT: v 229 LYS cc_start: 0.9166 (tttp) cc_final: 0.8900 (ttmt) outliers start: 66 outliers final: 20 residues processed: 433 average time/residue: 0.6576 time to fit residues: 331.0437 Evaluate side-chains 318 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain j residue 111 ASP Chi-restraints excluded: chain j residue 113 ARG Chi-restraints excluded: chain j residue 217 MET Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain o residue 120 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 35 VAL Chi-restraints excluded: chain s residue 68 GLU Chi-restraints excluded: chain t residue 64 GLU Chi-restraints excluded: chain t residue 105 ARG Chi-restraints excluded: chain v residue 64 GLU Chi-restraints excluded: chain v residue 163 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 129 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 325 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 chunk 241 optimal weight: 0.0980 chunk 212 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** d 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 218 ASN ** g 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 218 ASN ** h 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 218 ASN ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 218 ASN j 223 GLN ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 75 ASN ** r 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.145562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082984 restraints weight = 45143.271| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.56 r_work: 0.2930 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29728 Z= 0.105 Angle : 0.522 6.150 40320 Z= 0.270 Chirality : 0.041 0.186 4464 Planarity : 0.004 0.037 5216 Dihedral : 8.818 146.819 4320 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.75 % Allowed : 13.89 % Favored : 83.36 % 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: -1.72 (0.13), residues: 3624 helix: -0.86 (0.12), residues: 1760 sheet: -1.30 (0.20), residues: 672 loop : -1.13 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 107 TYR 0.016 0.001 TYR d 112 PHE 0.019 0.001 PHE r 139 TRP 0.023 0.002 TRP d 86 HIS 0.016 0.001 HIS F 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (29728) covalent geometry : angle 0.52233 / 0.27 (40320) hydrogen bonds : bond 0.03265 / 2.24 ( 1177) hydrogen bonds : angle 4.69161 / 3.32 ( 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 429 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 346 time to evaluate : 1.137 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 LYS cc_start: 0.6578 (mttt) cc_final: 0.6060 (mmtm) REVERT: F 14 LYS cc_start: 0.6519 (mttt) cc_final: 0.5802 (mmtm) REVERT: I 14 LYS cc_start: 0.6532 (mttt) cc_final: 0.6012 (mmtm) REVERT: I 178 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8402 (mt-10) REVERT: a 13 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6140 (pp20) REVERT: g 64 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: g 105 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7895 (mtt90) REVERT: g 161 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8560 (p) REVERT: g 229 LYS cc_start: 0.9274 (tttp) cc_final: 0.8935 (ttmt) REVERT: h 2 THR cc_start: 0.7982 (p) cc_final: 0.7663 (t) REVERT: h 8 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8617 (mt-10) REVERT: h 113 ARG cc_start: 0.8348 (mtp85) cc_final: 0.8146 (mtp85) REVERT: h 161 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8595 (p) REVERT: h 186 ASP cc_start: 0.9006 (m-30) cc_final: 0.8799 (m-30) REVERT: h 229 LYS cc_start: 0.9142 (tttp) cc_final: 0.8820 (ttmt) REVERT: i 105 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7926 (mtt90) REVERT: i 161 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8568 (p) REVERT: i 186 ASP cc_start: 0.9127 (m-30) cc_final: 0.8854 (m-30) REVERT: i 229 LYS cc_start: 0.9275 (tttp) cc_final: 0.8932 (ttmt) REVERT: j 2 THR cc_start: 0.7973 (p) cc_final: 0.7643 (t) REVERT: j 8 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8619 (mt-10) REVERT: j 19 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8661 (mt-10) REVERT: j 113 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8132 (mtp85) REVERT: j 229 LYS cc_start: 0.9155 (tttp) cc_final: 0.8835 (ttmt) REVERT: t 2 THR cc_start: 0.8245 (p) cc_final: 0.7997 (t) REVERT: t 64 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: t 161 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8624 (p) REVERT: u 2 THR cc_start: 0.8130 (p) cc_final: 0.7874 (t) REVERT: v 64 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8467 (pm20) REVERT: v 229 LYS cc_start: 0.9228 (tttp) cc_final: 0.8935 (ttmt) outliers start: 83 outliers final: 19 residues processed: 401 average time/residue: 0.6954 time to fit residues: 323.5776 Evaluate side-chains 308 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 163 ASP Chi-restraints excluded: chain i residue 103 MET Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 111 ASP Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 182 ASP Chi-restraints excluded: chain j residue 111 ASP Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain t residue 64 GLU Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 224 SER Chi-restraints excluded: chain v residue 64 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 54 optimal weight: 10.0000 chunk 337 optimal weight: 6.9990 chunk 330 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 306 