Starting phenix.real_space_refine on Mon Jun 23 01:37:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uhe_42278/06_2025/8uhe_42278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uhe_42278/06_2025/8uhe_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_42278/06_2025/8uhe_42278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uhe_42278/06_2025/8uhe_42278.map" model { file = "/net/cci-nas-00/data/ceres_data/8uhe_42278/06_2025/8uhe_42278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uhe_42278/06_2025/8uhe_42278.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.63, per 1000 atoms: 0.58 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: 6.90 Conformation dependent library (CDL) restraints added in 3.3 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: 2.25 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: 8.87 Time building geometry restraints manager: 8.03 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 57.870 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.150 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:14.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 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 : 13.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.039 0.002 TRP C 84 HIS 0.015 0.002 HIS N 155 PHE 0.042 0.003 PHE P 88 TYR 0.059 0.004 TYR K 626 ARG 0.045 0.001 ARG J 17 Details of bonding type rmsd hydrogen bonds : bond 0.11602 ( 1998) hydrogen bonds : angle 6.15572 ( 5952) covalent geometry : bond 0.01042 (27522) covalent geometry : angle 1.17039 (37298) Misc. bond : bond 0.04796 ( 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 : 2.646 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: 1.7834 time to fit residues: 1320.2416 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 : 3.049 ------------------------------------------------------------------------------- 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 277 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 298 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 K 564 HIS L 2 GLN L 10 ASN L 117 ASN M 52 GLN M 53 ASN M 79 GLN M 122 ASN 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 110 ASN R 117 ASN R 138 ASN S 63 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.227051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.206968 restraints weight = 31338.813| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 1.56 r_work: 0.4248 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4097 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27538 Z= 0.161 Angle : 0.730 10.294 37298 Z= 0.357 Chirality : 0.042 0.206 4096 Planarity : 0.006 0.071 4812 Dihedral : 10.253 104.675 4652 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.18 % Favored : 96.67 % Rotamer: Outliers : 6.74 % Allowed : 24.87 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3300 helix: 0.87 (0.10), residues: 2610 sheet: 1.95 (1.42), residues: 15 loop : -1.98 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 84 HIS 0.015 0.001 HIS K 29 PHE 0.026 0.002 PHE P 88 TYR 0.027 0.002 TYR L 151 ARG 0.007 0.001 ARG K 253 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 1998) hydrogen bonds : angle 4.93115 ( 5952) covalent geometry : bond 0.00355 (27522) covalent geometry : angle 0.72991 (37298) Misc. bond : bond 0.00046 ( 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 746 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 558 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5361 (mp0) cc_final: 0.4897 (mp0) REVERT: A 80 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.5264 (ttm170) REVERT: A 110 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6977 (mmmt) REVERT: A 152 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6014 (mm) REVERT: B 8 LEU cc_start: 0.6694 (mt) cc_final: 0.6462 (mp) REVERT: B 17 LYS cc_start: 0.6241 (pttp) cc_final: 0.5942 (pttp) REVERT: B 85 MET cc_start: 0.4075 (mmm) cc_final: 0.3610 (mmt) REVERT: C 25 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.6100 (mpt) REVERT: C 53 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.5645 (mtm-85) REVERT: C 82 MET cc_start: 0.4252 (OUTLIER) cc_final: 0.2950 (mmp) REVERT: C 98 ASP cc_start: 0.6131 (p0) cc_final: 0.5818 (p0) REVERT: C 146 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6074 (pp) REVERT: D 87 PHE cc_start: 0.7412 (m-80) cc_final: 0.7209 (m-80) REVERT: D 131 GLN cc_start: 0.6761 (pt0) cc_final: 0.6426 (pt0) REVERT: E 38 ARG cc_start: 0.6150 (ttp-170) cc_final: 0.5842 (ttp80) REVERT: E 99 ARG cc_start: 0.6111 (tmm-80) cc_final: 0.5880 (tmm-80) REVERT: F 3 ASP cc_start: 0.6377 (p0) cc_final: 0.6166 (p0) REVERT: F 100 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6352 (t0) REVERT: G 73 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5663 (ppp80) REVERT: G 98 GLU cc_start: 0.6258 (pm20) cc_final: 0.5621 (pm20) REVERT: H 54 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6911 (ttmm) REVERT: H 140 MET cc_start: 0.5170 (pmm) cc_final: 0.4682 (pp-130) REVERT: I 13 ARG cc_start: 0.6763 (mtp180) cc_final: 0.6526 (mtp180) REVERT: I 71 ASN cc_start: 0.7314 (t0) cc_final: 0.7113 (t160) REVERT: I 73 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: I 107 ARG cc_start: 0.6496 (tpt90) cc_final: 0.6223 (tpt170) REVERT: J 29 SER cc_start: 0.7978 (t) cc_final: 0.7614 (p) REVERT: J 39 LYS cc_start: 0.7370 (mtmt) cc_final: 0.7113 (mtmm) REVERT: J 83 LEU cc_start: 0.8062 (mp) cc_final: 0.7834 (mm) REVERT: J 141 ARG cc_start: 0.6562 (ptm160) cc_final: 0.6355 (ptp-170) REVERT: K 365 ARG cc_start: 0.7618 (ptt90) cc_final: 0.7388 (ptm160) REVERT: K 426 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6401 (tt0) REVERT: K 463 ASN cc_start: 0.7334 (t0) cc_final: 0.6934 (t0) REVERT: K 543 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5879 (mm-30) REVERT: K 622 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6134 (mt-10) REVERT: K 626 TYR cc_start: 0.5751 (m-80) cc_final: 0.5192 (m-80) REVERT: K 691 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6209 (pp20) REVERT: K 694 MET cc_start: 0.5159 (OUTLIER) cc_final: 0.4422 (mmm) REVERT: K 695 ARG cc_start: 0.4526 (OUTLIER) cc_final: 0.4248 (mtp180) REVERT: L 107 ARG cc_start: 0.5836 (tpp-160) cc_final: 0.5420 (ttm-80) REVERT: M 110 LYS cc_start: 0.6461 (mmmt) cc_final: 0.6140 (mmmt) REVERT: O 57 LYS cc_start: 0.4739 (ptmt) cc_final: 0.4045 (ptmt) REVERT: P 85 MET cc_start: 0.6505 (mmp) cc_final: 0.5819 (mtp) REVERT: P 135 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: Q 35 GLN cc_start: 0.6533 (tt0) cc_final: 0.5879 (tp-100) REVERT: Q 98 GLU cc_start: 0.5387 (pp20) cc_final: 0.5058 (pp20) REVERT: Q 103 ASP cc_start: 0.6839 (m-30) cc_final: 0.6637 (m-30) REVERT: R 97 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7512 (tp) REVERT: R 113 LYS cc_start: 0.6234 (OUTLIER) cc_final: 0.5991 (tmmt) REVERT: R 116 TYR cc_start: 0.7695 (m-10) cc_final: 0.7481 (m-10) outliers start: 188 outliers final: 64 residues processed: 675 average time/residue: 1.6062 time to fit residues: 1248.3634 Evaluate side-chains 607 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 525 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 LYS 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 12 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 45 SER 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 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 65 ILE 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 73 ARG 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 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 65 THR Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 153 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 578 VAL 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 103 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 M residue 153 ILE Chi-restraints excluded: chain N residue 15 GLN 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 P residue 36 LEU Chi-restraints excluded: chain P residue 43 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 89 ILE 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 97 LEU Chi-restraints excluded: chain R residue 113 LYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 74 optimal weight: 0.4980 chunk 195 optimal weight: 4.9990 chunk 283 optimal weight: 7.9990 chunk 328 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 326 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 122 ASN C 6 GLN C 10 ASN C 68 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 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS K 426 GLN K 451 GLN K 476 HIS L 47 ASN M 52 GLN M 79 GLN N 110 ASN O 53 ASN R 15 GLN R 28 GLN R 110 ASN R 117 ASN ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.224004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.203315 restraints weight = 31236.975| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 1.59 r_work: 0.4217 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4056 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27538 Z= 0.199 Angle : 0.772 10.733 37298 Z= 0.378 Chirality : 0.044 0.199 4096 Planarity : 0.006 0.066 4812 Dihedral : 9.743 101.999 4577 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.45 % Favored : 96.36 % Rotamer: Outliers : 8.24 % Allowed : 24.73 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3300 helix: 0.89 (0.10), residues: 2610 sheet: -0.40 (1.25), residues: 19 loop : -2.00 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 59 HIS 0.010 0.001 HIS K 29 PHE 0.018 0.002 PHE P 88 TYR 0.035 0.002 TYR H 152 ARG 0.007 0.001 ARG H 107 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 1998) hydrogen bonds : angle 5.01764 ( 5952) covalent geometry : bond 0.00450 (27522) covalent geometry : angle 0.77212 (37298) Misc. bond : bond 0.00073 ( 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 794 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 564 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.4945 (OUTLIER) cc_final: 0.4722 (mpt180) REVERT: A 110 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7013 (mmmt) REVERT: B 17 LYS cc_start: 0.6263 (pttp) cc_final: 0.5953 (pttp) REVERT: B 77 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7558 (mtp180) REVERT: B 85 MET cc_start: 0.4438 (mmm) cc_final: 0.4012 (mmt) REVERT: C 53 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.5718 (mtm-85) REVERT: C 79 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.6274 (mp10) REVERT: C 82 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.2824 (mmp) REVERT: C 98 ASP cc_start: 0.6397 (p0) cc_final: 0.6091 (p0) REVERT: C 130 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7014 (mp) REVERT: C 146 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6152 (pp) REVERT: D 76 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7545 (ptt90) REVERT: E 38 ARG cc_start: 0.6180 (ttp-170) cc_final: 0.5861 (ttp80) REVERT: E 60 GLU cc_start: 0.6047 (mt-10) cc_final: 0.5798 (mp0) REVERT: E 93 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6529 (mt) REVERT: E 99 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5824 (tmm-80) REVERT: F 3 ASP cc_start: 0.6474 (p0) cc_final: 0.6232 (p0) REVERT: F 42 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.4840 (tpp) REVERT: F 58 LYS cc_start: 0.6692 (ptmt) cc_final: 0.6399 (ptpt) REVERT: F 100 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6294 (t0) REVERT: G 28 ASP cc_start: 0.5659 (m-30) cc_final: 0.5387 (m-30) REVERT: G 47 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5895 (tt0) REVERT: G 73 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5708 (ppp80) REVERT: G 79 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.6023 (mp10) REVERT: G 98 GLU cc_start: 0.6409 (pm20) cc_final: 0.5790 (pm20) REVERT: G 106 THR cc_start: 0.6894 (OUTLIER) cc_final: 0.6659 (m) REVERT: H 54 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6914 (ttmm) REVERT: H 100 ASP cc_start: 0.5957 (t70) cc_final: 0.5552 (t0) REVERT: H 110 ASN cc_start: 0.6305 (t0) cc_final: 0.6090 (t0) REVERT: H 147 LYS cc_start: 0.5508 (pptt) cc_final: 0.4784 (mmtm) REVERT: I 107 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6286 (tpt170) REVERT: J 29 SER cc_start: 0.7947 (t) cc_final: 0.7635 (p) REVERT: J 39 LYS cc_start: 0.7264 (mtmt) cc_final: 0.7007 (mtmm) REVERT: J 141 ARG cc_start: 0.6653 (ptm160) cc_final: 0.6414 (ptp-170) REVERT: K 166 MET cc_start: 0.6004 (mmp) cc_final: 0.5587 (mmm) REVERT: K 342 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.4005 (mtp85) REVERT: K 365 ARG cc_start: 0.7638 (ptt90) cc_final: 0.7421 (ptm160) REVERT: K 388 LEU cc_start: 0.7835 (tp) cc_final: 0.7580 (tp) REVERT: K 463 ASN cc_start: 0.7332 (t0) cc_final: 0.6930 (t0) REVERT: K 543 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5941 (mm-30) REVERT: K 622 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6181 (mt-10) REVERT: K 626 TYR cc_start: 0.5853 (m-80) cc_final: 0.5226 (m-80) REVERT: K 691 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.6049 (pp20) REVERT: K 692 TYR cc_start: 0.6225 (t80) cc_final: 0.5929 (t80) REVERT: K 694 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4762 (mmp) REVERT: K 695 ARG cc_start: 0.4389 (OUTLIER) cc_final: 0.3019 (mtp180) REVERT: L 96 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6494 (ttm) REVERT: M 79 GLN cc_start: 0.6562 (mm110) cc_final: 0.6311 (mm-40) REVERT: M 98 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5463 (pm20) REVERT: M 110 LYS cc_start: 0.6654 (mmmt) cc_final: 0.6282 (mmmt) REVERT: M 111 GLU cc_start: 0.5690 (pm20) cc_final: 0.5408 (pm20) REVERT: N 76 ARG cc_start: 0.6155 (ptm-80) cc_final: 0.5661 (ttp80) REVERT: O 133 GLU cc_start: 0.4125 (OUTLIER) cc_final: 0.3586 (OUTLIER) REVERT: P 3 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.5328 (p0) REVERT: P 85 MET cc_start: 0.6559 (mmp) cc_final: 0.5810 (mtp) REVERT: Q 98 GLU cc_start: 0.5316 (pp20) cc_final: 0.5041 (pp20) REVERT: Q 125 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.4840 (tp30) REVERT: R 97 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7573 (tp) REVERT: R 113 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.6151 (tmmt) outliers start: 230 outliers final: 89 residues processed: 710 average time/residue: 1.4938 time to fit residues: 1218.0677 Evaluate side-chains 639 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 522 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 110 LYS 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 53 ARG Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 ARG 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 152 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 73 ARG 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 106 THR Chi-restraints excluded: chain G residue 130 LEU 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 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 107 ARG 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 276 ILE Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 501 HIS 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 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 103 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 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 M residue 153 ILE Chi-restraints excluded: chain N residue 15 GLN 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 102 GLU Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 79 GLN 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 49 SER Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 113 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 208 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 292 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 282 optimal weight: 0.0670 chunk 308 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 189 optimal weight: 0.0970 chunk 215 optimal weight: 0.9980 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 10 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 79 GLN G 115 ASN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN K 26 ASN K 29 HIS K 261 GLN L 47 ASN M 52 GLN O 35 GLN O 68 ASN ** 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 = 0.4562 r_free = 0.4562 target = 0.227460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.207809 restraints weight = 31468.849| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 1.55 r_work: 0.4266 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27538 Z= 0.132 Angle : 0.678 10.734 37298 Z= 0.330 Chirality : 0.040 0.241 4096 Planarity : 0.005 0.061 4812 Dihedral : 9.606 97.883 4571 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.00 % Favored : 96.85 % Rotamer: Outliers : 6.27 % Allowed : 27.20 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 3300 helix: 1.30 (0.10), residues: 2615 sheet: -0.29 (1.24), residues: 19 loop : -1.93 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 59 HIS 0.010 0.001 HIS K 29 PHE 0.019 0.001 PHE K 221 TYR 0.019 0.002 TYR L 152 ARG 0.008 0.001 ARG P 76 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 1998) hydrogen bonds : angle 4.67054 ( 5952) covalent geometry : bond 0.00286 (27522) covalent geometry : angle 0.67771 (37298) Misc. bond : bond 0.00033 ( 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 763 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 588 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 GLN cc_start: 0.5754 (mm-40) cc_final: 0.5535 (mm-40) REVERT: B 17 LYS cc_start: 0.6323 (pttp) cc_final: 0.6046 (pttp) REVERT: B 77 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7413 (mtp180) REVERT: B 85 MET cc_start: 0.4613 (mmm) cc_final: 0.4191 (mmt) REVERT: C 53 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5906 (mtm-85) REVERT: C 60 GLN cc_start: 0.5539 (OUTLIER) cc_final: 0.5291 (mp10) REVERT: C 109 MET cc_start: 0.6117 (tpp) cc_final: 0.5874 (tpt) REVERT: C 130 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7132 (mp) REVERT: C 146 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6046 (pp) REVERT: C 154 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6564 (mt) REVERT: D 32 ARG cc_start: 0.5968 (mpt-90) cc_final: 0.5628 (mtt-85) REVERT: D 100 ASP cc_start: 0.6360 (t70) cc_final: 0.5545 (m-30) REVERT: D 131 GLN cc_start: 0.6758 (pt0) cc_final: 0.6428 (pt0) REVERT: E 38 ARG cc_start: 0.6049 (ttp-170) cc_final: 0.5778 (ttp80) REVERT: E 93 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6281 (mt) REVERT: F 3 ASP cc_start: 0.6427 (p0) cc_final: 0.6180 (p0) REVERT: F 58 LYS cc_start: 0.6734 (ptmt) cc_final: 0.6437 (ptpt) REVERT: G 24 ARG cc_start: 0.6038 (ttp-170) cc_final: 0.5629 (ttm170) REVERT: G 28 ASP cc_start: 0.5674 (m-30) cc_final: 0.5470 (m-30) REVERT: G 79 GLN cc_start: 0.5944 (OUTLIER) cc_final: 