Starting phenix.real_space_refine on Sun Jul 5 08:16:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8uhe_42278/07_2026/8uhe_42278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uhe_42278/07_2026/8uhe_42278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uhe_42278/07_2026/8uhe_42278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uhe_42278/07_2026/8uhe_42278.map" model { file = "/net/cci-nas-00/data/ceres_data/8uhe_42278/07_2026/8uhe_42278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uhe_42278/07_2026/8uhe_42278.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8uhe_42278/07_2026/8uhe_42278.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8uhe_42278/07_2026/8uhe_42278.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 162 5.16 5 Cl 1 4.86 5 C 17061 2.51 5 N 4620 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27048 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1300 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "D" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "F" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1214 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "H" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1246 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "J" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1311 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 4727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4727 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 562} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1207 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 2, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "N" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "P" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "R" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1214 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'M1V': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CL': 1, 'M1V': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.08, per 1000 atoms: 0.19 Number of scatterers: 27048 At special positions: 0 Unit cell: (122.1, 123.75, 131.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 162 16.00 O 5204 8.00 N 4620 7.00 C 17061 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.40 Conformation dependent library (CDL) restraints added in 1.0 seconds 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6284 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 3 sheets defined 81.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 46 through 62 Processing helix chain 'A' and resid 71 through 96 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 119 through 138 Processing helix chain 'A' and resid 139 through 157 removed outlier: 4.259A pdb=" N TYR A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 20 through 47 removed outlier: 4.995A pdb=" N ASP B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 60 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 75 through 99 Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 122 through 142 Processing helix chain 'B' and resid 143 through 161 removed outlier: 3.806A pdb=" N TYR B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.694A pdb=" N GLU C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 32 through 62 Proline residue: C 48 - end of helix Processing helix chain 'C' and resid 71 through 96 removed outlier: 3.662A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 119 through 138 Processing helix chain 'C' and resid 142 through 156 removed outlier: 3.616A pdb=" N ILE C 146 " --> pdb=" O GLU C 142 " (cutoff:3.500A) Proline residue: C 148 - end of helix removed outlier: 3.824A pdb=" N GLU C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 14 Processing helix chain 'D' and resid 20 through 60 removed outlier: 4.601A pdb=" N ASP D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 99 Processing helix chain 'D' and resid 101 through 108 Processing helix chain 'D' and resid 108 through 120 removed outlier: 4.497A pdb=" N LYS D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 142 Processing helix chain 'D' and resid 143 through 161 removed outlier: 4.152A pdb=" N TYR D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 removed outlier: 4.108A pdb=" N GLU E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 32 through 62 removed outlier: 5.873A pdb=" N GLU E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.649A pdb=" N SER E 69 " --> pdb=" O PRO E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 96 Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'E' and resid 108 through 116 Processing helix chain 'E' and resid 119 through 138 Processing helix chain 'E' and resid 139 through 157 removed outlier: 3.879A pdb=" N TYR E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 15 Processing helix chain 'F' and resid 20 through 47 removed outlier: 4.821A pdb=" N ASP F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 60 Processing helix chain 'F' and resid 74 through 99 Processing helix chain 'F' and resid 101 through 108 Processing helix chain 'F' and resid 111 through 120 Processing helix chain 'F' and resid 122 through 142 Processing helix chain 'F' and resid 143 through 161 removed outlier: 3.790A pdb=" N TYR F 152 " --> pdb=" O GLU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 19 through 62 removed outlier: 5.053A pdb=" N GLU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.602A pdb=" N SER G 69 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 96 Processing helix chain 'G' and resid 98 through 106 Processing helix chain 'G' and resid 108 through 116 Processing helix chain 'G' and resid 119 through 138 Processing helix chain 'G' and resid 139 through 157 removed outlier: 3.747A pdb=" N TYR G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 16 Processing helix chain 'H' and resid 20 through 60 removed outlier: 5.145A pdb=" N ASP H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N SER H 49 " --> pdb=" O SER H 45 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 99 Processing helix chain 'H' and resid 101 through 108 Processing helix chain 'H' and resid 111 through 120 Processing helix chain 'H' and resid 122 through 142 removed outlier: 3.711A pdb=" N MET H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H 142 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 161 removed outlier: 4.434A pdb=" N TYR H 152 " --> pdb=" O GLU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 14 Processing helix chain 'I' and resid 19 through 62 Proline residue: I 34 - end of helix removed outlier: 5.416A pdb=" N GLU I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLU I 49 " --> pdb=" O SER I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 96 Processing helix chain 'I' and resid 98 through 105 Processing helix chain 'I' and resid 108 through 116 Processing helix chain 'I' and resid 119 through 137 Processing helix chain 'I' and resid 139 through 156 Proline residue: I 148 - end of helix Processing helix chain 'J' and resid 3 through 16 Processing helix chain 'J' and resid 20 through 63 removed outlier: 4.485A pdb=" N ALA J 35 " --> pdb=" O PHE J 31 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN J 36 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA J 49 " --> pdb=" O SER J 45 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 75 through 100 Processing helix chain 'J' and resid 102 through 109 Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'J' and resid 123 through 146 removed outlier: 3.684A pdb=" N THR J 127 " --> pdb=" O PRO J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 165 Processing helix chain 'K' and resid 19 through 31 removed outlier: 3.623A pdb=" N ALA K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 63 removed outlier: 4.578A pdb=" N LEU K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLN K 52 " --> pdb=" O ARG K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 71 Processing helix chain 'K' and resid 153 through 158 Processing helix chain 'K' and resid 158 through 183 Processing helix chain 'K' and resid 185 through 193 Processing helix chain 'K' and resid 203 through 221 Processing helix chain 'K' and resid 228 through 244 Processing helix chain 'K' and resid 266 through 273 Processing helix chain 'K' and resid 286 through 302 Processing helix chain 'K' and resid 314 through 323 removed outlier: 3.717A pdb=" N GLY K 323 " --> pdb=" O SER K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 337 Processing helix chain 'K' and resid 338 through 346 Processing helix chain 'K' and resid 350 through 364 Processing helix chain 'K' and resid 369 through 394 removed outlier: 3.546A pdb=" N PHE K 373 " --> pdb=" O CYS K 369 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N SER K 386 " --> pdb=" O ASP K 382 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA K 387 " --> pdb=" O GLN K 383 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 388 " --> pdb=" O GLY K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 402 Processing helix chain 'K' and resid 422 through 431 removed outlier: 3.717A pdb=" N LYS K 431 " --> pdb=" O LEU K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 437 Processing helix chain 'K' and resid 440 through 450 removed outlier: 3.540A pdb=" N THR K 444 " --> pdb=" O PRO K 440 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG K 450 " --> pdb=" O PHE K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 464 removed outlier: 3.629A pdb=" N ASN K 463 " --> pdb=" O GLY K 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 554 Processing helix chain 'K' and resid 559 through 563 Processing helix chain 'K' and resid 564 through 573 Processing helix chain 'K' and resid 577 through 587 Processing helix chain 'K' and resid 588 through 596 Processing helix chain 'K' and resid 600 through 614 Processing helix chain 'K' and resid 619 through 633 Processing helix chain 'K' and resid 634 through 644 Processing helix chain 'K' and resid 645 through 652 Processing helix chain 'K' and resid 664 through 671 Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 20 through 47 removed outlier: 4.661A pdb=" N ASP L 