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 357 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 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 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.142381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079978 restraints weight = 45050.767| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.53 r_work: 0.2868 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29728 Z= 0.126 Angle : 0.544 9.373 40320 Z= 0.277 Chirality : 0.042 0.192 4464 Planarity : 0.004 0.034 5216 Dihedral : 8.744 147.166 4320 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.92 % Allowed : 15.25 % Favored : 81.83 % 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: -1.08 (0.14), residues: 3624 helix: -0.22 (0.12), residues: 1776 sheet: -1.08 (0.20), residues: 688 loop : -0.98 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 107 TYR 0.015 0.002 TYR o 112 PHE 0.035 0.002 PHE L 139 TRP 0.033 0.002 TRP d 86 HIS 0.011 0.001 HIS F 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (29728) covalent geometry : angle 0.54414 / 0.28 (40320) hydrogen bonds : bond 0.03319 / 2.26 ( 1177) hydrogen bonds : angle 4.46522 / 3.17 ( 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 395 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 307 time to evaluate : 1.144 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5782 (pp20) REVERT: C 14 LYS cc_start: 0.6552 (mttt) cc_final: 0.5849 (mmtm) REVERT: C 65 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6595 (pp20) REVERT: F 146 ILE cc_start: 0.3785 (pp) cc_final: 0.3514 (mp) REVERT: I 13 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5841 (pp20) REVERT: L 14 LYS cc_start: 0.6621 (mttt) cc_final: 0.5894 (mmtm) REVERT: a 13 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6360 (pp20) REVERT: a 14 LYS cc_start: 0.6712 (mttt) cc_final: 0.5894 (mmtm) REVERT: g 58 ASP cc_start: 0.9010 (t70) cc_final: 0.8678 (t0) REVERT: g 105 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7908 (mtt90) REVERT: g 229 LYS cc_start: 0.9259 (tttp) cc_final: 0.8881 (ttmt) REVERT: h 2 THR cc_start: 0.7966 (p) cc_final: 0.7662 (t) REVERT: h 8 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8569 (mt-10) REVERT: h 105 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7943 (mtt90) REVERT: h 113 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8236 (mtp85) REVERT: h 229 LYS cc_start: 0.9143 (tttp) cc_final: 0.8822 (ttmt) REVERT: i 6 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8542 (tt) REVERT: i 58 ASP cc_start: 0.8990 (t70) cc_final: 0.8643 (t0) REVERT: i 68 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.7962 (tp30) REVERT: i 105 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7902 (mtt90) REVERT: i 229 LYS cc_start: 0.9278 (tttp) cc_final: 0.8937 (ttmt) REVERT: j 2 THR cc_start: 0.7968 (p) cc_final: 0.7665 (t) REVERT: j 8 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8581 (mt-10) REVERT: j 105 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7954 (mtt90) REVERT: j 229 LYS cc_start: 0.9155 (tttp) cc_final: 0.8841 (ttmt) REVERT: s 93 GLU cc_start: 0.8571 (pt0) cc_final: 0.8338 (pm20) REVERT: t 2 THR cc_start: 0.8225 (p) cc_final: 0.7975 (t) REVERT: t 64 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8418 (pm20) REVERT: u 93 GLU cc_start: 0.8557 (pt0) cc_final: 0.8308 (pm20) REVERT: v 64 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: v 105 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8015 (mtt90) REVERT: v 229 LYS cc_start: 0.9202 (tttp) cc_final: 0.8900 (ttmt) outliers start: 88 outliers final: 45 residues processed: 370 average time/residue: 0.7200 time to fit residues: 310.0706 Evaluate side-chains 343 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain g residue 14 LYS Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 163 ASP Chi-restraints excluded: chain h residue 166 ASP Chi-restraints excluded: chain h residue 182 ASP Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 14 LYS Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 111 ASP Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 111 ASP Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain j residue 163 ASP Chi-restraints excluded: chain j residue 166 ASP Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 22 LEU Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain t residue 64 GLU Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 224 SER Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 161 THR Chi-restraints excluded: chain u residue 163 ASP Chi-restraints excluded: chain v residue 64 GLU Chi-restraints excluded: chain v residue 105 ARG Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 224 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 285 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 340 optimal weight: 8.9990 chunk 313 optimal weight: 7.9990 chunk 358 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 31 optimal weight: 40.0000 chunk 274 optimal weight: 0.0980 chunk 195 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN a 11 ASN d 11 ASN ** i 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN o 101 GLN ** o 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 11 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.140434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.079090 restraints weight = 44717.671| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.44 r_work: 0.2844 