0.5702 (mp10) REVERT: G 98 GLU cc_start: 0.6325 (pm20) cc_final: 0.5717 (pm20) REVERT: G 127 MET cc_start: 0.6897 (tpp) cc_final: 0.6550 (mpm) REVERT: G 135 MET cc_start: 0.5830 (mmp) cc_final: 0.5573 (mmp) REVERT: H 54 LYS cc_start: 0.7050 (mmtt) cc_final: 0.6787 (ttmm) REVERT: H 100 ASP cc_start: 0.5963 (t70) cc_final: 0.5535 (t0) REVERT: I 13 ARG cc_start: 0.6860 (mtp180) cc_final: 0.6579 (mtp180) REVERT: I 73 GLN cc_start: 0.6854 (tt0) cc_final: 0.6636 (tt0) REVERT: J 21 ARG cc_start: 0.2003 (OUTLIER) cc_final: 0.0920 (tpt170) REVERT: J 29 SER cc_start: 0.7892 (t) cc_final: 0.7641 (p) REVERT: J 39 LYS cc_start: 0.7348 (mtmt) cc_final: 0.7087 (mtmm) REVERT: K 281 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6617 (ttp) REVERT: K 365 ARG cc_start: 0.7615 (ptt90) cc_final: 0.7139 (ptm160) REVERT: K 388 LEU cc_start: 0.7828 (tp) cc_final: 0.7591 (tp) REVERT: K 441 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6519 (pt0) REVERT: K 463 ASN cc_start: 0.7298 (t0) cc_final: 0.6944 (t0) REVERT: K 660 GLU cc_start: 0.6858 (tt0) cc_final: 0.6546 (tt0) REVERT: K 693 MET cc_start: 0.6341 (mmm) cc_final: 0.6095 (mmm) REVERT: K 694 MET cc_start: 0.5037 (OUTLIER) cc_final: 0.4631 (mmp) REVERT: K 695 ARG cc_start: 0.4193 (OUTLIER) cc_final: 0.3273 (mtp180) REVERT: L 107 ARG cc_start: 0.5676 (OUTLIER) cc_final: 0.5409 (mmt90) REVERT: M 52 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: M 110 LYS cc_start: 0.6513 (mmmt) cc_final: 0.6301 (mmmt) REVERT: M 135 MET cc_start: 0.0711 (mmt) cc_final: 0.0197 (mmt) REVERT: N 76 ARG cc_start: 0.6097 (ptm-80) cc_final: 0.5659 (ttp80) REVERT: O 29 PHE cc_start: 0.6224 (t80) cc_final: 0.5808 (t80) REVERT: O 125 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6413 (mt-10) REVERT: O 133 GLU cc_start: 0.4155 (OUTLIER) cc_final: 0.3827 (mp0) REVERT: O 152 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5469 (mm) REVERT: O 153 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6552 (mt) REVERT: P 85 MET cc_start: 0.6584 (mmp) cc_final: 0.5944 (mtt) REVERT: Q 35 GLN cc_start: 0.6559 (tt0) cc_final: 0.5713 (tm130) REVERT: Q 125 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5035 (tp30) REVERT: R 76 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5798 (ptt90) REVERT: S 54 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6088 (tp30) outliers start: 175 outliers final: 66 residues processed: 700 average time/residue: 1.6649 time to fit residues: 1344.8557 Evaluate side-chains 616 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 531 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR 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 C residue 53 ARG Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 56 VAL 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 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 G residue 30 VAL Chi-restraints excluded: chain G residue 37 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 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 21 ARG 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 276 ILE Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE 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 107 ARG 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 52 GLN 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 M residue 152 LEU Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain O residue 153 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 54 LYS 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 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 76 ARG Chi-restraints excluded: chain R residue 149 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 189 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 155 HIS C 68 ASN D 2 GLN D 10 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 68 ASN J 101 ASN K 29 HIS ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 GLN K 469 GLN L 28 GLN L 47 ASN M 52 GLN O 35 GLN O 68 ASN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN R 138 ASN S 41 GLN S 63 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.222866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.202166 restraints weight = 31264.780| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 1.59 r_work: 0.4207 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27538 Z= 0.220 Angle : 0.796 10.978 37298 Z= 0.392 Chirality : 0.045 0.221 4096 Planarity : 0.006 0.063 4812 Dihedral : 9.490 97.417 4563 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 7.24 % Allowed : 26.77 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3300 helix: 0.96 (0.10), residues: 2606 sheet: -0.26 (1.29), residues: 19 loop : -2.12 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 59 HIS 0.009 0.002 HIS K 29 PHE 0.019 0.002 PHE S 37 TYR 0.033 0.003 TYR H 152 ARG 0.012 0.001 ARG Q 99 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 1998) hydrogen bonds : angle 5.07232 ( 5952) covalent geometry : bond 0.00505 (27522) covalent geometry : angle 0.79627 (37298) Misc. bond : bond 0.00083 ( 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 761 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 559 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: A 110 LYS cc_start: 0.7557 (mmmt) cc_final: 0.7283 (mmmt) REVERT: A 121 ARG cc_start: 0.4867 (OUTLIER) cc_final: 0.4609 (mmp80) REVERT: B 2 GLN cc_start: 0.5832 (mm-40) cc_final: 0.5600 (mm-40) REVERT: B 17 LYS cc_start: 0.6210 (pttp) cc_final: 0.5896 (pttp) REVERT: B 73 TYR cc_start: 0.5851 (t80) cc_final: 0.5495 (t80) REVERT: B 85 MET cc_start: 0.4890 (mmm) cc_final: 0.4589 (mmt) REVERT: C 25 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.5796 (tpt) REVERT: C 53 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.5718 (mtm-85) REVERT: C 130 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7158 (mp) REVERT: C 146 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6172 (pp) REVERT: D 1 MET cc_start: 0.5778 (OUTLIER) cc_final: 0.5497 (pmt) REVERT: D 32 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5357 (mpt-90) REVERT: E 38 ARG cc_start: 0.6111 (ttp-170) cc_final: 0.5779 (ttp80) REVERT: E 60 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5621 (mp0) REVERT: E 93 