35 " --> pdb=" O PHE L 31 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU L 36 " --> pdb=" O ARG L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 60 Processing helix chain 'L' and resid 75 through 99 Processing helix chain 'L' and resid 101 through 108 Processing helix chain 'L' and resid 111 through 120 removed outlier: 3.513A pdb=" N THR L 115 " --> pdb=" O GLY L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 142 Processing helix chain 'L' and resid 142 through 160 removed outlier: 4.243A pdb=" N TYR L 152 " --> pdb=" O GLU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 12 Processing helix chain 'M' and resid 19 through 46 removed outlier: 5.335A pdb=" N GLU M 34 " --> pdb=" O VAL M 30 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLN M 35 " --> pdb=" O LYS M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 62 Processing helix chain 'M' and resid 65 through 69 removed outlier: 3.515A pdb=" N ASN M 68 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER M 69 " --> pdb=" O PRO M 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 65 through 69' Processing helix chain 'M' and resid 71 through 96 removed outlier: 3.528A pdb=" N THR M 75 " --> pdb=" O VAL M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 108 through 116 Processing helix chain 'M' and resid 119 through 137 Processing helix chain 'M' and resid 139 through 157 removed outlier: 4.043A pdb=" N TYR M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 20 through 47 removed outlier: 5.597A pdb=" N ASP N 35 " --> pdb=" O PHE N 31 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU N 36 " --> pdb=" O ARG N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 60 Processing helix chain 'N' and resid 75 through 99 Processing helix chain 'N' and resid 101 through 108 Processing helix chain 'N' and resid 111 through 120 Processing helix chain 'N' and resid 122 through 142 removed outlier: 3.845A pdb=" N MET N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY N 142 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 161 removed outlier: 3.842A pdb=" N TYR N 152 " --> pdb=" O GLU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 12 Processing helix chain 'O' and resid 19 through 62 removed outlier: 5.048A pdb=" N GLU O 34 " --> pdb=" O VAL O 30 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN O 35 " --> pdb=" O LYS O 31 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLU O 48 " --> pdb=" O ALA O 44 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 96 Processing helix chain 'O' and resid 98 through 105 Processing helix chain 'O' and resid 108 through 116 Processing helix chain 'O' and resid 119 through 138 removed outlier: 3.767A pdb=" N ILE O 123 " --> pdb=" O PRO O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 157 removed outlier: 4.057A pdb=" N TYR O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 16 removed outlier: 3.577A pdb=" N GLN P 15 " --> pdb=" O THR P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 60 removed outlier: 5.145A pdb=" N ASP P 35 " --> pdb=" O PHE P 31 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU P 36 " --> pdb=" O ARG P 32 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER P 49 " --> pdb=" O SER P 45 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 99 Processing helix chain 'P' and resid 101 through 108 Processing helix chain 'P' and resid 111 through 120 Processing helix chain 'P' and resid 122 through 142 Processing helix chain 'P' and resid 143 through 161 removed outlier: 4.111A pdb=" N TYR P 152 " --> pdb=" O GLU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 12 Processing helix chain 'Q' and resid 19 through 62 removed outlier: 5.137A pdb=" N GLU Q 34 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLU Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 96 removed outlier: 3.583A pdb=" N THR Q 75 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 105 Processing helix chain 'Q' and resid 108 through 116 Processing helix chain 'Q' and resid 119 through 138 removed outlier: 3.548A pdb=" N ILE Q 123 " --> pdb=" O PRO Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 157 removed outlier: 3.908A pdb=" N TYR Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 16 removed outlier: 3.770A pdb=" N GLN R 15 " --> pdb=" O THR R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 47 removed outlier: 5.776A pdb=" N ASP R 35 " --> pdb=" O PHE R 31 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU R 36 " --> pdb=" O ARG R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 60 Processing helix chain 'R' and resid 75 through 99 Processing helix chain 'R' and resid 101 through 108 Processing helix chain 'R' and resid 111 through 120 Processing helix chain 'R' and resid 122 through 161 removed outlier: 6.195A pdb=" N ALA R 143 " --> pdb=" O ASP R 139 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N GLU R 144 " --> pdb=" O MET R 140 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU R 148 " --> pdb=" O GLU R 144 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL R 149 " --> pdb=" O ALA R 145 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR R 152 " --> pdb=" O GLU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 46 removed outlier: 4.312A pdb=" N PHE S 37 " --> pdb=" O TYR S 33 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 251 through 253 Processing sheet with id=AA2, first strand: chain 'K' and resid 497 through 498 Processing sheet with id=AA3, first strand: chain 'S' and resid 26 through 32 removed outlier: 7.266A pdb=" N CYS S 9 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE S 50 " --> pdb=" O CYS S 9 " (cutoff:3.500A) 1998 hydrogen bonds defined for protein. 5952 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: 4.09 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.23: 252 1.23 - 1.39: 10590 1.39 - 1.54: 16219 1.54 - 1.70: 205 1.70 - 1.86: 256 Bond restraints: 27522 Sorted by residual: bond pdb=" CG PRO Q 66 " pdb=" CD PRO Q 66 " ideal model delta sigma weight residual 1.503 1.141 0.362 3.40e-02 8.65e+02 1.13e+02 bond pdb=" CG1 ILE I 4 " pdb=" CD1 ILE I 4 " ideal model delta sigma weight residual 1.513 1.124 0.389 3.90e-02 6.57e+02 9.96e+01 bond pdb=" CD GLU L 29 " pdb=" OE1 GLU L 29 " ideal model delta sigma weight residual 1.249 1.072 0.177 1.90e-02 2.77e+03 8.69e+01 bond pdb=" CG1 ILE M 25 " pdb=" CD1 ILE M 25 " ideal model delta sigma weight residual 1.513 1.163 0.350 3.90e-02 6.57e+02 8.04e+01 bond pdb=" CD GLU L 144 " pdb=" OE2 GLU L 144 " ideal model delta sigma weight residual 1.249 1.088 0.161 1.90e-02 2.77e+03 7.18e+01 ... (remaining 27517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 36965 4.91 - 9.82: 284 9.82 - 14.73: 27 14.73 - 19.63: 20 19.63 - 24.54: 2 Bond angle restraints: 37298 Sorted by residual: angle pdb=" CA PRO Q 66 " pdb=" N PRO Q 66 " pdb=" CD PRO Q 66 " ideal model delta sigma weight residual 112.00 93.51 18.49 1.40e+00 5.10e-01 1.75e+02 angle pdb=" N SER C 163 " pdb=" CA SER C 163 " pdb=" C SER C 163 " ideal model delta sigma weight residual 109.96 125.85 -15.89 1.49e+00 4.50e-01 1.14e+02 angle pdb=" N PRO Q 66 " pdb=" CD PRO Q 66 " pdb=" CG PRO Q 66 " ideal model delta sigma weight residual 103.20 88.11 15.09 1.50e+00 4.44e-01 1.01e+02 angle pdb=" CA LEU C 157 " pdb=" C LEU C 157 " pdb=" O LEU C 157 " ideal model delta sigma weight residual 119.51 129.65 -10.14 1.04e+00 9.25e-01 9.51e+01 angle pdb=" CA PRO C 63 " pdb=" N PRO C 63 " pdb=" CD PRO C 63 " ideal model delta sigma weight residual 112.00 101.17 10.83 1.40e+00 5.10e-01 5.99e+01 ... (remaining 37293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 14862 22.02 - 44.04: 1679 44.04 - 66.05: 355 66.05 - 88.07: 90 88.07 - 110.09: 12 Dihedral angle restraints: 16998 sinusoidal: 7201 harmonic: 9797 Sorted by residual: dihedral pdb=" CA MET K 694 " pdb=" C MET K 694 " pdb=" N ARG K 695 " pdb=" CA ARG K 695 " ideal model delta harmonic sigma weight residual -180.00 -146.72 -33.28 0 5.00e+00 4.00e-02 4.43e+01 dihedral pdb=" CA THR B 74 " pdb=" C THR B 74 " pdb=" N CYS B 75 " pdb=" CA CYS B 75 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ARG L 32 " pdb=" C ARG L 32 " pdb=" N SER L 33 " pdb=" CA SER L 33 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 16995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 4052 0.204 - 0.408: 41 0.408 - 0.612: 2 0.612 - 0.816: 0 0.816 - 1.020: 1 Chirality restraints: 4096 Sorted by residual: chirality pdb=" CG LEU L 36 " pdb=" CB LEU L 36 " pdb=" CD1 LEU L 36 " pdb=" CD2 LEU L 36 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA ARG C 159 " pdb=" N ARG C 159 " pdb=" C ARG C 159 " pdb=" CB ARG C 159 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CB THR F 55 " pdb=" CA THR F 55 " pdb=" OG1 THR F 55 " pdb=" CG2 THR F 55 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.89e+00 ... (remaining 4093 not shown) Planarity restraints: 4812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A M1V K 801 " 0.109 2.00e-02 2.50e+03 2.88e-01 1.87e+03 pdb=" C2A M1V K 801 " -0.095 2.00e-02 2.50e+03 pdb=" C3A M1V K 801 " 0.105 2.00e-02 2.50e+03 pdb=" C4A M1V K 801 " -0.057 2.00e-02 2.50e+03 pdb=" CAA M1V K 801 " 0.464 2.00e-02 2.50e+03 pdb=" CHA M1V K 801 " -0.449 2.00e-02 2.50e+03 pdb=" CMA M1V K 801 " -0.463 2.00e-02 2.50e+03 pdb=" NA M1V K 801 " 0.249 2.00e-02 2.50e+03 pdb=" OA M1V K 801 " 0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C M1V C 201 " -0.007 2.00e-02 2.50e+03 2.39e-01 1.29e+03 pdb=" C2C M1V C 201 " 0.108 2.00e-02 2.50e+03 pdb=" C3C M1V C 201 " -0.012 2.00e-02 2.50e+03 pdb=" C4C M1V C 201 " 0.101 2.00e-02 2.50e+03 pdb=" CAC M1V C 201 " 0.251 2.00e-02 2.50e+03 pdb=" CHB M1V C 201 " -0.453 2.00e-02 2.50e+03 pdb=" CHC M1V C 201 " -0.079 2.00e-02 2.50e+03 pdb=" CMC M1V C 201 " -0.281 2.00e-02 2.50e+03 pdb=" NC M1V C 201 " 0.373 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C M1V K 801 " -0.011 2.00e-02 2.50e+03 2.02e-01 9.22e+02 pdb=" C2C M1V K 801 " -0.057 2.00e-02 2.50e+03 pdb=" C3C M1V K 801 " 0.014 2.00e-02 2.50e+03 pdb=" C4C M1V K 801 " -0.077 2.00e-02 2.50e+03 pdb=" CAC M1V K 801 " -0.169 2.00e-02 2.50e+03 pdb=" CHB M1V K 801 " 0.367 2.00e-02 2.50e+03 