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29728 Z= 0.148 Angle : 0.552 10.869 40320 Z= 0.283 Chirality : 0.043 0.194 4464 Planarity : 0.004 0.034 5216 Dihedral : 8.835 154.002 4320 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.48 % Allowed : 15.29 % Favored : 81.23 % 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: -0.74 (0.14), residues: 3624 helix: 0.16 (0.12), residues: 1776 sheet: -0.95 (0.20), residues: 688 loop : -0.94 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 107 TYR 0.016 0.002 TYR o 112 PHE 0.022 0.002 PHE a 139 TRP 0.019 0.002 TRP F 141 HIS 0.012 0.001 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (29728) covalent geometry : angle 0.55236 / 0.28 (40320) hydrogen bonds : bond 0.03463 / 2.36 ( 1177) hydrogen bonds : angle 4.37917 / 3.11 ( 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 404 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 299 time to evaluate : 1.072 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: symmetry clash REVERT: C 65 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6697 (pp20) REVERT: I 65 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6668 (pp20) REVERT: L 13 GLU cc_start: 0.7143 (tt0) cc_final: 0.6453 (pp20) REVERT: L 14 LYS cc_start: 0.6628 (mttt) cc_final: 0.5755 (mmtm) REVERT: a 13 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6711 (pp20) REVERT: a 14 LYS cc_start: 0.6690 (mttt) cc_final: 0.6339 (mmmm) REVERT: d 157 MET cc_start: 0.5325 (OUTLIER) cc_final: 0.4651 (tmm) REVERT: g 58 ASP cc_start: 0.9037 (t70) cc_final: 0.8720 (t0) REVERT: g 68 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: g 105 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7938 (mtt90) REVERT: g 120 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: g 229 LYS cc_start: 0.9236 (tttp) cc_final: 0.8856 (ttmt) REVERT: h 2 THR cc_start: 0.7982 (p) cc_final: 0.7662 (t) REVERT: h 8 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8590 (mt-10) REVERT: h 105 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7981 (mtt90) REVERT: h 229 LYS cc_start: 0.9138 (tttp) cc_final: 0.8823 (ttmt) REVERT: i 6 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8520 (tt) REVERT: i 58 ASP cc_start: 0.9012 (t70) cc_final: 0.8684 (t0) REVERT: i 68 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: i 105 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7951 (mtt90) REVERT: i 186 ASP cc_start: 0.9004 (m-30) cc_final: 0.8759 (m-30) REVERT: i 225 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: i 229 LYS cc_start: 0.9251 (tttp) cc_final: 0.8870 (ttmt) REVERT: j 2 THR cc_start: 0.7962 (p) cc_final: 0.7641 (t) REVERT: j 8 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8593 (mt-10) REVERT: j 41 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: j 105 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7995 (mtt90) REVERT: j 229 LYS cc_start: 0.9149 (tttp) cc_final: 0.8837 (ttmt) REVERT: r 14 LYS cc_start: 0.6646 (mttt) cc_final: 0.6228 (mmtm) REVERT: r 157 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4565 (tmm) REVERT: s 41 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: t 2 THR cc_start: 0.8178 (p) cc_final: 0.7932 (t) REVERT: t 64 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: t 105 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8039 (mtt90) REVERT: u 93 GLU cc_start: 0.8578 (pt0) cc_final: 0.8378 (pm20) REVERT: u 105 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8003 (mtt90) REVERT: v 64 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: v 68 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: v 105 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8046 (mtt90) REVERT: v 229 LYS cc_start: 0.9156 (tttp) cc_final: 0.8891 (ttmt) outliers start: 105 outliers final: 53 residues processed: 368 average time/residue: 0.7401 time to fit residues: 316.4782 Evaluate side-chains 349 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 276 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 157 MET Chi-restraints excluded: chain g residue 68 GLU Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 111 ASP Chi-restraints excluded: chain g residue 120 TYR Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 163 ASP Chi-restraints excluded: chain h residue 182 ASP Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 111 ASP Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain i residue 225 GLN Chi-restraints excluded: chain j residue 41 GLN Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 111 ASP Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain j residue 163 ASP Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 35 VAL Chi-restraints excluded: chain r residue 46 VAL Chi-restraints excluded: chain r residue 157 MET Chi-restraints excluded: chain s residue 41 GLN Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain s residue 163 ASP Chi-restraints excluded: chain t residue 64 GLU Chi-restraints excluded: chain t residue 105 ARG Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 224 SER Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 161 THR Chi-restraints excluded: chain u residue 163 ASP Chi-restraints excluded: chain v residue 64 GLU Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain v residue 105 ARG Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 224 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 297 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 265 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 