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6464 (mt) REVERT: F 58 LYS cc_start: 0.6704 (ptmt) cc_final: 0.6405 (ptpt) REVERT: G 24 ARG cc_start: 0.6033 (ttp-170) cc_final: 0.5610 (ttm170) REVERT: G 28 ASP cc_start: 0.5671 (m-30) cc_final: 0.5393 (m-30) REVERT: G 73 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.5796 (ppp80) REVERT: G 79 GLN cc_start: 0.5733 (mp10) cc_final: 0.5404 (mp-120) REVERT: G 98 GLU cc_start: 0.6452 (pm20) cc_final: 0.5988 (pm20) REVERT: G 127 MET cc_start: 0.7034 (tpp) cc_final: 0.6544 (mpm) REVERT: G 135 MET cc_start: 0.6167 (mmp) cc_final: 0.5704 (mmp) REVERT: G 142 ASP cc_start: 0.5088 (m-30) cc_final: 0.4800 (m-30) REVERT: H 54 LYS cc_start: 0.7123 (mmtt) cc_final: 0.6894 (ttmm) REVERT: H 100 ASP cc_start: 0.6098 (t70) cc_final: 0.5635 (t0) REVERT: H 147 LYS cc_start: 0.5284 (pptt) cc_final: 0.4530 (mmmm) REVERT: I 13 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6709 (mtp180) REVERT: I 53 LYS cc_start: 0.7653 (mtpt) cc_final: 0.7439 (mtpm) REVERT: I 89 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7137 (tt) REVERT: I 152 TYR cc_start: 0.7493 (t80) cc_final: 0.6549 (t80) REVERT: J 21 ARG cc_start: 0.2121 (OUTLIER) cc_final: 0.1165 (tpt170) REVERT: J 24 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5555 (mp) REVERT: J 29 SER cc_start: 0.7925 (t) cc_final: 0.7610 (m) REVERT: J 39 LYS cc_start: 0.7218 (mtmt) cc_final: 0.6955 (mtmm) REVERT: J 78 ARG cc_start: 0.7099 (mmm-85) cc_final: 0.6738 (mtm-85) REVERT: K 163 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5082 (tmtt) REVERT: K 166 MET cc_start: 0.5993 (mmp) cc_final: 0.5539 (mmm) REVERT: K 388 LEU cc_start: 0.7904 (tp) cc_final: 0.7664 (tp) REVERT: K 463 ASN cc_start: 0.7366 (t0) cc_final: 0.6947 (t0) REVERT: K 502 ARG cc_start: 0.5149 (mmm-85) cc_final: 0.4928 (mmm-85) REVERT: K 543 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5876 (mm-30) REVERT: K 622 GLU cc_start: 0.6495 (mt-10) cc_final: 0.5662 (mt-10) REVERT: K 626 TYR cc_start: 0.5850 (m-80) cc_final: 0.4904 (m-80) REVERT: K 691 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6100 (pp20) REVERT: K 694 MET cc_start: 0.5071 (OUTLIER) cc_final: 0.4308 (mmm) REVERT: K 695 ARG cc_start: 0.4394 (OUTLIER) cc_final: 0.3242 (mtp180) REVERT: L 24 LEU cc_start: 0.5510 (mt) cc_final: 0.5305 (mp) REVERT: L 96 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6504 (ttm) REVERT: M 98 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5511 (pm20) REVERT: M 110 LYS cc_start: 0.6628 (mmmt) cc_final: 0.6294 (mmmt) REVERT: N 76 ARG cc_start: 0.5950 (ptm-80) cc_final: 0.5503 (ttp80) REVERT: N 131 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6746 (tp-100) REVERT: O 29 PHE cc_start: 0.6316 (t80) cc_final: 0.5968 (t80) REVERT: O 98 GLU cc_start: 0.6072 (mt-10) cc_final: 0.5850 (mt-10) REVERT: O 133 GLU cc_start: 0.4222 (OUTLIER) cc_final: 0.3700 (OUTLIER) REVERT: O 152 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.5322 (mt) REVERT: O 153 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6593 (mt) REVERT: P 3 ASP cc_start: 0.5682 (OUTLIER) cc_final: 0.5253 (p0) REVERT: P 15 GLN cc_start: 0.5398 (mp10) cc_final: 0.5189 (mp10) REVERT: P 85 MET cc_start: 0.6746 (mmp) cc_final: 0.5976 (mtp) REVERT: Q 125 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5278 (tp30) REVERT: R 76 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5922 (ptt90) REVERT: R 96 MET cc_start: 0.7391 (tmm) cc_final: 0.7037 (ttp) REVERT: R 97 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7579 (tp) outliers start: 202 outliers final: 90 residues processed: 684 average time/residue: 1.8228 time to fit residues: 1435.6973 Evaluate side-chains 634 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 517 time to evaluate : 5.478 ------------------------------------------------------------------------------- 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 121 ARG 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 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 158 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 32 ARG Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 60 GLU 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 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 140 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 75 THR 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 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 126 CYS 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 24 ILE Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 52 SER 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 163 LYS Chi-restraints excluded: chain K residue 328 MET Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 543 GLU Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 666 ARG 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 118 SER 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 50 ILE 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 M residue 98 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain N residue 15 GLN 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 102 GLU 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 O residue 153 ILE Chi-restraints excluded: chain P residue 3 ASP 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 114 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 79 GLN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN K 26 ASN K 29 HIS K 476 HIS L 47 ASN L 117 ASN M 52 GLN N 10 ASN ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.225954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.206339 restraints weight = 31242.918| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 1.53 r_work: 0.4248 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4100 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27538 Z= 0.145 Angle : 0.699 10.974 37298 Z= 0.344 Chirality : 0.041 0.205 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.374 93.792 4563 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.09 % Favored : 96.76 % Rotamer: Outliers : 5.95 % Allowed : 28.60 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3300 helix: 1.26 (0.10), residues: 2611 sheet: -0.05 (1.29), residues: 19 loop : -2.02 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 59 