pdb=" CHC M1V K 801 " 0.141 2.00e-02 2.50e+03 pdb=" CMC M1V K 801 " 0.174 2.00e-02 2.50e+03 pdb=" NC M1V K 801 " -0.382 2.00e-02 2.50e+03 ... (remaining 4809 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 599 2.66 - 3.22: 26163 3.22 - 3.78: 49070 3.78 - 4.34: 63469 4.34 - 4.90: 102295 Nonbonded interactions: 241596 Sorted by model distance: nonbonded pdb=" OG SER E 139 " pdb=" OD1 ASP E 142 " model vdw 2.105 3.040 nonbonded pdb=" OG SER M 2 " pdb=" OD2 ASP N 3 " model vdw 2.142 3.040 nonbonded pdb=" O ILE P 51 " pdb=" OG1 THR P 55 " model vdw 2.147 3.040 nonbonded pdb=" O SER K 268 " pdb=" OG SER K 272 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" O LYS B 17 " model vdw 2.185 3.040 ... (remaining 241591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'G' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = (chain 'B' and (resid 2 through 160 or resid 201)) selection = (chain 'D' and (resid 2 through 160 or resid 201)) selection = (chain 'F' and (resid 2 through 160 or resid 201)) selection = (chain 'H' and (resid 2 through 160 or resid 201)) selection = chain 'L' selection = (chain 'N' and (resid 2 through 160 or resid 201)) selection = (chain 'P' and (resid 2 through 160 or resid 201)) selection = (chain 'R' and (resid 2 through 160 or resid 201)) } 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.500 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 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 : 0.010 0.389 27538 Z= 0.452 Angle : 1.170 24.543 37298 Z= 0.585 Chirality : 0.061 1.020 4096 Planarity : 0.013 0.288 4812 Dihedral : 19.110 110.088 10714 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.88 % Favored : 96.91 % Rotamer: Outliers : 4.23 % Allowed : 29.75 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 3300 helix: 0.09 (0.09), residues: 2599 sheet: 1.58 (1.47), residues: 17 loop : -2.03 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG J 17 TYR 0.059 0.004 TYR K 626 PHE 0.042 0.003 PHE P 88 TRP 0.039 0.002 TRP C 84 HIS 0.015 0.002 HIS N 155 Details of bonding type rmsd/Z covalent geometry : bond 0.01042 / 0.44 (27522) covalent geometry : angle 1.17039 / 0.58 (37298) hydrogen bonds : bond 0.11602 / 7.38 ( 1998) hydrogen bonds : angle 6.15572 / 4.46 ( 5952) Misc. bond : bond 0.04796 / 3.13 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 558 time to evaluate : 0.694 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: A 26 PHE cc_start: 0.5069 (t80) cc_final: 0.4607 (m-80) REVERT: A 110 LYS cc_start: 0.6989 (mmmm) cc_final: 0.6701 (mmmt) REVERT: B 8 LEU cc_start: 0.6634 (mt) cc_final: 0.6368 (mp) REVERT: B 17 LYS cc_start: 0.5863 (pttp) cc_final: 0.5606 (pttp) REVERT: B 119 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6246 (mp) REVERT: C 82 MET cc_start: 0.4292 (mmt) cc_final: 0.3140 (mmt) REVERT: E 38 ARG cc_start: 0.5892 (ttp-170) cc_final: 0.5602 (ttp80) REVERT: E 111 GLU cc_start: 0.6635 (pm20) cc_final: 0.6164 (tm-30) REVERT: E 152 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.5552 (mm) REVERT: I 89 ILE cc_start: 0.7240 (mt) cc_final: 0.6914 (tt) REVERT: J 3 ASP cc_start: 0.3055 (OUTLIER) cc_final: 0.2851 (p0) REVERT: J 39 LYS cc_start: 0.7209 (mtmt) cc_final: 0.6949 (mtmm) REVERT: J 153 ILE cc_start: 0.6039 (OUTLIER) cc_final: 0.5622 (tp) REVERT: K 547 LEU cc_start: 0.7788 (mt) cc_final: 0.7462 (mt) REVERT: K 694 MET cc_start: 0.5005 (OUTLIER) cc_final: 0.4086 (tmm) REVERT: N 17 LYS cc_start: 0.6323 (ptpp) cc_final: 0.6005 (ptmm) REVERT: O 133 GLU cc_start: 0.3605 (OUTLIER) cc_final: 0.3273 (mp0) REVERT: P 85 MET cc_start: 0.6612 (mmp) cc_final: 0.6168 (mtt) REVERT: Q 35 GLN cc_start: 0.6509 (tt0) cc_final: 0.5912 (tp-100) REVERT: Q 98 GLU cc_start: 0.5366 (pp20) cc_final: 0.5142 (pp20) REVERT: Q 103 ASP cc_start: 0.6604 (m-30) cc_final: 0.6380 (m-30) outliers start: 118 outliers final: 65 residues processed: 644 average time/residue: 0.6620 time to fit residues: 491.9822 Evaluate side-chains 588 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 517 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 258 LYS Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 694 MET Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 79 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN B 117 ASN C 79 GLN E 35 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 27 GLN G 122 ASN H 117 ASN I 6 GLN I 44 ASN I 46 ASN I 68 ASN I 71 ASN K 29 HIS K 37 HIS K 63 HIS K 261 GLN K 396 GLN K 426 GLN K 441 GLN K 469 GLN K 476 HIS K 484 GLN L 2 GLN L 10 ASN L 117 ASN M 52 GLN M 53 ASN M 79 GLN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN O 115 ASN P 110 ASN Q 53 ASN Q 79 GLN Q 82 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN R 138 ASN S 63 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.228258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.208372 restraints weight = 31620.004| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 1.56 r_work: 0.4271 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4120 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27538 Z= 0.141 Angle : 0.700 10.246 37298 Z= 0.342 Chirality : 0.041 0.198 4096 Planarity : 0.005 0.070 4812 Dihedral : 10.148 104.713 4652 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.82 % Rotamer: Outliers : 6.09 % Allowed : 24.95 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3300 helix: 0.97 (0.10), residues: 2616 sheet: 2.00 (1.39), residues: 15 loop : -1.96 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 253 TYR 0.026 0.002 TYR L 151 PHE 0.026 0.001 PHE P 88 TRP 0.008 0.001 TRP A 59 HIS 0.013 0.001 HIS K 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (27522) covalent geometry : angle 0.69980 / 0.34 (37298) hydrogen bonds : bond 0.04035 / 2.66 ( 1998) hydrogen bonds : angle 4.82275 / 3.49 ( 5952) Misc. bond : bond 0.00035 / 0.02 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 574 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5270 (mp0) cc_final: 0.4937 (mp0) REVERT: A 38 ARG cc_start: 0.6974 (ttp80) cc_final: 0.6600 (ttp80) REVERT: A 110 LYS cc_start: 0.7274 (mmmm) cc_final: 0.6946 (mmmt) REVERT: A 121 ARG cc_start: 0.4538 (mpt180) cc_final: 0.4326 (mmt-90) REVERT: A 152 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5979 (mm) REVERT: B 17 LYS cc_start: 0.6213 (pttp) cc_final: 0.5967 (pttp) REVERT: B 85 MET cc_start: 0.4014 (mmm) cc_final: 0.3523 (mmt) REVERT: C 25 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.6103 (mpt) REVERT: C 53 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5576 (mtm-85) REVERT: C 82 MET cc_start: 0.4192 (OUTLIER) cc_final: 0.2877 (mmt) REVERT: C 98 ASP cc_start: 0.6030 (p0) cc_final: 0.5818 (p0) REVERT: C 146 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6069 (pp) REVERT: D 87 PHE cc_start: 0.7453 (m-80) cc_final: 0.7199 (m-80) REVERT: D 131 GLN cc_start: 0.6728 (pt0) cc_final: 0.6415 (pt0) REVERT: E 99 ARG cc_start: 0.5981 (tmm-80) cc_final: 0.5709 (tmm-80) REVERT: F 100 ASP cc_start: 0.6523 (OUTLIER) cc_final: 0.6299 (t0) REVERT: G 98 GLU cc_start: 0.6149 (pm20) cc_final: 0.5486 (pm20) REVERT: H 54 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6843 (ttmm) REVERT: H 140 MET cc_start: 0.4994 (pmm) cc_final: 0.4489 (pp-130) REVERT: I 13 ARG cc_start: 0.6759 (mtp180) cc_final: 0.6364 (mtt180) REVERT: J 29 SER cc_start: 0.8009 (t) cc_final: 0.7657 (p) REVERT: J 39 LYS cc_start: 0.7395 (mtmt) cc_final: 0.7003 (mtmm) REVERT: J 65 GLU cc_start: 0.5555 (tm-30) cc_final: 0.5273 (tm-30) REVERT: J 83 LEU cc_start: 0.8029 (mp) cc_final: 0.7757 (mm) REVERT: K 281 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6566 (ttp) REVERT: K 426 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: K 463 ASN cc_start: 0.7343 (t0) cc_final: 0.6936 (t0) REVERT: K 543 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5734 (mm-30) REVERT: K 626 TYR cc_start: 0.5731 (m-80) cc_final: 0.5247 (m-80) REVERT: K 660 GLU cc_start: 0.6731 (tt0) cc_final: 0.6445 (tt0) REVERT: K 691 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.6154 (pp20) REVERT: K 694 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4553 (mmm) REVERT: K 695 ARG cc_start: 0.4653 (OUTLIER) cc_final: 0.4400 (mtp180) REVERT: L 85 MET cc_start: 0.4932 (mmp) cc_final: 0.4505 (mpm) REVERT: L 107 ARG cc_start: 0.5741 (tpp-160) cc_final: 0.5443 (ttm-80) REVERT: M 73 ARG cc_start: 0.6683 (tmm160) cc_final: 0.6455 (ttp-110) REVERT: M 110 LYS cc_start: 0.6312 (mmmt) cc_final: 0.5978 (mmmt) REVERT: N 1 MET cc_start: 0.4692 (OUTLIER) cc_final: 0.4140 (tmt) REVERT: N 17 LYS cc_start: 0.6134 (ptpp) cc_final: 0.5905 (ptmm) REVERT: O 29 PHE cc_start: 0.6139 (t80) cc_final: 0.5814 (t80) REVERT: O 57 LYS cc_start: 0.4842 (ptmt) cc_final: 0.4398 (ptpt) REVERT: O 133 GLU cc_start: 0.3988 (OUTLIER) cc_final: 0.3634 (mp0) REVERT: P 42 MET cc_start: 0.5109 (mtt) cc_final: 0.4732 (mtm) REVERT: P 85 MET cc_start: 0.6486 (mmp) cc_final: 0.5832 (mtt) REVERT: P 135 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: Q 35 GLN cc_start: 0.6450 (tt0) cc_final: 0.5848 (tp-100) outliers start: 170 outliers final: 57 residues processed: 676 average time/residue: 0.6081 time to fit residues: 475.2175 Evaluate side-chains 590 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 518 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 276 ILE Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 426 GLN Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 543 GLU Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain K residue 694 MET Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 49 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 122 ASN B 117 ASN C 6 GLN C 10 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 79 GLN H 110 ASN H 117 ASN I 71 ASN I 73 GLN K 29 HIS K 426 GLN K 469 GLN K 476 HIS L 47 ASN L 117 ASN M 52 GLN M 122 ASN N 110 ASN O 53 ASN P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN R 138 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.227466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.207800 restraints weight = 31272.864| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 1.55 r_work: 0.4254 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27538 