352 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 ASN a 11 ASN ** d 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078543 restraints weight = 44240.477| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.43 r_work: 0.2834 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29728 Z= 0.150 Angle : 0.549 9.880 40320 Z= 0.281 Chirality : 0.043 0.191 4464 Planarity : 0.004 0.035 5216 Dihedral : 8.823 156.170 4320 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.22 % Allowed : 16.28 % Favored : 80.50 % 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: -0.47 (0.14), residues: 3624 helix: 0.41 (0.13), residues: 1728 sheet: -0.75 (0.21), residues: 616 loop : -0.92 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 107 TYR 0.015 0.002 TYR I 112 PHE 0.030 0.002 PHE r 139 TRP 0.020 0.002 TRP L 141 HIS 0.014 0.001 HIS F 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (29728) covalent geometry : angle 0.54901 / 0.28 (40320) hydrogen bonds : bond 0.03389 / 2.31 ( 1177) hydrogen bonds : angle 4.34684 / 3.09 ( 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 391 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 294 time to evaluate : 1.213 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5980 (pp20) REVERT: C 157 MET cc_start: 0.4652 (tmm) cc_final: 0.4301 (tmm) REVERT: I 13 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.5975 (pp20) REVERT: I 157 MET cc_start: 0.4673 (tmm) cc_final: 0.4323 (tmm) REVERT: L 13 GLU cc_start: 0.7069 (tt0) cc_final: 0.6403 (pp20) REVERT: L 14 LYS cc_start: 0.6496 (mttt) cc_final: 0.6041 (mmtm) REVERT: a 13 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6609 (pp20) REVERT: a 14 LYS cc_start: 0.6257 (mttt) cc_final: 0.5920 (mmmm) REVERT: d 157 MET cc_start: 0.4913 (OUTLIER) cc_final: 0.4264 (tmm) REVERT: g 58 ASP cc_start: 0.9017 (t70) cc_final: 0.8712 (t0) REVERT: g 68 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: g 105 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7941 (mtt90) REVERT: g 229 LYS cc_start: 0.9221 (tttp) cc_final: 0.8836 (ttmt) REVERT: h 2 THR cc_start: 0.7928 (p) cc_final: 0.7624 (t) REVERT: h 8 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8559 (mt-10) REVERT: h 19 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8603 (mt-10) REVERT: h 105 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7979 (mtt90) REVERT: h 229 LYS cc_start: 0.9077 (tttp) cc_final: 0.8765 (ttmt) REVERT: i 68 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: i 105 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7948 (mtt90) REVERT: i 186 ASP cc_start: 0.8964 (m-30) cc_final: 0.8696 (m-30) REVERT: i 229 LYS cc_start: 0.9227 (tttp) cc_final: 0.8835 (ttmt) REVERT: j 2 THR cc_start: 0.7927 (p) cc_final: 0.7620 (t) REVERT: j 8 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8538 (mt-10) REVERT: j 105 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7974 (mtt90) REVERT: j 225 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: j 229 LYS cc_start: 0.9094 (tttp) cc_final: 0.8783 (ttmt) REVERT: o 156 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: r 157 MET cc_start: 0.4795 (tmm) cc_final: 0.4112 (tmm) REVERT: t 2 THR cc_start: 0.8173 (p) cc_final: 0.7932 (t) REVERT: t 64 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: t 68 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.7831 (tp30) REVERT: t 105 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8046 (mtt90) REVERT: u 105 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7997 (mtt90) REVERT: v 64 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8503 (pm20) REVERT: v 105 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8026 (mtt90) REVERT: v 229 LYS cc_start: 0.9143 (tttp) cc_final: 0.8883 (ttmt) outliers start: 97 outliers final: 51 residues processed: 367 average time/residue: 0.7448 time to fit residues: 317.6184 Evaluate side-chains 341 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 272 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 65 GLU Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 157 MET Chi-restraints excluded: chain g residue 68 GLU Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 111 ASP Chi-restraints excluded: chain g residue 120 TYR Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 163 ASP Chi-restraints excluded: chain h residue 182 ASP Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 111 ASP Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 111 ASP Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain j residue 163 ASP Chi-restraints excluded: chain j residue 225 GLN Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 22 LEU Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain o residue 156 GLU Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 35 VAL Chi-restraints excluded: chain r residue 46 VAL Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain t residue 64 GLU Chi-restraints excluded: chain t residue 68 GLU Chi-restraints excluded: chain t residue 105 ARG Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 224 SER Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain u residue 161 THR Chi-restraints excluded: chain u residue 163 ASP Chi-restraints excluded: chain v residue 64 GLU Chi-restraints excluded: chain v residue 105 ARG Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 224 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 268 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 