HIS 0.008 0.001 HIS K 29 PHE 0.018 0.001 PHE K 221 TYR 0.031 0.002 TYR B 152 ARG 0.010 0.001 ARG Q 99 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 1998) hydrogen bonds : angle 4.79414 ( 5952) covalent geometry : bond 0.00320 (27522) covalent geometry : angle 0.69913 (37298) Misc. bond : bond 0.00038 ( 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 744 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 578 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6780 (pm20) REVERT: B 2 GLN cc_start: 0.5776 (mm-40) cc_final: 0.5516 (mm-40) REVERT: B 17 LYS cc_start: 0.6232 (pttp) cc_final: 0.5951 (pttp) REVERT: B 27 LEU cc_start: 0.4666 (OUTLIER) cc_final: 0.4414 (pp) REVERT: B 85 MET cc_start: 0.4634 (mmm) cc_final: 0.4321 (mmt) REVERT: B 105 ASP cc_start: 0.6926 (m-30) cc_final: 0.6654 (t0) REVERT: C 25 MET cc_start: 0.6104 (mpt) cc_final: 0.5803 (tpt) REVERT: C 53 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.5785 (mtm-85) REVERT: C 82 MET cc_start: 0.4771 (mmm) cc_final: 0.4137 (mpm) REVERT: C 130 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7199 (mp) REVERT: C 146 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6065 (pp) REVERT: D 76 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7529 (ptt90) REVERT: D 100 ASP cc_start: 0.6328 (t70) cc_final: 0.5630 (m-30) REVERT: E 38 ARG cc_start: 0.6031 (ttp-170) cc_final: 0.5555 (ttp80) REVERT: E 60 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5590 (mp0) REVERT: E 93 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6319 (mt) REVERT: E 135 MET cc_start: 0.5804 (mmm) cc_final: 0.5227 (mmt) REVERT: E 142 ASP cc_start: 0.6100 (m-30) cc_final: 0.5341 (m-30) REVERT: F 58 LYS cc_start: 0.6768 (ptmt) cc_final: 0.6466 (ptpt) REVERT: G 24 ARG cc_start: 0.6023 (ttp-170) cc_final: 0.5520 (ttm170) REVERT: G 28 ASP cc_start: 0.5722 (m-30) cc_final: 0.5396 (m-30) REVERT: G 98 GLU cc_start: 0.6271 (pm20) cc_final: 0.5738 (pm20) REVERT: G 127 MET cc_start: 0.6911 (tpp) cc_final: 0.5811 (mpm) REVERT: G 135 MET cc_start: 0.6044 (mmp) cc_final: 0.5644 (mmp) REVERT: G 150 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.4833 (t80) REVERT: H 28 GLN cc_start: 0.5651 (mm110) cc_final: 0.5275 (mm110) REVERT: H 54 LYS cc_start: 0.7026 (mmtt) cc_final: 0.6793 (ttmm) REVERT: H 100 ASP cc_start: 0.5945 (t70) cc_final: 0.5446 (t0) REVERT: J 21 ARG cc_start: 0.2034 (OUTLIER) cc_final: 0.0951 (tpt170) REVERT: J 29 SER cc_start: 0.7935 (t) cc_final: 0.7648 (p) REVERT: J 39 LYS cc_start: 0.7278 (mtmt) cc_final: 0.7010 (mtmm) REVERT: K 166 MET cc_start: 0.5729 (mmp) cc_final: 0.5319 (mmm) REVERT: K 388 LEU cc_start: 0.7907 (tp) cc_final: 0.7660 (tp) REVERT: K 463 ASN cc_start: 0.7327 (t0) cc_final: 0.6967 (t0) REVERT: K 593 GLN cc_start: 0.6988 (mm110) cc_final: 0.6657 (mm110) REVERT: K 693 MET cc_start: 0.6287 (mmm) cc_final: 0.6002 (mmm) REVERT: K 695 ARG cc_start: 0.4071 (OUTLIER) cc_final: 0.2966 (mtp180) REVERT: L 24 LEU cc_start: 0.5471 (mt) cc_final: 0.5257 (mp) REVERT: L 107 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.5292 (mmt90) REVERT: N 76 ARG cc_start: 0.5880 (ptm-80) cc_final: 0.5521 (ttp80) REVERT: N 131 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6709 (tp-100) REVERT: N 134 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6535 (tttt) REVERT: N 135 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6917 (mm-30) REVERT: O 29 PHE cc_start: 0.6332 (t80) cc_final: 0.6028 (t80) REVERT: O 98 GLU cc_start: 0.6106 (mt-10) cc_final: 0.5901 (mt-10) REVERT: O 133 GLU cc_start: 0.4160 (OUTLIER) cc_final: 0.3880 (mp0) REVERT: O 152 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5237 (mt) REVERT: O 153 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6511 (mt) REVERT: P 54 LYS cc_start: 0.7028 (ptpp) cc_final: 0.6820 (ptpp) REVERT: P 85 MET cc_start: 0.6688 (mmp) cc_final: 0.6030 (mtt) REVERT: Q 125 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.5144 (tp30) REVERT: R 76 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5827 (ptt90) REVERT: R 96 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6992 (ttp) REVERT: S 54 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6316 (tp30) outliers start: 166 outliers final: 75 residues processed: 685 average time/residue: 1.8910 time to fit residues: 1513.2338 Evaluate side-chains 626 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 532 time to evaluate : 3.960 ------------------------------------------------------------------------------- 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 B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU 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 158 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 60 GLU 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 E residue 152 LEU 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 140 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 33 SER 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 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 666 ARG Chi-restraints excluded: chain K residue 679 ILE 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 107 ARG Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 118 SER 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 71 VAL Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN 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 102 GLU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain O residue 153 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 125 GLU 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 76 ARG Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 149 VAL 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 95 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 259 optimal weight: 0.9980 chunk 299 optimal weight: 0.5980 chunk 323 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 35 GLN G 79 GLN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN J 101 ASN K 26 ASN K 29 HIS K 320 GLN 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 110 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 = 0.4551 r_free = 0.4551 target = 0.225931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.206100 restraints weight = 31167.265| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 