Z= 0.155 Angle : 0.708 10.699 37298 Z= 0.345 Chirality : 0.041 0.182 4096 Planarity : 0.005 0.076 4812 Dihedral : 9.663 100.996 4576 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.09 % Favored : 96.73 % Rotamer: Outliers : 7.06 % Allowed : 25.02 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3300 helix: 1.20 (0.10), residues: 2614 sheet: -0.27 (1.25), residues: 19 loop : -1.94 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 16 TYR 0.028 0.002 TYR H 152 PHE 0.018 0.002 PHE P 88 TRP 0.007 0.001 TRP A 59 HIS 0.014 0.001 HIS K 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (27522) covalent geometry : angle 0.70817 / 0.35 (37298) hydrogen bonds : bond 0.03967 / 2.61 ( 1998) hydrogen bonds : angle 4.76972 / 3.46 ( 5952) Misc. bond : bond 0.00046 / 0.02 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 564 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5518 (mp0) cc_final: 0.5214 (mp0) REVERT: A 110 LYS cc_start: 0.7360 (mmmm) cc_final: 0.7009 (mmmt) REVERT: A 121 ARG cc_start: 0.4529 (mpt180) cc_final: 0.4198 (mmt-90) REVERT: B 17 LYS cc_start: 0.6276 (pttp) cc_final: 0.5994 (pttp) REVERT: B 77 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7440 (mtp180) REVERT: B 85 MET cc_start: 0.4164 (mmm) cc_final: 0.3727 (mmt) REVERT: C 53 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.5572 (mtm-85) REVERT: C 79 GLN cc_start: 0.6482 (OUTLIER) cc_final: 0.6279 (mp10) REVERT: C 98 ASP cc_start: 0.6064 (p0) cc_final: 0.5764 (p0) REVERT: C 130 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7153 (mp) REVERT: C 146 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6091 (pp) REVERT: D 32 ARG cc_start: 0.5896 (mpt-90) cc_final: 0.5577 (mtt-85) REVERT: E 38 ARG cc_start: 0.6080 (ttp-170) cc_final: 0.5655 (ttp80) REVERT: E 93 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6408 (mt) REVERT: E 99 ARG cc_start: 0.6073 (tmm-80) cc_final: 0.5871 (tmm-80) REVERT: F 100 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6273 (t0) REVERT: G 73 ARG cc_start: 0.5809 (tmm-80) cc_final: 0.5505 (ppp80) REVERT: G 98 GLU cc_start: 0.6382 (pm20) cc_final: 0.5652 (pm20) REVERT: G 106 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6530 (m) REVERT: G 127 MET cc_start: 0.7002 (tpp) cc_final: 0.6489 (mpt) REVERT: H 54 LYS cc_start: 0.7121 (mmtt) cc_final: 0.6850 (ttmm) REVERT: H 100 ASP cc_start: 0.5967 (t70) cc_final: 0.5698 (t70) REVERT: I 13 ARG cc_start: 0.6824 (mtp180) cc_final: 0.6361 (mtt180) REVERT: J 21 ARG cc_start: 0.1910 (OUTLIER) cc_final: 0.0859 (tpt170) REVERT: J 29 SER cc_start: 0.7965 (t) cc_final: 0.7691 (p) REVERT: J 39 LYS cc_start: 0.7305 (mtmt) cc_final: 0.7054 (mtmm) REVERT: J 65 GLU cc_start: 0.5574 (tm-30) cc_final: 0.5275 (tm-30) REVERT: K 166 MET cc_start: 0.5892 (mmp) cc_final: 0.5456 (mmm) REVERT: K 388 LEU cc_start: 0.7799 (tp) cc_final: 0.7546 (tp) REVERT: K 426 GLN cc_start: 0.6983 (tt0) cc_final: 0.6466 (tt0) REVERT: K 463 ASN cc_start: 0.7296 (t0) cc_final: 0.6899 (t0) REVERT: K 543 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5798 (mm-30) REVERT: K 626 TYR cc_start: 0.5766 (m-80) cc_final: 0.5259 (m-80) REVERT: K 691 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.6091 (pp20) REVERT: K 694 MET cc_start: 0.5129 (OUTLIER) cc_final: 0.4720 (mmm) REVERT: L 96 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6484 (ttm) REVERT: M 98 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5449 (pm20) REVERT: M 110 LYS cc_start: 0.6538 (mmmt) cc_final: 0.6224 (mmmt) REVERT: N 8 LEU cc_start: 0.6724 (mt) cc_final: 0.6508 (mp) REVERT: N 17 LYS cc_start: 0.6177 (ptpp) cc_final: 0.5939 (ptmm) REVERT: N 135 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6848 (mm-30) REVERT: O 29 PHE cc_start: 0.6340 (t80) cc_final: 0.6042 (t80) REVERT: O 57 LYS cc_start: 0.4834 (ptmt) cc_final: 0.4472 (ptpt) REVERT: P 1 MET cc_start: 0.4402 (tmt) cc_final: 0.3046 (tmt) REVERT: P 85 MET cc_start: 0.6606 (mmp) cc_final: 0.5893 (mtp) REVERT: Q 35 GLN cc_start: 0.6526 (tt0) cc_final: 0.5853 (tp-100) REVERT: Q 79 GLN cc_start: 0.5786 (OUTLIER) cc_final: 0.5156 (mp-120) REVERT: Q 125 GLU cc_start: 0.5652 (OUTLIER) cc_final: 0.4826 (tp30) REVERT: R 97 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7531 (tp) outliers start: 197 outliers final: 72 residues processed: 691 average time/residue: 0.6489 time to fit residues: 517.0332 Evaluate side-chains 605 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 517 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 543 GLU Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 590 SER Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain K residue 694 MET Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 285 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 79 GLN H 117 ASN I 68 ASN J 101 ASN K 29 HIS ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 261 GLN K 451 GLN K 564 HIS L 47 ASN L 117 ASN M 52 GLN O 53 ASN O 68 ASN P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN S 63 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.227029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.207314 restraints weight = 31085.160| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 1.55 r_work: 0.4248 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27538 Z= 0.158 Angle : 0.708 10.982 37298 Z= 0.345 Chirality : 0.041 0.246 4096 Planarity : 0.005 0.062 4812 Dihedral : 9.527 98.311 4567 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Rotamer: Outliers : 6.59 % Allowed : 26.52 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.89 (0.15), residues: 3300 helix: 1.25 (0.10), residues: 2615 sheet: -0.30 (1.24), residues: 19 loop : -1.99 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 365 TYR 0.025 0.002 TYR H 152 PHE 0.018 0.002 PHE K 221 TRP 0.008 0.001 TRP O 59 HIS 0.009 0.001 HIS K 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (27522) covalent geometry : angle 0.70752 / 0.35 (37298) hydrogen bonds : bond 0.03902 / 2.57 ( 1998) hydrogen bonds : angle 4.76223 / 3.46 ( 5952) Misc. bond : bond 0.00050 / 0.03 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 545 time to evaluate : 0.958 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: A 22 GLU cc_start: 0.5580 (mp0) cc_final: 0.5369 (mp0) REVERT: A 110 LYS cc_start: 0.7425 (mmmm) cc_final: 0.7080 (mmmt) REVERT: A 121 ARG cc_start: 0.4467 (mpt180) cc_final: 0.4178 (mmt-90) REVERT: B 17 LYS cc_start: 0.6327 (pttp) cc_final: 0.6044 (pttp) REVERT: B 27 LEU cc_start: 0.4365 (OUTLIER) cc_final: 0.4013 (pp) REVERT: B 77 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7529 (mtp180) REVERT: B 85 MET cc_start: 0.4195 (mmm) cc_final: 0.3820 (mmt) REVERT: B 113 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7489 (tppp) REVERT: C 9 SER cc_start: 0.7652 (OUTLIER) cc_final: 0.7326 (t) REVERT: C 25 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6256 (mpt) REVERT: C 53 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.5547 (mtm-85) REVERT: C 102 ARG cc_start: 0.5792 (mtm110) cc_final: 0.5371 (mtm180) REVERT: C 130 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7201 (mp) REVERT: C 146 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6162 (pp) REVERT: D 10 ASN cc_start: 0.6233 (m-40) cc_final: 0.5346 (m110) REVERT: E 93 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6398 (mt) REVERT: E 99 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5842 (tmm-80) REVERT: E 135 MET cc_start: 0.4980 (OUTLIER) cc_final: 0.4699 (tpp) REVERT: E 142 ASP cc_start: 0.6172 (m-30) cc_final: 0.5807 (m-30) REVERT: F 58 LYS cc_start: 0.6743 (ptmt) cc_final: 0.6445 (ptpt) REVERT: F 100 ASP cc_start: 0.6431 (OUTLIER) cc_final: 0.6197 (t0) REVERT: G 28 ASP cc_start: 0.5712 (m-30) cc_final: 0.5507 (m-30) REVERT: G 73 ARG cc_start: 0.5818 (tmm-80) cc_final: 0.5530 (ppp80) REVERT: G 79 GLN cc_start: 0.6202 (OUTLIER) cc_final: 0.5997 (mp10) REVERT: G 98 GLU cc_start: 0.6413 (pm20) cc_final: 0.5758 (pm20) REVERT: G 106 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6565 (m) REVERT: G 127 MET cc_start: 0.6923 (tpp) cc_final: 0.6505 (mpm) REVERT: G 135 MET cc_start: 0.5815 (mmp) cc_final: 0.5591 (mmp) REVERT: H 28 GLN cc_start: 0.5819 (mm110) cc_final: 0.5514 (mm110) REVERT: H 54 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6820 (ttmm) REVERT: H 100 ASP cc_start: 0.6012 (t70) cc_final: 0.5597 (t0) REVERT: I 13 ARG cc_start: 0.6899 (mtp180) cc_final: 0.6644 (mtp180) REVERT: J 21 ARG cc_start: 0.1927 (OUTLIER) cc_final: 0.0970 (tpt170) REVERT: J 29 SER cc_start: 0.7960 (t) cc_final: 0.7685 (p) REVERT: J 39 LYS cc_start: 0.7285 (mtmt) cc_final: 0.7022 (mtmm) REVERT: J 65 GLU cc_start: 0.5615 (tm-30) cc_final: 0.5353 (tm-30) REVERT: K 166 MET cc_start: 0.5851 (mmp) cc_final: 0.5413 (mmm) REVERT: K 214 MET cc_start: 0.6741 (mtt) cc_final: 0.6541 (mtp) REVERT: K 281 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6675 (ttp) REVERT: K 388 LEU cc_start: 0.7829 (tp) cc_final: 0.7607 (tp) REVERT: K 463 ASN cc_start: 0.7300 (t0) cc_final: 0.6936 (t0) REVERT: K 502 ARG cc_start: 0.5297 (mtp180) cc_final: 0.4958 (mtt180) REVERT: K 626 TYR cc_start: 0.5719 (m-80) cc_final: 0.5092 (m-80) REVERT: K 691 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5987 (pp20) REVERT: K 694 MET cc_start: 0.5098 (OUTLIER) cc_final: 0.4616 (mmm) REVERT: K 695 ARG cc_start: 0.4267 (OUTLIER) cc_final: 0.3189 (mtp180) REVERT: L 96 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6505 (ttm) REVERT: L 107 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.5432 (mmt90) REVERT: M 73 ARG cc_start: 0.6655 (tmm160) cc_final: 0.6169 (tmm160) REVERT: M 98 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5471 (pm20) REVERT: M 110 LYS cc_start: 0.6537 (mmmt) cc_final: 0.6301 (mmmt) REVERT: N 17 LYS cc_start: 0.6153 (ptpp) cc_final: 0.5947 (ptmm) REVERT: N 76 ARG cc_start: 0.6111 (ptm-80) cc_final: 0.5612 (ttp80) REVERT: O 29 PHE cc_start: 0.6350 (t80) cc_final: 0.5835 (t80) REVERT: O 133 GLU cc_start: 0.3939 (OUTLIER) cc_final: 0.3524 (mp0) REVERT: O 153 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6527 (mt) REVERT: P 1 MET cc_start: 0.4442 (OUTLIER) cc_final: 