15 optimal weight: 40.0000 chunk 151 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 338 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 278 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 ASN a 8 ASN a 11 ASN d 8 ASN ** d 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 8 ASN o 11 ASN ** o 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 8 ASN ** r 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.142861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081649 restraints weight = 44190.546| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.48 r_work: 0.2908 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29728 Z= 0.098 Angle : 0.522 9.500 40320 Z= 0.266 Chirality : 0.042 0.213 4464 Planarity : 0.004 0.034 5216 Dihedral : 8.575 157.027 4320 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.39 % Allowed : 17.74 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3624 helix: 0.68 (0.13), residues: 1728 sheet: -0.88 (0.20), residues: 672 loop : -0.71 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 107 TYR 0.012 0.001 TYR u 83 PHE 0.021 0.001 PHE a 139 TRP 0.024 0.002 TRP C 141 HIS 0.013 0.001 HIS F 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (29728) covalent geometry : angle 0.52217 / 0.27 (40320) hydrogen bonds : bond 0.02780 / 1.91 ( 1177) hydrogen bonds : angle 4.23684 / 3.00 ( 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 403 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 331 time to evaluate : 1.148 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.6675 (tt0) cc_final: 0.6079 (pp20) REVERT: C 157 MET cc_start: 0.4456 (tmm) cc_final: 0.4199 (tmm) REVERT: I 157 MET cc_start: 0.4428 (tmm) cc_final: 0.4189 (tmm) REVERT: L 13 GLU cc_start: 0.7173 (tt0) cc_final: 0.6406 (pp20) REVERT: L 14 LYS cc_start: 0.6027 (mttt) cc_final: 0.5761 (mmmm) REVERT: a 13 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6891 (pp20) REVERT: d 157 MET cc_start: 0.4950 (OUTLIER) cc_final: 0.4250 (tmm) REVERT: g 58 ASP cc_start: 0.8932 (t70) cc_final: 0.8603 (t0) REVERT: g 229 LYS cc_start: 0.9204 (tttp) cc_final: 0.8883 (ttmt) REVERT: h 2 THR cc_start: 0.7955 (p) cc_final: 0.7664 (t) REVERT: h 8 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8601 (mt-10) REVERT: h 105 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7853 (mtt90) REVERT: h 161 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8481 (t) REVERT: h 229 LYS cc_start: 0.9093 (tttp) cc_final: 0.8789 (ttmt) REVERT: i 58 ASP cc_start: 0.8957 (t70) cc_final: 0.8628 (t0) REVERT: i 161 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8528 (t) REVERT: i 186 ASP cc_start: 0.8977 (m-30) cc_final: 0.8704 (m-30) REVERT: i 229 LYS cc_start: 0.9212 (tttp) cc_final: 0.8890 (ttmt) REVERT: j 2 THR cc_start: 0.7946 (p) cc_final: 0.7654 (t) REVERT: j 8 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8587 (mt-10) REVERT: j 105 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7857 (mtt90) REVERT: j 229 LYS cc_start: 0.9096 (tttp) cc_final: 0.8796 (ttmt) REVERT: o 157 MET cc_start: 0.5549 (ttm) cc_final: 0.5248 (ttm) REVERT: r 157 MET cc_start: 0.5025 (OUTLIER) cc_final: 0.4437 (tmm) REVERT: t 2 THR cc_start: 0.8201 (p) cc_final: 0.7972 (t) REVERT: t 64 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8430 (pm20) REVERT: t 93 GLU cc_start: 0.8521 (pt0) cc_final: 0.8260 (pm20) REVERT: t 105 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7992 (mtt90) REVERT: t 161 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8510 (t) REVERT: u 105 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7988 (mtt90) REVERT: v 64 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: v 68 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: v 93 GLU cc_start: 0.8536 (pt0) cc_final: 0.8275 (pm20) REVERT: v 105 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8008 (mtt90) REVERT: v 229 LYS cc_start: 0.9135 (tttp) cc_final: 0.8859 (ttmt) outliers start: 72 outliers final: 35 residues processed: 384 average time/residue: 0.6566 time to fit residues: 293.3281 Evaluate side-chains 346 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 65 GLU Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 157 MET Chi-restraints excluded: chain g residue 111 ASP Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 163 ASP Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 111 ASP Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain j residue 163 ASP Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 22 LEU Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 157 MET Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain t residue 64 GLU Chi-restraints excluded: chain t residue 105 ARG Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 224 SER Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain v residue 64 GLU Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain v residue 105 ARG Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 224 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 238 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 205 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 ASN a 8 ASN d 8 ASN o 8 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 8 ASN ** r 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.140146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.078855 restraints weight = 43727.008| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.45 r_work: 0.2831 