1.53 r_work: 0.4249 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4097 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27538 Z= 0.153 Angle : 0.719 13.310 37298 Z= 0.353 Chirality : 0.042 0.298 4096 Planarity : 0.005 0.061 4812 Dihedral : 9.232 92.508 4558 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.12 % Favored : 96.73 % Rotamer: Outliers : 5.73 % Allowed : 29.35 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3300 helix: 1.29 (0.10), residues: 2611 sheet: 0.14 (1.33), residues: 19 loop : -2.03 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 84 HIS 0.008 0.001 HIS N 155 PHE 0.018 0.001 PHE K 221 TYR 0.034 0.002 TYR B 152 ARG 0.010 0.001 ARG P 76 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 1998) hydrogen bonds : angle 4.80180 ( 5952) covalent geometry : bond 0.00344 (27522) covalent geometry : angle 0.71852 (37298) Misc. bond : bond 0.00045 ( 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 714 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 554 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.6059 (mt) cc_final: 0.5835 (tt) REVERT: A 98 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: B 2 GLN cc_start: 0.5686 (mm-40) cc_final: 0.5424 (mm-40) REVERT: B 6 THR cc_start: 0.6579 (m) cc_final: 0.5986 (p) REVERT: B 17 LYS cc_start: 0.6221 (pttp) cc_final: 0.5952 (pttp) REVERT: B 27 LEU cc_start: 0.4673 (OUTLIER) cc_final: 0.4431 (pp) REVERT: B 85 MET cc_start: 0.4562 (mmm) cc_final: 0.4198 (mmt) REVERT: B 105 ASP cc_start: 0.6953 (m-30) cc_final: 0.6668 (t0) REVERT: B 152 TYR cc_start: 0.6588 (m-80) cc_final: 0.6365 (m-80) REVERT: C 24 GLU cc_start: 0.6768 (tp30) cc_final: 0.6434 (tp30) REVERT: C 25 MET cc_start: 0.6161 (mpt) cc_final: 0.5828 (tpt) REVERT: C 53 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.5807 (mtm-85) REVERT: C 82 MET cc_start: 0.4781 (mmm) cc_final: 0.4145 (mpm) REVERT: C 109 MET cc_start: 0.6247 (tpp) cc_final: 0.5962 (tpt) REVERT: C 130 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7214 (mp) REVERT: C 146 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6105 (pp) REVERT: D 1 MET cc_start: 0.4936 (pmt) cc_final: 0.4064 (ppp) REVERT: D 7 THR cc_start: 0.6518 (t) cc_final: 0.5936 (m) REVERT: D 100 ASP cc_start: 0.6268 (t70) cc_final: 0.5593 (m-30) REVERT: D 140 MET cc_start: 0.6017 (ppp) cc_final: 0.5737 (ppp) REVERT: E 38 ARG cc_start: 0.6026 (ttp-170) cc_final: 0.5606 (ttp80) REVERT: E 60 GLU cc_start: 0.5754 (OUTLIER) cc_final: 0.5457 (mp0) REVERT: E 93 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6264 (mt) REVERT: E 131 LYS cc_start: 0.6428 (tmmm) cc_final: 0.5760 (ttmt) REVERT: E 142 ASP cc_start: 0.6138 (m-30) cc_final: 0.5360 (m-30) REVERT: F 58 LYS cc_start: 0.6766 (ptmt) cc_final: 0.6466 (ptpt) REVERT: G 24 ARG cc_start: 0.6046 (ttp-170) cc_final: 0.5627 (ttm170) REVERT: G 28 ASP cc_start: 0.5749 (m-30) cc_final: 0.5496 (m-30) REVERT: G 73 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5703 (ppp80) REVERT: G 98 GLU cc_start: 0.6267 (pm20) cc_final: 0.5737 (pm20) REVERT: G 127 MET cc_start: 0.6915 (tpp) cc_final: 0.5800 (mpm) REVERT: G 135 MET cc_start: 0.6006 (mmp) cc_final: 0.5638 (mmp) REVERT: G 150 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.4725 (t80) REVERT: H 28 GLN cc_start: 0.5651 (mm110) cc_final: 0.5313 (mm110) REVERT: H 54 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6755 (ttmm) REVERT: H 100 ASP cc_start: 0.6018 (t70) cc_final: 0.5511 (t0) REVERT: H 147 LYS cc_start: 0.5137 (pptt) cc_final: 0.4346 (mmmm) REVERT: I 13 ARG cc_start: 0.6838 (mtp180) cc_final: 0.6546 (mtp180) REVERT: I 137 MET cc_start: 0.6182 (mtt) cc_final: 0.5772 (mtp) REVERT: I 158 MET cc_start: 0.5734 (tpp) cc_final: 0.5035 (ptt) REVERT: J 21 ARG cc_start: 0.1997 (OUTLIER) cc_final: 0.1386 (tpt170) REVERT: J 29 SER cc_start: 0.7926 (t) cc_final: 0.7641 (p) REVERT: J 39 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7040 (mtmm) REVERT: J 58 LYS cc_start: 0.6080 (ttmt) cc_final: 0.5622 (mtmt) REVERT: K 29 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6547 (t-170) REVERT: K 162 MET cc_start: 0.5652 (mmt) cc_final: 0.5385 (mmt) REVERT: K 295 ARG cc_start: 0.6282 (mtm-85) cc_final: 0.5891 (mtm110) REVERT: K 365 ARG cc_start: 0.7612 (ptm-80) cc_final: 0.7292 (ptm160) REVERT: K 377 PHE cc_start: 0.7393 (t80) cc_final: 0.7002 (t80) REVERT: K 463 ASN cc_start: 0.7339 (t0) cc_final: 0.6994 (t0) REVERT: K 593 GLN cc_start: 0.6951 (mm110) cc_final: 0.6628 (mm110) REVERT: K 691 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5846 (pp20) REVERT: K 693 MET cc_start: 0.6349 (mmm) cc_final: 0.5949 (mmm) REVERT: K 695 ARG cc_start: 0.4016 (OUTLIER) cc_final: 0.2659 (mtp180) REVERT: L 24 LEU cc_start: 0.5418 (mt) cc_final: 0.5210 (mp) REVERT: L 96 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6400 (ttm) REVERT: M 73 ARG cc_start: 0.6444 (ttp-110) cc_final: 0.6242 (tmm160) REVERT: M 74 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7056 (mptp) REVERT: M 110 LYS cc_start: 0.6498 (mmmt) cc_final: 0.6294 (tppp) REVERT: N 17 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5885 (ptmm) REVERT: N 76 ARG cc_start: 0.5888 (ptm-80) cc_final: 0.5564 (ttp80) REVERT: N 131 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6708 (tp-100) REVERT: N 134 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6527 (tttt) REVERT: N 135 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6949 (mm-30) REVERT: O 29 PHE cc_start: 0.6521 (t80) cc_final: 0.6198 (t80) REVERT: O 98 GLU cc_start: 0.6097 (mt-10) cc_final: 0.5888 (mt-10) REVERT: O 125 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6137 (mt-10) REVERT: O 127 MET cc_start: 0.5892 (mmm) cc_final: 0.5596 (mpm) REVERT: O 133 GLU cc_start: 0.4237 (OUTLIER) cc_final: 0.3690 (OUTLIER) REVERT: O 152 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5169 (mt) REVERT: P 28 GLN cc_start: 0.5504 (OUTLIER) cc_final: 0.4713 (mp-120) REVERT: P 54 LYS cc_start: 0.6985 (ptpp) cc_final: 0.6769 (ptpp) REVERT: P 85 MET cc_start: 0.6786 (mmp) cc_final: 0.5973 (mtt) REVERT: R 76 ARG cc_start: 0.6240 (OUTLIER) cc_final: 0.5839 (ptt90) REVERT: R 96 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6979 (ttp) REVERT: S 54 