0.3116 (tmt) REVERT: P 85 MET cc_start: 0.6645 (mmp) cc_final: 0.5924 (mtp) REVERT: Q 35 GLN cc_start: 0.6593 (tt0) cc_final: 0.5808 (tm-30) REVERT: R 97 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7552 (tp) outliers start: 184 outliers final: 77 residues processed: 667 average time/residue: 0.6179 time to fit residues: 475.8916 Evaluate side-chains 617 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 515 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 476 HIS Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 590 SER Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain K residue 694 MET Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 153 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 195 optimal weight: 5.9990 chunk 241 optimal weight: 0.0970 chunk 131 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN D 2 GLN D 10 ASN E 115 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN H 117 ASN J 101 ASN K 29 HIS K 476 HIS L 47 ASN L 117 ASN M 52 GLN O 35 GLN O 68 ASN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN S 63 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.228367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.209047 restraints weight = 31274.287| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 1.54 r_work: 0.4277 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27538 Z= 0.129 Angle : 0.667 10.706 37298 Z= 0.326 Chirality : 0.040 0.216 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.471 95.358 4564 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Rotamer: Outliers : 5.56 % Allowed : 28.06 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 1.21 (0.15), residues: 3300 helix: 1.48 (0.10), residues: 2617 sheet: -0.19 (1.28), residues: 19 loop : -1.90 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 33 TYR 0.026 0.001 TYR L 152 PHE 0.019 0.001 PHE K 221 TRP 0.012 0.001 TRP A 59 HIS 0.009 0.001 HIS K 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (27522) covalent geometry : angle 0.66745 / 0.33 (37298) hydrogen bonds : bond 0.03584 / 2.35 ( 1998) hydrogen bonds : angle 4.59848 / 3.34 ( 5952) Misc. bond : bond 0.00034 / 0.02 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 565 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5656 (mp0) cc_final: 0.5399 (mp0) REVERT: A 98 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: A 110 LYS cc_start: 0.7404 (mmmm) cc_final: 0.7106 (mmmt) REVERT: B 2 GLN cc_start: 0.5720 (mm-40) cc_final: 0.5422 (mm110) REVERT: B 17 LYS cc_start: 0.6319 (pttp) cc_final: 0.6059 (pttp) REVERT: B 27 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.4179 (pp) REVERT: B 77 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7454 (mtp180) REVERT: B 85 MET cc_start: 0.4272 (mmm) cc_final: 0.3972 (mmt) REVERT: B 113 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7517 (tppp) REVERT: C 9 SER cc_start: 0.7595 (m) cc_final: 0.7256 (t) REVERT: C 53 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5980 (mtm-85) REVERT: C 82 MET cc_start: 0.4697 (mmm) cc_final: 0.4096 (mpm) REVERT: C 102 ARG cc_start: 0.5769 (mtm110) cc_final: 0.5480 (mtm180) REVERT: C 130 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7185 (mp) REVERT: C 146 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6058 (pp) REVERT: D 100 ASP cc_start: 0.6378 (t70) cc_final: 0.5565 (m-30) REVERT: E 60 GLU cc_start: 0.6048 (mt-10) cc_final: 0.5825 (mp0) REVERT: F 58 LYS cc_start: 0.6788 (ptmt) cc_final: 0.6253 (ptpp) REVERT: F 100 ASP cc_start: 0.6380 (OUTLIER) cc_final: 0.6170 (t0) REVERT: G 24 ARG cc_start: 0.6006 (ttp-170) cc_final: 0.5560 (ttm170) REVERT: G 73 ARG cc_start: 0.5712 (tmm-80) cc_final: 0.5425 (ppp80) REVERT: G 98 GLU cc_start: 0.6303 (pm20) cc_final: 0.5710 (pm20) REVERT: G 127 MET cc_start: 0.6877 (tpp) cc_final: 0.6509 (mpm) REVERT: G 135 MET cc_start: 0.5834 (mmp) cc_final: 0.5608 (mmp) REVERT: H 28 GLN cc_start: 0.5856 (mm110) cc_final: 0.5647 (mm110) REVERT: H 54 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6734 (ttmm) REVERT: I 13 ARG cc_start: 0.6859 (mtp180) cc_final: 0.6369 (mtt180) REVERT: J 29 SER cc_start: 0.7956 (t) cc_final: 0.7723 (p) REVERT: J 39 LYS cc_start: 0.7356 (mtmt) cc_final: 0.6947 (mtmm) REVERT: J 65 GLU cc_start: 0.5625 (tm-30) cc_final: 0.5261 (tm-30) REVERT: K 33 ARG cc_start: 0.6848 (ptt90) cc_final: 0.6501 (ptt90) REVERT: K 281 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6510 (ttp) REVERT: K 388 LEU cc_start: 0.7876 (tp) cc_final: 0.7631 (tp) REVERT: K 441 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6571 (pt0) REVERT: K 463 ASN cc_start: 0.7343 (t0) cc_final: 0.7008 (t0) REVERT: K 691 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.6036 (pp20) REVERT: K 693 MET cc_start: 0.6252 (mmm) cc_final: 0.5838 (mmm) REVERT: M 110 LYS cc_start: 0.6491 (mmmt) cc_final: 0.6277 (mmmt) REVERT: N 76 ARG cc_start: 0.6068 (ptm-80) cc_final: 0.5722 (ttp80) REVERT: N 131 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6679 (tp-100) REVERT: O 29 PHE cc_start: 0.6539 (t80) cc_final: 0.6037 (t80) REVERT: O 153 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6432 (mt) REVERT: P 1 MET cc_start: 0.4529 (OUTLIER) cc_final: 0.3209 (tmt) REVERT: P 85 MET cc_start: 0.6597 (mmp) cc_final: 0.5930 (mtt) REVERT: Q 35 GLN cc_start: 0.6586 (tt0) cc_final: 0.5910 (tm-30) REVERT: Q 98 GLU cc_start: 0.5107 (pp20) cc_final: 0.4830 (pp20) REVERT: S 54 GLU cc_start: 0.6642 (mm-30) cc_final: 0.5955 (tp30) outliers start: 155 outliers final: 60 residues processed: 663 average time/residue: 0.6380 time to fit residues: 487.8802 Evaluate side-chains 582 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 510 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain K residue 554 PHE Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 590 SER Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 153 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 246 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 115 ASN H 117 ASN I 46 ASN I 60 GLN J 101 ASN K 26 ASN K 29 HIS ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 GLN ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 68 ASN P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN R 117 ASN R 138 ASN S 63 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.223387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.202718 restraints weight = 31274.052| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 1.58 r_work: 0.4213 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4058 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27538 Z= 0.223 Angle : 0.797 12.140 37298 Z= 0.393 Chirality : 0.045 0.254 4096 Planarity : 0.006 0.063 4812 Dihedral : 9.295 96.823 4557 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.70 % Favored : 96.12 % Rotamer: Outliers : 6.67 % Allowed : 27.99 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3300 helix: 1.04 (0.10), residues: 2611 sheet: -0.10 (1.29), residues: 19 loop : -2.06 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 53 TYR 0.034 0.003 TYR L 152 PHE 0.019 0.002 PHE K 265 TRP 0.016 0.002 TRP O 59 HIS 0.008 0.002 HIS N 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (27522) covalent geometry : angle 0.79726 / 0.39 (37298) hydrogen bonds : bond 0.04464 / 2.94 ( 1998) hydrogen bonds : angle 5.03085 / 3.65 ( 5952) Misc. bond : bond 0.00094 / 0.05 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 550 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.6586 (OUTLIER) cc_final: 0.6268 (tt) REVERT: A 98 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: A 110 LYS cc_start: 0.7445 (mmmm) cc_final: 0.7077 (mmmt) REVERT: B 2 GLN cc_start: 0.5622 (mm-40) cc_final: 0.5389 (mm110) REVERT: B 17 LYS cc_start: 0.6336 (pttp) cc_final: 0.6035 (pttp) REVERT: B 27 LEU cc_start: 0.4524 (OUTLIER) cc_final: 0.4175 (pp) REVERT: B 73 TYR cc_start: 0.5927 (t80) cc_final: 0.5574 (t80) REVERT: B 85 MET cc_start: 0.4355 (mmm) cc_final: 0.4062 (mmt) REVERT: B 113 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7405 (tppp) REVERT: B 128 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5768 (mtm-85) REVERT: C 25 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.5708 (tpt) REVERT: C 53 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.5708 (mtm-85) REVERT: C 102 ARG cc_start: 0.5800 (mtm110) cc_final: 0.5259 (mtm180) REVERT: C 130 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7178 (mp) REVERT: C 146 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6147 (pp) REVERT: D 32 ARG cc_start: 0.6005 (mmt90) cc_final: 0.5764 (mtt-85) REVERT: E 38 ARG cc_start: 0.6046 (ttp-110) cc_final: 0.5688 (ttp80) REVERT: E 93 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6491 (mt) REVERT: F 58 LYS cc_start: 0.6707 (ptmt) cc_final: 0.6396 (ptpt) REVERT: F 100 ASP cc_start: 0.6528 (OUTLIER) cc_final: 0.6202 (t0) REVERT: G 16 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6352 (ptm160) REVERT: G 24 ARG cc_start: 0.5973 (ttp-170) cc_final: 0.5528 (ttm170) REVERT: G 28 ASP cc_start: 0.5623 (m-30) cc_final: 0.5335 (m-30) REVERT: G 73 ARG cc_start: 0.6007 (tmm-80) cc_final: 0.5721 (ppp80) REVERT: G 79 GLN cc_start: 0.6187 (OUTLIER) cc_final: 0.5837 (mp10) REVERT: G 98 GLU cc_start: 0.6365 (pm20) cc_final: 0.5871 (pm20) REVERT: G 127 MET cc_start: 0.7012 (tpp) cc_final: 0.6395 (mpt) REVERT: G 135 MET cc_start: 0.6288 (mmp) cc_final: 0.5842 (mmp) REVERT: H 54 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6900 (ttmm) REVERT: H 100 ASP cc_start: 0.5897 (t70) cc_final: 0.5396 (t0) REVERT: I 89 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7170 (tt) REVERT: I 152 TYR cc_start: 0.7468 (t80) cc_final: 0.6524 (t80) REVERT: J 21 ARG cc_start: 0.1805 (OUTLIER) cc_final: 0.0973 (tpt170) REVERT: J 29 SER cc_start: 0.7983 (t) cc_final: 0.7659 (m) REVERT: J 39 LYS cc_start: 0.7185 (mtmt) cc_final: 0.6941 (mtmm) REVERT: J 78 ARG cc_start: 0.7031 (mmm-85) cc_final: 0.6700 (mtm-85) REVERT: K 166 MET cc_start: 0.5952 (mmp) cc_final: 0.5491 (mmm) REVERT: K 388 LEU cc_start: 0.7937 (tp) cc_final: 0.7709 (tp) REVERT: K 463 ASN cc_start: 0.7375 (t0) cc_final: 0.6984 (t0) REVERT: K 502 ARG cc_start: 0.5200 (mtp180) cc_final: 0.4932 (mtt180) REVERT: K 691 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6035 (pp20) REVERT: L 24 LEU cc_start: 0.5525 (mt) cc_final: 0.5307 (mp) REVERT: M 73 ARG cc_start: 0.6719 (tmm160) cc_final: 0.6352 (tmm160) REVERT: M 98 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5452 (pm20) REVERT: M 110 LYS cc_start: 0.6624 (mmmt) cc_final: 0.6263 (mmmt) REVERT: M 111 GLU cc_start: 0.5568 (pm20) cc_final: 0.5333 (pm20) REVERT: N 76 ARG cc_start: 0.6079 (ptm-80) cc_final: 0.5680 (ttp80) REVERT: N 131 GLN cc_start: 0.7312 (mm-40) cc_final: 0.6744 (tp-100) REVERT: O 29 PHE cc_start: 0.6544 (t80) cc_final: 0.6194 (t80) REVERT: O 133 GLU cc_start: 0.4236 (OUTLIER) cc_final: 0.3858 (mp0) REVERT: O 153 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6666 (mt) REVERT: P 1 MET cc_start: 0.4490 (OUTLIER) cc_final: 0.3416 (tmt) REVERT: P 11 THR cc_start: 0.7020 (p) cc_final: 0.6563 (p) REVERT: Q 35 GLN cc_start: 0.6792 (tt0) cc_final: 0.5990 (tm-30) REVERT: Q 127 MET cc_start: 0.5922 (mmp) cc_final: 0.5593 (mmp) REVERT: R 15 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6918 (mt0) REVERT: R 76 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5915 (ptt90) REVERT: R 96 MET cc_start: 0.7414 (tmm) cc_final: 0.7161 (ttp) REVERT: R 97 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7591 (tp) outliers start: 186 outliers final: 83 residues processed: 670 average time/residue: 0.7004 time to fit residues: 536.9596 Evaluate side-chains 633 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 527 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 554 PHE Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 590 SER Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 688 THR Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 153 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 35 ASN Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 165 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 311 optimal weight: 7.9990 chunk 320 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN G 35 GLN G 79 GLN H 117 ASN I 60 GLN J 101 ASN K 26 ASN K 29 HIS K 383 GLN M 52 GLN ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 68 ASN P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN R 117 ASN R 138 ASN S 63 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.225117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.205113 restraints weight = 30891.489| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 1.54 r_work: 0.4236 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4080 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27538 Z= 0.167 Angle : 0.736 12.745 37298 Z= 0.362 Chirality : 0.043 0.300 4096 Planarity : 0.005 0.061 4812 Dihedral : 9.150 94.193 4555 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.27 % Favored : 96.55 % Rotamer: Outliers : 5.56 % Allowed : 29.50 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.80 (0.15), residues: 3300 helix: 1.20 (0.10), residues: 2617 sheet: -0.03 (1.32), residues: 19 loop : -2.05 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 33 TYR 0.031 0.002 TYR L 152 PHE 0.018 0.002 PHE K 221 TRP 0.017 0.001 TRP A 59 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (27522) covalent geometry : angle 0.73631 / 0.36 (37298) hydrogen bonds : bond 0.04014 / 2.63 ( 1998) hydrogen bonds : angle 4.85711 / 3.53 ( 5952) Misc. bond : bond 0.00054 / 0.03 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 556 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6828 (pm20) REVERT: A 110 LYS cc_start: 0.7510 (mmmm) cc_final: 0.7135 (mmmt) REVERT: A 121 ARG cc_start: 0.4480 (mpt180) cc_final: 0.4260 (mmt-90) REVERT: B 2 GLN cc_start: 0.5558 (mm-40) cc_final: 0.5322 (mm-40) REVERT: B 6 THR cc_start: 0.6647 (m) cc_final: 0.6058 (p) REVERT: B 17 LYS cc_start: 0.6273 (pttp) cc_final: 0.5999 (pttp) REVERT: B 27 LEU cc_start: 0.4556 (OUTLIER) cc_final: 0.4271 (pp) REVERT: B 73 TYR cc_start: 0.5749 (t80) cc_final: 0.5376 (t80) REVERT: B 113 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7495 (tppp) REVERT: C 25 MET cc_start: 0.6156 (mpt) cc_final: 0.5798 (tpt) REVERT: C 53 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.5769 (mtm-85) REVERT: C 102 ARG cc_start: 0.5762 (mtm110) cc_final: 0.5296 (mtm180) REVERT: C 130 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7207 (mp) REVERT: C 146 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6094 (pp) REVERT: D 32 ARG cc_start: 0.6012 (mmt90) cc_final: 0.5787 (mtt-85) REVERT: D 140 MET cc_start: 0.6056 (OUTLIER) cc_final: 0.5764 (ppp) REVERT: E 14 GLU cc_start: 0.5752 (tt0) cc_final: 0.5552 (tt0) REVERT: E 38 ARG cc_start: 0.5982 (ttp-110) cc_final: 0.5600 (ttp80) REVERT: E 93 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6389 (mt) REVERT: E 121 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5500 (ppp80) REVERT: F 58 LYS cc_start: 0.6753 (ptmt) cc_final: 0.6456 (ptpt) REVERT: G 24 ARG cc_start: 0.5997 (ttp-170) cc_final: 0.5525 (ttm170) REVERT: G 28 ASP cc_start: 0.5674 (m-30) cc_final: 0.5339 (m-30) REVERT: G 73 ARG cc_start: 0.5883 (tmm-80) cc_final: 0.5642 (ppp80) REVERT: G 98 GLU cc_start: 0.6311 (pm20) cc_final: 0.5817 (pm20) REVERT: G 127 MET cc_start: 0.6900 (tpp) cc_final: 0.6250 (mpt) REVERT: G 135 MET cc_start: 0.6202 (mmp) cc_final: 0.5706 (mmp) REVERT: H 54 LYS cc_start: 0.7075 (mmtt) cc_final: 0.6832 (ttmm) REVERT: H 100 ASP cc_start: 0.6010 (t70) cc_final: 0.5474 (t0) REVERT: J 21 ARG cc_start: 0.1772 (OUTLIER) cc_final: 0.0918 (tpt170) REVERT: J 29 SER cc_start: 0.7966 (t) cc_final: 0.7670 (m) REVERT: J 39 LYS cc_start: 0.7257 (mtmt) cc_final: 0.7001 (mtmm) REVERT: J 68 ARG cc_start: 0.5569 (mmp-170) cc_final: 0.5355 (mmp-170) REVERT: K 166 MET cc_start: 0.5886 (mmp) cc_final: 0.5437 (mmm) REVERT: K 388 LEU cc_start: 0.7952 (tp) cc_final: 0.7696 (tp) REVERT: K 463 ASN cc_start: 0.7319 (t0) cc_final: 0.6942 (t0) REVERT: K 589 ARG cc_start: 0.6997 (tpt-90) cc_final: 0.6754 (tpt-90) REVERT: K 593 GLN cc_start: 0.7116 (mm110) cc_final: 0.6633 (mm110) REVERT: K 691 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6097 (pp20) REVERT: L 24 LEU cc_start: 0.5430 (mt) cc_final: 0.5202 (mp) REVERT: L 96 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6403 (ttm) REVERT: M 73 ARG cc_start: 0.6701 (tmm160) cc_final: 0.6373 (tmm160) REVERT: M 110 LYS cc_start: 0.6567 (mmmt) cc_final: 0.6362 (mmmt) REVERT: N 76 ARG cc_start: 0.5990 (ptm-80) cc_final: 0.5650 (ttp80) REVERT: N 131 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6726 (tp-100) REVERT: O 29 PHE cc_start: 0.6660 (t80) cc_final: 0.6422 (t80) REVERT: O 133 GLU cc_start: 0.4056 (OUTLIER) cc_final: 0.3719 (mp0) REVERT: O 153 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6654 (mt) REVERT: P 3 ASP cc_start: 0.5639 (OUTLIER) cc_final: 0.5199 (p0) REVERT: P 28 GLN cc_start: 0.5512 (OUTLIER) cc_final: 0.4729 (mp-120) REVERT: P 85 MET cc_start: 0.6871 (mmt) cc_final: 0.6048 (mtp) REVERT: Q 35 GLN cc_start: 0.6654 (tt0) cc_final: 0.5945 (tm-30) REVERT: R 15 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6900 (mt0) REVERT: R 76 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5833 (ptt90) REVERT: R 96 MET cc_start: 0.7374 (tmm) cc_final: 0.7052 (ttp) outliers start: 155 outliers final: 73 residues processed: 653 average time/residue: 0.6650 time to fit residues: 499.1305 Evaluate side-chains 623 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 532 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 234 ARG Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 554 PHE Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 590 SER Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 688 THR Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 153 ILE Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 35 ASN Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 321 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 131 GLN G 35 GLN H 117 ASN I 60 GLN J 101 ASN K 26 ASN K 29 HIS ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 GLN K 320 GLN K 383 GLN M 52 GLN ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 GLN R 110 ASN R 117 ASN R 138 ASN S 63 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.223847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.203722 restraints weight = 31045.921| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 1.54 r_work: 0.4223 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4065 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 27538 Z= 0.207 Angle : 0.794 11.893 37298 Z= 0.392 Chirality : 0.045 0.290 4096 Planarity : 0.006 0.062 4812 Dihedral : 9.116 94.397 4553 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 5.84 % Allowed : 29.07 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.53 (0.14), residues: 3300 helix: 0.99 (0.10), residues: 2617 sheet: -0.17 (1.30), residues: 19 loop : -2.10 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 33 TYR 0.040 0.003 TYR B 152 PHE 0.018 0.002 PHE S 37 TRP 0.014 0.002 TRP C 84 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (27522) covalent geometry : angle 0.79351 / 0.39 (37298) hydrogen bonds : bond 0.04372 / 2.87 ( 1998) hydrogen bonds : angle 5.03131 / 3.65 ( 5952) Misc. bond : bond 0.00086 / 0.05 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 538 time to evaluate : 0.940 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: A 50 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.6213 (tt) REVERT: A 98 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: A 110 LYS cc_start: 0.7521 (mmmm) cc_final: 0.7142 (mmmt) REVERT: A 121 ARG cc_start: 0.4641 (mpt180) cc_final: 0.4332 (mmt-90) REVERT: B 6 THR cc_start: 0.6608 (m) cc_final: 0.6330 (p) REVERT: B 17 LYS cc_start: 0.6263 (pttp) cc_final: 0.5982 (pttp) REVERT: B 27 LEU cc_start: 0.4657 (OUTLIER) cc_final: 0.4341 (pp) REVERT: B 85 MET cc_start: 0.4541 (mmm) cc_final: 0.3882 (mmm) REVERT: B 113 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7438 (tppp) REVERT: C 9 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7417 (t) REVERT: C 25 MET cc_start: 0.6210 (mpt) cc_final: 0.5922 (tpt) REVERT: C 102 ARG cc_start: 0.5728 (mtm110) cc_final: 0.5306 (mtm180) REVERT: C 109 MET cc_start: 0.6363 (tpp) cc_final: 0.6132 (tpt) REVERT: C 130 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7200 (mp) REVERT: C 146 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6164 (pp) REVERT: D 140 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.5751 (ppp) REVERT: E 38 ARG cc_start: 0.5973 (ttp-110) cc_final: 0.5576 (ttp80) REVERT: E 93 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6405 (mt) REVERT: E 121 ARG cc_start: 0.5830 (OUTLIER) cc_final: 0.5593 (ppp80) REVERT: E 131 LYS cc_start: 0.6521 (tmmm) cc_final: 0.5948 (ttmt) REVERT: F 42 MET cc_start: 0.5162 (OUTLIER) cc_final: 0.4816 (tpp) REVERT: F 58 LYS cc_start: 0.6715 (ptmt) cc_final: 0.6417 (ptpt) REVERT: G 16 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6581 (ptm160) REVERT: G 24 ARG cc_start: 0.6027 (ttp-170) cc_final: 0.5691 (ttm170) REVERT: G 28 ASP cc_start: 0.5668 (m-30) cc_final: 0.5450 (m-30) REVERT: G 73 ARG cc_start: 0.5987 (tmm-80) cc_final: 0.5745 (ppp80) REVERT: G 79 GLN cc_start: 0.6082 (OUTLIER) cc_final: 0.5767 (tp40) REVERT: G 98 GLU cc_start: 0.6349 (pm20) cc_final: 0.5944 (pm20) REVERT: G 127 MET cc_start: 0.6937 (tpp) cc_final: 0.5624 (mpt) REVERT: G 142 ASP cc_start: 0.4940 (m-30) cc_final: 0.4644 (m-30) REVERT: G 150 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.4891 (t80) REVERT: H 54 LYS cc_start: 0.7088 (mmtt) cc_final: 0.6834 (ttmm) REVERT: H 100 ASP cc_start: 0.5942 (t70) cc_final: 0.5435 (t0) REVERT: I 13 ARG cc_start: 0.6954 (mtp180) cc_final: 0.6663 (mtp180) REVERT: J 21 ARG cc_start: 0.1835 (OUTLIER) cc_final: 0.1091 (tpt170) REVERT: J 29 SER cc_start: 0.7964 (t) cc_final: 0.7656 (m) REVERT: J 39 LYS cc_start: 0.7177 (mtmt) cc_final: 0.6917 (mtmm) REVERT: J 68 ARG cc_start: 0.5597 (mmp-170) cc_final: 0.5359 (mmp-170) REVERT: J 140 GLU cc_start: 0.5601 (pp20) cc_final: 0.5254 (pt0) REVERT: K 32 ASP cc_start: 0.5952 (t0) cc_final: 0.5488 (t70) REVERT: K 388 LEU cc_start: 0.7955 (tp) cc_final: 0.7706 (tp) REVERT: K 463 ASN cc_start: 0.7403 (t0) cc_final: 0.7008 (t0) REVERT: K 589 ARG cc_start: 0.6925 (tpt-90) cc_final: 0.6645 (tpt-90) REVERT: K 593 GLN cc_start: 0.7159 (mm110) cc_final: 0.6701 (mm110) REVERT: K 691 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6135 (pp20) REVERT: L 24 LEU cc_start: 0.5444 (mt) cc_final: 0.5209 (mp) REVERT: L 96 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6442 (ttm) REVERT: M 73 ARG cc_start: 0.6730 (tmm160) cc_final: 0.6461 (tmm160) REVERT: M 101 LEU cc_start: 0.7328 (tp) cc_final: 0.6919 (tt) REVERT: M 110 LYS cc_start: 0.6613 (mmmt) cc_final: 0.6408 (mmmt) REVERT: N 131 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6729 (tp-100) REVERT: N 134 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6514 (tttt) REVERT: O 29 PHE cc_start: 0.6658 (t80) cc_final: 0.6400 (t80) REVERT: O 127 MET cc_start: 0.5807 (mmm) cc_final: 0.5537 (mpm) REVERT: O 133 GLU cc_start: 0.4112 (OUTLIER) cc_final: 0.3788 (mp0) REVERT: O 153 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6784 (mt) REVERT: P 53 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7427 (m) REVERT: P 85 MET cc_start: 0.6852 (mmt) cc_final: 0.6021 (mtp) REVERT: Q 35 GLN cc_start: 0.6707 (tt0) cc_final: 0.6039 (tm-30) REVERT: Q 125 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5306 (tp30) REVERT: R 15 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6930 (mt0) REVERT: R 76 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5850 (ptt90) REVERT: R 96 MET cc_start: 0.7370 (tmm) cc_final: 0.7048 (ttp) REVERT: R 97 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7622 (tp) outliers start: 163 outliers final: 85 residues processed: 641 average time/residue: 0.6647 time to fit residues: 489.1279 Evaluate side-chains 628 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 518 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 234 ARG Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 476 HIS Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 554 PHE Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 590 SER Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 688 THR Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 153 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 35 ASN Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 126 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 107 optimal weight: 0.0570 chunk 109 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 79 GLN H 117 ASN I 60 GLN J 101 ASN K 29 HIS K 383 GLN K 609 HIS ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN R 138 ASN S 63 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.227821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.208281 restraints weight = 31032.545| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 1.53 r_work: 0.4260 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4110 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27538 Z= 0.143 Angle : 0.720 12.473 37298 Z= 0.355 Chirality : 0.042 0.281 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.114 91.561 4553 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.24 % Favored : 96.61 % Rotamer: Outliers : 4.27 % Allowed : 31.04 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.15), residues: 3300 helix: 1.33 (0.10), residues: 2617 sheet: -0.06 (1.31), residues: 19 loop : -1.99 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 33 TYR 0.032 0.002 TYR B 152 PHE 0.020 0.001 PHE K 221 TRP 0.015 0.001 TRP A 59 HIS 0.011 0.001 HIS K 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (27522) covalent geometry : angle 0.71985 / 0.35 (37298) hydrogen bonds : bond 0.03800 / 2.50 ( 1998) hydrogen bonds : angle 4.78444 / 3.48 ( 5952) Misc. bond : bond 0.00041 / 0.03 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 559 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5633 (mp0) cc_final: 0.5016 (pm20) REVERT: A 58 PHE cc_start: 0.6067 (t80) cc_final: 0.5840 (t80) REVERT: A 98 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: A 110 LYS cc_start: 0.7507 (mmmm) cc_final: 0.7167 (mmmt) REVERT: B 6 THR cc_start: 0.6689 (m) cc_final: 0.6371 (p) REVERT: B 17 LYS cc_start: 0.6335 (pttp) cc_final: 0.6064 (pttp) REVERT: B 27 LEU cc_start: 0.4676 (OUTLIER) cc_final: 0.4419 (pp) REVERT: B 73 TYR cc_start: 0.5720 (t80) cc_final: 0.5347 (t80) REVERT: B 85 MET cc_start: 0.4507 (mmm) cc_final: 0.3838 (mmm) REVERT: B 113 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7525 (tppp) REVERT: B 152 TYR cc_start: 0.6464 (m-80) cc_final: 0.6225 (m-80) REVERT: C 24 GLU cc_start: 0.6644 (tp30) cc_final: 0.6323 (tp30) REVERT: C 25 MET cc_start: 0.6099 (mpt) cc_final: 0.5790 (tpt) REVERT: C 26 ILE cc_start: 0.7085 (mt) cc_final: 0.6817 (tp) REVERT: C 53 ARG cc_start: 0.6259 (mtm-85) cc_final: 0.6004 (mtm-85) REVERT: C 79 GLN cc_start: 0.6062 (OUTLIER) cc_final: 0.5735 (mm110) REVERT: C 82 MET cc_start: 0.4727 (mmm) cc_final: 0.4098 (mpm) REVERT: C 102 ARG cc_start: 0.5642 (mtm110) cc_final: 0.5332 (mtm180) REVERT: C 109 MET cc_start: 0.6167 (tpp) cc_final: 0.5901 (tpt) REVERT: C 130 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7212 (mp) REVERT: C 146 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6066 (pp) REVERT: D 1 MET cc_start: 0.5800 (ptp) cc_final: 0.5539 (pmt) REVERT: D 7 THR cc_start: 0.6477 (t) cc_final: 0.6115 (m) REVERT: D 58 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6894 (ptmt) REVERT: D 140 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5729 (ppp) REVERT: E 38 ARG cc_start: 0.5974 (ttp-110) cc_final: 0.5547 (ttp80) REVERT: E 60 GLU cc_start: 0.6145 (mt-10) cc_final: 0.5888 (mp0) REVERT: F 58 LYS cc_start: 0.6807 (ptmt) cc_final: 0.6512 (ptpt) REVERT: F 119 LEU cc_start: 0.6425 (mm) cc_final: 0.6221 (mp) REVERT: G 16 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6392 (ptm160) REVERT: G 24 ARG cc_start: 0.6039 (ttp-170) cc_final: 0.5553 (ttm170) REVERT: G 28 ASP cc_start: 0.5632 (m-30) cc_final: 0.5309 (m-30) REVERT: G 73 ARG cc_start: 0.5830 (tmm-80) cc_final: 0.5624 (ppp80) REVERT: G 98 GLU cc_start: 0.6216 (pm20) cc_final: 0.5843 (pm20) REVERT: G 127 MET cc_start: 0.6891 (tpp) cc_final: 0.6362 (mpm) REVERT: G 135 MET cc_start: 0.6089 (mmp) cc_final: 0.5609 (mmp) REVERT: H 54 LYS cc_start: 0.6969 (mmtt) cc_final: 0.6743 (ttmm) REVERT: H 76 ARG cc_start: 0.5689 (OUTLIER) cc_final: 0.5488 (ppp-140) REVERT: H 100 ASP cc_start: 0.5942 (t70) cc_final: 0.5415 (t0) REVERT: J 21 ARG cc_start: 0.1918 (OUTLIER) cc_final: 0.1029 (tpt170) REVERT: J 29 SER cc_start: 0.7932 (t) cc_final: 0.7658 (p) REVERT: J 39 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6869 (mtmm) REVERT: J 140 GLU cc_start: 0.5480 (pp20) cc_final: 0.5240 (pt0) REVERT: K 29 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.6130 (t-170) REVERT: K 32 ASP cc_start: 0.5900 (t0) cc_final: 0.5431 (t70) REVERT: K 33 ARG cc_start: 0.6580 (ptt90) cc_final: 0.6357 (ptt90) REVERT: K 166 MET cc_start: 0.5709 (mmp) cc_final: 0.5360 (mmm) REVERT: K 281 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6716 (ttp) REVERT: K 377 PHE cc_start: 0.7360 (t80) cc_final: 0.6987 (t80) REVERT: K 383 GLN cc_start: 0.6951 (pt0) cc_final: 0.6747 (pt0) REVERT: K 388 LEU cc_start: 0.7998 (tp) cc_final: 0.7729 (tp) REVERT: K 463 ASN cc_start: 0.7307 (t0) cc_final: 0.6971 (t0) REVERT: K 593 GLN cc_start: 0.6984 (mm110) cc_final: 0.6669 (mm110) REVERT: K 691 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.6104 (pp20) REVERT: L 24 LEU cc_start: 0.5353 (mt) cc_final: 0.5108 (mp) REVERT: L 140 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.4820 (pp-130) REVERT: M 73 ARG cc_start: 0.6661 (tmm160) cc_final: 0.6332 (tmm160) REVERT: M 101 LEU cc_start: 0.7306 (tp) cc_final: 0.6899 (tt) REVERT: N 17 LYS cc_start: 0.6196 (ptmm) cc_final: 0.5769 (ptmm) REVERT: N 131 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6672 (tp-100) REVERT: N 140 MET cc_start: 0.3803 (pmt) cc_final: 0.2905 (pmm) REVERT: O 24 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.4913 (tpm170) REVERT: O 29 PHE cc_start: 0.6655 (t80) cc_final: 0.6120 (t80) REVERT: O 68 ASN cc_start: 0.5052 (OUTLIER) cc_final: 0.4800 (p0) REVERT: O 133 GLU cc_start: 0.4139 (OUTLIER) cc_final: 0.3673 (mp0) REVERT: O 153 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6646 (mt) REVERT: P 1 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.3311 (tmt) REVERT: P 53 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7293 (m) REVERT: P 85 MET cc_start: 0.6797 (mmt) cc_final: 0.6008 (mtp) REVERT: Q 35 GLN cc_start: 0.6628 (tt0) cc_final: 0.5956 (tm-30) REVERT: Q 152 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5840 (tp) REVERT: R 15 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: R 76 ARG cc_start: 0.6184 (OUTLIER) cc_final: 0.5725 (ptt90) REVERT: R 96 MET cc_start: 0.7203 (tmm) cc_final: 0.6969 (ttp) REVERT: S 46 MET cc_start: 0.6382 (mtm) cc_final: 0.5990 (ptt) outliers start: 119 outliers final: 56 residues processed: 632 average time/residue: 0.6422 time to fit residues: 466.6434 Evaluate side-chains 604 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 524 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 554 PHE Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 590 SER Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 688 THR Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 24 ARG Chi-restraints excluded: chain O residue 68 ASN Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 153 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 6 optimal weight: 0.0070 chunk 133 optimal weight: 9.9990 chunk 274 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 281 optimal weight: 0.8980 chunk 272 optimal weight: 0.9980 chunk 302 optimal weight: 0.9990 chunk 325 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 79 GLN J 101 ASN K 26 ASN ** K 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN S 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.227702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.208139 restraints weight = 31051.568| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 1.52 r_work: 0.4264 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4111 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 27538 Z= 0.186 Angle : 0.843 59.200 37298 Z= 0.447 Chirality : 0.046 1.077 4096 Planarity : 0.006 0.143 4812 Dihedral : 9.116 91.563 4552 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.36 % Favored : 96.52 % Rotamer: Outliers : 3.44 % Allowed : 32.22 % Favored : 64.34 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 1.03 (0.15), residues: 3300 helix: 1.36 (0.10), residues: 2617 sheet: -0.03 (1.32), residues: 19 loop : -1.98 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 16 TYR 0.038 0.002 TYR H 91 PHE 0.019 0.001 PHE K 221 TRP 0.020 0.001 TRP C 84 HIS 0.221 0.006 HIS K 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (27522) covalent geometry : angle 0.84313 / 0.45 (37298) hydrogen bonds : bond 0.03836 / 2.53 ( 1998) hydrogen bonds : angle 4.79425 / 3.49 ( 5952) Misc. bond : bond 0.00050 / 0.04 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 526 time to evaluate : 1.058 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: A 22 GLU cc_start: 0.5639 (mp0) cc_final: 0.4987 (pm20) REVERT: A 58 PHE cc_start: 0.6081 (t80) cc_final: 0.5867 (t80) REVERT: A 98 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: A 110 LYS cc_start: 0.7496 (mmmm) cc_final: 0.7155 (mmmt) REVERT: B 6 THR cc_start: 0.6680 (m) cc_final: 0.6361 (p) REVERT: B 17 LYS cc_start: 0.6310 (pttp) cc_final: 0.6039 (pttp) REVERT: B 27 LEU cc_start: 0.4710 (OUTLIER) cc_final: 0.4452 (pp) REVERT: B 73 TYR cc_start: 0.5715 (t80) cc_final: 0.5338 (t80) REVERT: B 85 MET cc_start: 0.4542 (mmm) cc_final: 0.4260 (mmt) REVERT: B 113 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7521 (tppp) REVERT: C 24 GLU cc_start: 0.6645 (tp30) cc_final: 0.6278 (tp30) REVERT: C 25 MET cc_start: 0.6077 (mpt) cc_final: 0.5803 (tpt) REVERT: C 26 ILE cc_start: 0.7086 (mt) cc_final: 0.6837 (tp) REVERT: C 79 GLN cc_start: 0.6067 (OUTLIER) cc_final: 0.5742 (mm110) REVERT: C 82 MET cc_start: 0.4733 (mmm) cc_final: 0.4125 (mpm) REVERT: C 102 ARG cc_start: 0.5627 (mtm110) cc_final: 0.5180 (mtm180) REVERT: C 109 MET cc_start: 0.6228 (tpp) cc_final: 0.5943 (tpt) REVERT: C 130 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7223 (mp) REVERT: C 146 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6067 (pp) REVERT: D 1 MET cc_start: 0.5785 (ptp) cc_final: 0.5559 (pmt) REVERT: D 7 THR cc_start: 0.6472 (t) cc_final: 0.6110 (m) REVERT: D 58 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6895 (ptmt) REVERT: D 140 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.5713 (ppp) REVERT: E 38 ARG cc_start: 0.5960 (ttp-110) cc_final: 0.5546 (ttp80) REVERT: E 93 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6335 (mt) REVERT: F 58 LYS cc_start: 0.6810 (ptmt) cc_final: 0.6517 (ptpt) REVERT: G 16 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6374 (ptm160) REVERT: G 24 ARG cc_start: 0.6036 (ttp-170) cc_final: 0.5537 (ttm170) REVERT: G 28 ASP cc_start: 0.5667 (m-30) cc_final: 0.5344 (m-30) REVERT: G 73 ARG cc_start: 0.5827 (tmm-80) cc_final: 0.5615 (ppp80) REVERT: G 79 GLN cc_start: 0.5885 (OUTLIER) cc_final: 0.5290 (mp10) REVERT: G 98 GLU cc_start: 0.6208 (pm20) cc_final: 0.5837 (pm20) REVERT: G 127 MET cc_start: 0.6898 (tpp) cc_final: 0.6421 (mpm) REVERT: G 135 MET cc_start: 0.6064 (mmp) cc_final: 0.5577 (mmp) REVERT: H 54 LYS cc_start: 0.6942 (mmtt) cc_final: 0.6718 (ttmm) REVERT: H 76 ARG cc_start: 0.5701 (OUTLIER) cc_final: 0.5481 (ppp-140) REVERT: H 100 ASP cc_start: 0.5970 (t70) cc_final: 0.5448 (t0) REVERT: I 53 LYS cc_start: 0.7647 (mtpm) cc_final: 0.7248 (ttpt) REVERT: J 21 ARG cc_start: 0.1931 (OUTLIER) cc_final: 0.1053 (tpt170) REVERT: J 29 SER cc_start: 0.7933 (t) cc_final: 0.7669 (p) REVERT: J 39 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6878 (mtmm) REVERT: J 78 ARG cc_start: 0.6947 (mmm-85) cc_final: 0.6654 (mtm-85) REVERT: J 140 GLU cc_start: 0.5514 (pp20) cc_final: 0.5241 (pt0) REVERT: K 29 HIS cc_start: 0.6493 (OUTLIER) cc_final: 0.6101 (t-170) REVERT: K 32 ASP cc_start: 0.5886 (t0) cc_final: 0.5445 (t70) REVERT: K 33 ARG cc_start: 0.6586 (ptt90) cc_final: 0.6355 (ptt90) REVERT: K 162 MET cc_start: 0.5469 (mmt) cc_final: 0.4937 (mmm) REVERT: K 166 MET cc_start: 0.5690 (mmp) cc_final: 0.5363 (mmm) REVERT: K 281 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6722 (ttp) REVERT: K 377 PHE cc_start: 0.7380 (t80) cc_final: 0.7003 (t80) REVERT: K 388 LEU cc_start: 0.8022 (tp) cc_final: 0.7751 (tp) REVERT: K 463 ASN cc_start: 0.7288 (t0) cc_final: 0.6958 (t0) REVERT: K 593 GLN cc_start: 0.6968 (mm110) cc_final: 0.6536 (mm110) REVERT: K 691 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6064 (pp20) REVERT: L 24 LEU cc_start: 0.5332 (mt) cc_final: 0.5112 (mp) REVERT: L 84 ASP cc_start: 0.6696 (m-30) cc_final: 0.6485 (m-30) REVERT: L 140 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.4791 (pp-130) REVERT: M 73 ARG cc_start: 0.6667 (tmm160) cc_final: 0.6346 (tmm160) REVERT: M 101 LEU cc_start: 0.7303 (tp) cc_final: 0.6885 (tt) REVERT: N 17 LYS cc_start: 0.6174 (ptmm) cc_final: 0.5753 (ptmm) REVERT: N 131 GLN cc_start: 0.7256 (mm-40) cc_final: 0.6676 (tp-100) REVERT: N 140 MET cc_start: 0.3790 (pmt) cc_final: 0.3062 (pmm) REVERT: O 24 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.4921 (tpm170) REVERT: O 29 PHE cc_start: 0.6681 (t80) cc_final: 0.6141 (t80) REVERT: O 133 GLU cc_start: 0.4003 (OUTLIER) cc_final: 0.3668 (mp0) REVERT: O 153 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6676 (mt) REVERT: P 1 MET cc_start: 0.4302 (OUTLIER) cc_final: 0.3307 (tmt) REVERT: P 53 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7291 (m) REVERT: P 85 MET cc_start: 0.6781 (mmt) cc_final: 0.5992 (mtp) REVERT: Q 35 GLN cc_start: 0.6633 (tt0) cc_final: 0.6006 (tm-30) REVERT: Q 152 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5865 (tp) REVERT: R 15 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6651 (mp10) REVERT: R 76 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5727 (ptt90) REVERT: R 96 MET cc_start: 0.7204 (tmm) cc_final: 0.6961 (ttp) REVERT: S 46 MET cc_start: 0.6434 (mtm) cc_final: 0.6043 (ptt) outliers start: 96 outliers final: 63 residues processed: 588 average time/residue: 0.6826 time to fit residues: 460.0912 Evaluate side-chains 609 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 521 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 554 PHE Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 590 SER Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 688 THR Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 24 ARG Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 153 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 135 MET Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 236 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN H 131 GLN J 101 ASN K 26 ASN K 383 GLN ** K 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN S 63 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.227650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.208173 restraints weight = 30831.866| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 1.52 r_work: 0.4266 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 27538 Z= 0.186 Angle : 0.843 59.200 37298 Z= 0.447 Chirality : 0.046 1.077 4096 Planarity : 0.006 0.143 4812 Dihedral : 9.116 91.563 4552 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.36 % Favored : 96.52 % Rotamer: Outliers : 3.33 % Allowed : 32.44 % Favored : 64.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 1.03 (0.15), residues: 3300 helix: 1.36 (0.10), residues: 2617 sheet: -0.03 (1.32), residues: 19 loop : -1.98 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 16 TYR 0.038 0.002 TYR H 91 PHE 0.019 0.001 PHE K 221 TRP 0.020 0.001 TRP C 84 HIS 0.221 0.006 HIS K 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (27522) covalent geometry : angle 0.84313 / 0.45 (37298) hydrogen bonds : bond 0.03836 / 2.53 ( 1998) hydrogen bonds : angle 4.79425 / 3.49 ( 5952) Misc. bond : bond 0.00050 / 0.04 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10605.26 seconds wall clock time: 196 minutes 58.61 seconds (11818.61 seconds total)