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29728 Z= 0.135 Angle : 0.552 12.132 40320 Z= 0.280 Chirality : 0.043 0.212 4464 Planarity : 0.004 0.034 5216 Dihedral : 8.690 158.697 4320 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.22 % Allowed : 18.37 % Favored : 79.41 % 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: -0.11 (0.14), residues: 3624 helix: 0.75 (0.13), residues: 1728 sheet: -0.77 (0.20), residues: 672 loop : -0.67 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 107 TYR 0.014 0.001 TYR a 112 PHE 0.026 0.001 PHE L 139 TRP 0.021 0.002 TRP C 141 HIS 0.019 0.001 HIS L 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (29728) covalent geometry : angle 0.55161 / 0.28 (40320) hydrogen bonds : bond 0.03219 / 2.21 ( 1177) hydrogen bonds : angle 4.22795 / 2.99 ( 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 366 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 299 time to evaluate : 1.163 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 TYR cc_start: 0.7802 (t80) cc_final: 0.7281 (t80) REVERT: C 13 GLU cc_start: 0.6735 (tt0) cc_final: 0.6117 (pp20) REVERT: C 146 ILE cc_start: 0.3589 (pp) cc_final: 0.3257 (mp) REVERT: C 157 MET cc_start: 0.4368 (tmm) cc_final: 0.4145 (tmm) REVERT: F 7 TYR cc_start: 0.7832 (t80) cc_final: 0.7486 (t80) REVERT: F 157 MET cc_start: 0.4459 (OUTLIER) cc_final: 0.4040 (tmm) REVERT: I 13 GLU cc_start: 0.7062 (tt0) cc_final: 0.6411 (pp20) REVERT: L 13 GLU cc_start: 0.7084 (tt0) cc_final: 0.6529 (pp20) REVERT: a 13 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7005 (pp20) REVERT: a 14 LYS cc_start: 0.7240 (mmtt) cc_final: 0.7001 (mmtt) REVERT: d 157 MET cc_start: 0.4806 (OUTLIER) cc_final: 0.4115 (tmm) REVERT: g 58 ASP cc_start: 0.8975 (t70) cc_final: 0.8669 (t0) REVERT: g 105 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7874 (mtt90) REVERT: g 229 LYS cc_start: 0.9152 (tttp) cc_final: 0.8827 (ttmt) REVERT: h 2 THR cc_start: 0.7937 (p) cc_final: 0.7625 (t) REVERT: h 8 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8550 (mt-10) REVERT: h 105 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7933 (mtt90) REVERT: h 229 LYS cc_start: 0.9062 (tttp) cc_final: 0.8753 (ttmt) REVERT: i 58 ASP cc_start: 0.8970 (t70) cc_final: 0.8657 (t0) REVERT: i 105 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7878 (mtt90) REVERT: i 186 ASP cc_start: 0.8929 (m-30) cc_final: 0.8656 (m-30) REVERT: i 229 LYS cc_start: 0.9178 (tttp) cc_final: 0.8846 (ttmt) REVERT: j 2 THR cc_start: 0.7944 (p) cc_final: 0.7627 (t) REVERT: j 8 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8537 (mt-10) REVERT: j 105 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7922 (mtt90) REVERT: j 229 LYS cc_start: 0.9065 (tttp) cc_final: 0.8758 (ttmt) REVERT: r 157 MET cc_start: 0.4859 (OUTLIER) cc_final: 0.4226 (tmm) REVERT: t 2 THR cc_start: 0.8184 (p) cc_final: 0.7956 (t) REVERT: t 64 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8418 (pm20) REVERT: t 93 GLU cc_start: 0.8492 (pt0) cc_final: 0.8207 (pm20) REVERT: t 105 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7962 (mtt90) REVERT: u 105 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7931 (mtt90) REVERT: v 64 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: v 68 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: v 105 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7983 (mtt90) REVERT: v 229 LYS cc_start: 0.9109 (tttp) cc_final: 0.8865 (ttmt) outliers start: 67 outliers final: 39 residues processed: 348 average time/residue: 0.7088 time to fit residues: 285.3474 Evaluate side-chains 339 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 286 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 157 MET Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 111 ASP Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 163 ASP Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 111 ASP Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain j residue 163 ASP Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 22 LEU Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 35 VAL Chi-restraints excluded: chain r residue 157 MET Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain t residue 64 GLU Chi-restraints excluded: chain t residue 105 ARG Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 224 SER Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain v residue 64 GLU Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain v residue 105 ARG Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 224 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 16 optimal weight: 6.9990 chunk 358 optimal weight: 2.9990 chunk 286 optimal weight: 0.0270 chunk 231 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 230 optimal weight: 0.1980 chunk 334 optimal weight: 0.8980 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 ASN d 101 GLN o 8 ASN o 11 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 101 GLN r 8 ASN r 172 HIS ** s 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.141629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.080905 restraints weight = 43899.401| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.46 r_work: 0.2885 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29728 Z= 0.105 Angle : 0.533 12.469 40320 Z= 0.271 Chirality : 0.042 0.203 4464 Planarity : 0.004 0.034 5216 Dihedral : 8.637 158.329 4320 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.09 % Allowed : 18.87 % Favored : 79.05 % 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: -0.06 (0.14), residues: 3624 helix: 0.76 (0.13), residues: 1776 sheet: -0.69 (0.20), residues: 672 loop : -0.69 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 170 TYR 0.017 0.001 TYR d 30 PHE 0.024 0.001 PHE o 139 TRP 0.023 0.002 TRP C 141 HIS 0.007 0.001 HIS F 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (29728) covalent geometry : angle 0.53329 / 0.27 (40320) hydrogen bonds : bond 0.02863 / 1.97 ( 1177) hydrogen bonds : angle 4.16211 / 2.94 ( 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 354 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 291 time to evaluate : 1.114 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 146 ILE cc_start: 0.3569 (pp) cc_final: 0.3280 (mp) REVERT: F 157 MET cc_start: 0.4264 (OUTLIER) cc_final: 0.3930 (tmm) REVERT: I 7 TYR cc_start: 0.7716 (t80) cc_final: 0.7038 (t80) REVERT: I 13 GLU cc_start: 0.7109 (tt0) cc_final: 0.6522 (pp20) REVERT: I 128 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7466 (tm-30) REVERT: I 146 ILE cc_start: 0.3494 (pp) cc_final: 0.3215 (mp) REVERT: L 13 GLU cc_start: 0.7064 (tt0) cc_final: 0.6569 (pp20) REVERT: a 13 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7002 (pp20) REVERT: d 157 MET cc_start: 0.4857 (OUTLIER) cc_final: 0.4187 (tmm) REVERT: g 58 ASP cc_start: 0.8960 (t70) cc_final: 0.8636 (t0) REVERT: g 68 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: g 105 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7954 (mtt90) REVERT: g 229 LYS cc_start: 0.9164 (tttp) cc_final: 0.8853 (ttmt) REVERT: h 2 THR cc_start: 0.7970 (p) cc_final: 0.7669 (t) REVERT: h 8 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8552 (mt-10) REVERT: h 105 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7978 (mtt90) REVERT: h 122 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7828 (pptt) REVERT: h 229 LYS cc_start: 0.9023 (tttp) cc_final: 0.8725 (ttmt) REVERT: i 58 ASP cc_start: 0.8953 (t70) cc_final: 0.8633 (t0) REVERT: i 68 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: i 105 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7910 (mtt90) REVERT: i 186 ASP cc_start: 0.8974 (m-30) cc_final: 0.8693 (m-30) REVERT: i 229 LYS cc_start: 0.9176 (tttp) cc_final: 0.8858 (ttmt) REVERT: j 2 THR cc_start: 0.7975 (p) cc_final: 0.7674 (t) REVERT: j 8 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8527 (mt-10) REVERT: j 105 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7969 (mtt90) REVERT: j 122 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7837 (pptt) REVERT: j 229 LYS cc_start: 0.9036 (tttp) cc_final: 0.8740 (ttmt) REVERT: o 157 MET cc_start: 0.5417 (ttm) cc_final: 0.5149 (ttm) REVERT: r 157 MET cc_start: 0.4773 (OUTLIER) cc_final: 0.4169 (tmm) REVERT: t 2 THR cc_start: 0.8204 (p) cc_final: 0.7987 (t) REVERT: t 64 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: t 93 GLU cc_start: 0.8506 (pt0) cc_final: 0.8253 (pm20) REVERT: t 105 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7977 (mtt90) REVERT: u 105 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7978 (mtt90) REVERT: v 68 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: v 105 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8014 (mtt90) REVERT: v 229 LYS cc_start: 0.9116 (tttp) cc_final: 0.8844 (ttmt) outliers start: 63 outliers final: 32 residues processed: 339 average time/residue: 0.7339 time to fit residues: 288.0125 Evaluate side-chains 323 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 157 MET Chi-restraints excluded: chain g residue 68 GLU Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 111 ASP Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 122 LYS Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain h residue 163 ASP Chi-restraints excluded: chain i residue 68 GLU Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 111 ASP Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 122 LYS Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain j residue 163 ASP Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 22 LEU Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 157 MET Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain t residue 64 GLU Chi-restraints excluded: chain t residue 105 ARG Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 224 SER Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain v residue 105 ARG Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 224 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 312 optimal weight: 0.8980 chunk 310 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 169 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 351 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN d 8 ASN d 75 ASN o 8 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 8 ASN r 66 HIS r 101 GLN ** s 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.140474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.079499 restraints weight = 43381.242| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.46 r_work: 0.2878 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29728 Z= 0.114 Angle : 0.540 12.509 40320 Z= 0.273 Chirality : 0.042 0.200 4464 Planarity : 0.004 0.035 5216 Dihedral : 8.623 160.803 4320 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.72 % Allowed : 19.33 % Favored : 78.95 % 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: 0.03 (0.14), residues: 3624 helix: 0.82 (0.13), residues: 1776 sheet: -0.51 (0.21), residues: 664 loop : -0.71 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 107 TYR 0.013 0.001 TYR a 112 PHE 0.021 0.001 PHE o 139 TRP 0.023 0.002 TRP C 141 HIS 0.009 0.001 HIS a 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (29728) covalent geometry : angle 0.54036 / 0.27 (40320) hydrogen bonds : bond 0.02983 / 2.05 ( 1177) hydrogen bonds : angle 4.13380 / 2.92 ( 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 334 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 1.045 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 146 ILE cc_start: 0.3572 (pp) cc_final: 0.3312 (mp) REVERT: F 172 HIS cc_start: 0.6105 (m90) cc_final: 0.5841 (p90) REVERT: I 146 ILE cc_start: 0.3451 (pp) cc_final: 0.3186 (mp) REVERT: L 13 GLU cc_start: 0.7019 (tt0) cc_final: 0.6393 (pp20) REVERT: a 13 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7071 (pp20) REVERT: g 58 ASP cc_start: 0.8969 (t70) cc_final: 0.8650 (t0) REVERT: g 68 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: g 229 LYS cc_start: 0.9168 (tttp) cc_final: 0.8853 (ttmt) REVERT: h 2 THR cc_start: 0.7970 (p) cc_final: 0.7672 (t) REVERT: h 8 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8562 (mt-10) REVERT: h 105 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7981 (mtt90) REVERT: h 229 LYS cc_start: 0.9057 (tttp) cc_final: 0.8749 (ttmt) REVERT: i 58 ASP cc_start: 0.8966 (t70) cc_final: 0.8652 (t0) REVERT: i 105 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7939 (mtt90) REVERT: i 186 ASP cc_start: 0.8968 (m-30) cc_final: 0.8725 (m-30) REVERT: i 229 LYS cc_start: 0.9168 (tttp) cc_final: 0.8859 (ttmt) REVERT: j 2 THR cc_start: 0.7970 (p) cc_final: 0.7681 (t) REVERT: j 8 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8553 (mt-10) REVERT: j 105 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7984 (mtt90) REVERT: j 122 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7880 (pptt) REVERT: j 229 LYS cc_start: 0.9058 (tttp) cc_final: 0.8754 (ttmt) REVERT: t 2 THR cc_start: 0.8214 (p) cc_final: 0.8001 (t) REVERT: t 58 ASP cc_start: 0.8935 (t70) cc_final: 0.8647 (t0) REVERT: t 68 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.7663 (tp30) REVERT: t 93 GLU cc_start: 0.8506 (pt0) cc_final: 0.8231 (pm20) REVERT: t 105 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7986 (mtt90) REVERT: u 105 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7987 (mtt90) REVERT: v 68 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: v 105 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8015 (mtt90) REVERT: v 229 LYS cc_start: 0.9103 (tttp) cc_final: 0.8845 (ttpt) outliers start: 52 outliers final: 30 residues processed: 325 average time/residue: 0.7192 time to fit residues: 270.4901 Evaluate side-chains 313 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain g residue 68 GLU Chi-restraints excluded: chain g residue 111 ASP Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain h residue 120 TYR Chi-restraints excluded: chain h residue 161 THR Chi-restraints excluded: chain i residue 105 ARG Chi-restraints excluded: chain i residue 120 TYR Chi-restraints excluded: chain i residue 161 THR Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain j residue 111 ASP Chi-restraints excluded: chain j residue 120 TYR Chi-restraints excluded: chain j residue 122 LYS Chi-restraints excluded: chain j residue 161 THR Chi-restraints excluded: chain j residue 163 ASP Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain s residue 120 TYR Chi-restraints excluded: chain t residue 68 GLU Chi-restraints excluded: chain t residue 105 ARG Chi-restraints excluded: chain t residue 120 TYR Chi-restraints excluded: chain t residue 161 THR Chi-restraints excluded: chain t residue 224 SER Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain u residue 120 TYR Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain v residue 105 ARG Chi-restraints excluded: chain v residue 120 TYR Chi-restraints excluded: chain v residue 161 THR Chi-restraints excluded: chain v residue 224 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 286 optimal weight: 0.0170 chunk 343 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 334 optimal weight: 0.7980 chunk 298 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 GLN d 66 HIS o 8 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.137338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.077257 restraints weight = 43606.988| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.40 r_work: 0.2818 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29728 Z= 0.178 Angle : 0.593 12.480 40320 Z= 0.302 Chirality : 0.045 0.218 4464 Planarity : 0.004 0.034 5216 Dihedral : 8.847 161.230 4320 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.02 % Allowed : 19.23 % Favored : 78.75 % 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: -0.03 (0.14), residues: 3624 helix: 0.78 (0.13), residues: 1728 sheet: -0.52 (0.21), residues: 664 loop : -0.73 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 107 TYR 0.015 0.002 TYR a 112 PHE 0.022 0.002 PHE L 139 TRP 0.025 0.002 TRP d 141 HIS 0.008 0.001 HIS o 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (29728) covalent geometry : angle 0.59329 / 0.30 (40320) hydrogen bonds : bond 0.03733 / 2.55 ( 1177) hydrogen bonds : angle 4.24498 / 3.01 ( 3387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12286.74 seconds wall clock time: 209 minutes 12.17 seconds (12552.17 seconds total)