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6042 (tp30) outliers start: 160 outliers final: 77 residues processed: 652 average time/residue: 1.5040 time to fit residues: 1126.0960 Evaluate side-chains 630 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 532 time to evaluate : 2.727 ------------------------------------------------------------------------------- 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 B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 124 LEU 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 158 VAL 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 E residue 3 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 60 GLU 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 36 LEU Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 33 SER 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 97 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 443 VAL 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 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 691 GLU 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 96 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 118 SER 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 74 LYS Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 17 LYS 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 102 GLU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 64 ASP 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 3 LEU Chi-restraints excluded: chain Q residue 79 GLN 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 76 ARG Chi-restraints excluded: chain R residue 96 MET 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 20 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 141 optimal weight: 0.0670 chunk 176 optimal weight: 7.9990 chunk 309 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN J 101 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 GLN K 215 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.228062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.208660 restraints weight = 31280.240| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 1.52 r_work: 0.4270 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27538 Z= 0.137 Angle : 0.698 11.910 37298 Z= 0.345 Chirality : 0.041 0.291 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.171 91.431 4556 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 4.73 % Allowed : 30.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3300 helix: 1.44 (0.10), residues: 2612 sheet: 0.30 (1.35), residues: 19 loop : -1.93 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 84 HIS 0.006 0.001 HIS K 29 PHE 0.018 0.001 PHE K 221 TYR 0.029 0.002 TYR L 152 ARG 0.010 0.001 ARG P 76 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 1998) hydrogen bonds : angle 4.72092 ( 5952) covalent geometry : bond 0.00304 (27522) covalent geometry : angle 0.69791 (37298) Misc. bond : bond 0.00035 ( 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 691 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 559 time to evaluate : 2.921 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: 0.5705 (mp0) cc_final: 0.5112 (pm20) REVERT: A 26 PHE cc_start: 0.5234 (t80) cc_final: 0.4985 (t80) REVERT: A 50 ILE cc_start: 0.6190 (mt) cc_final: 0.5942 (tt) REVERT: A 88 LEU cc_start: 0.6225 (mt) cc_final: 0.5892 (mp) REVERT: A 98 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: A 110 LYS cc_start: 0.7374 (mmmt) cc_final: 0.7079 (mmmt) REVERT: A 135 MET cc_start: 0.4625 (mpm) cc_final: 0.3880 (mpm) REVERT: B 2 GLN cc_start: 0.5688 (mm-40) cc_final: 0.5377 (mm-40) REVERT: B 6 THR cc_start: 0.6573 (m) cc_final: 0.5968 (p) REVERT: B 17 LYS cc_start: 0.6225 (pttp) cc_final: 0.5963 (pttp) REVERT: B 27 LEU cc_start: 0.4723 (OUTLIER) cc_final: 0.4498 (pp) REVERT: B 85 MET cc_start: 0.4586 (mmm) cc_final: 0.4132 (mmt) REVERT: B 105 ASP cc_start: 0.6934 (m-30) cc_final: 0.6640 (t0) REVERT: B 151 TYR cc_start: 0.5423 (t80) cc_final: 0.4806 (t80) REVERT: B 152 TYR cc_start: 0.6281 (m-80) cc_final: 0.5566 (m-80) REVERT: C 24 GLU cc_start: 0.6669 (tp30) cc_final: 0.6375 (tp30) REVERT: C 25 MET cc_start: 0.6109 (mpt) cc_final: 0.5789 (tpt) REVERT: C 26 ILE cc_start: 0.7041 (mt) cc_final: 0.6785 (tp) REVERT: C 53 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5774 (mtm-85) REVERT: C 79 GLN cc_start: 0.6017 (OUTLIER) cc_final: 0.5755 (mm110) REVERT: C 82 MET cc_start: 0.4509 (mmm) cc_final: 0.4095 (mpm) REVERT: C 109 MET cc_start: 0.6088 (tpp) cc_final: 0.5868 (tpt) REVERT: C 146 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6106 (pp) REVERT: C 154 ILE cc_start: 0.6744 (OUTLIER) cc_final: 0.6395 (mp) REVERT: D 1 MET cc_start: 0.4835 (pmt) cc_final: 0.4148 (ppp) REVERT: D 58 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6883 (ptmt) REVERT: E 38 ARG cc_start: 0.5988 (ttp-170) cc_final: 0.5569 (ttp80) REVERT: E 93 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6256 (mt) REVERT: E 121 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.5448 (ppp80) REVERT: E 142 ASP cc_start: 0.6255 (m-30) cc_final: 0.5436 (m-30) REVERT: F 58 LYS cc_start: 0.6798 (ptmt) cc_final: 0.6492 (ptpt) REVERT: G 24 ARG cc_start: 0.6012 (ttp-170) cc_final: 0.5589 (ttm170) REVERT: G 28 ASP cc_start: 0.5686 (m-30) cc_final: 0.5441 (m-30) REVERT: G 73 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.5657 (ppp80) REVERT: G 98 GLU cc_start: 0.6198 (pm20) cc_final: 0.5670 (pm20) REVERT: G 127 MET cc_start: 0.6915 (tpp) cc_final: 0.6438 (mpm) REVERT: G 135 MET cc_start: 0.5966 (mmp) cc_final: 0.5651 (mmp) REVERT: H 28 GLN cc_start: 0.5531 (mm110) cc_final: 0.5193 (mm110) REVERT: H 54 LYS cc_start: 0.6907 (mmtt) cc_final: 0.6693 (ttmm) REVERT: H 100 ASP cc_start: 0.5982 (t70) cc_final: 0.5481 (t0) REVERT: I 137 MET cc_start: 0.6214 (mtt) cc_final: 0.5818 (mtp) REVERT: I 158 MET cc_start: 0.5653 (tpp) cc_final: 0.4955 (ptm) REVERT: J 21 ARG cc_start: 0.1944 (OUTLIER) cc_final: 0.0886 (tpt170) REVERT: J 29 SER cc_start: 0.7867 (t) cc_final: 0.7610 (p) REVERT: J 39 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6962 (mtmm) REVERT: J 78 ARG cc_start: 0.6951 (mmm-85) cc_final: 0.6671 (mtm-85) REVERT: K 38 SER cc_start: 0.1857 (OUTLIER) cc_final: 0.1637 (p) REVERT: K 295 ARG cc_start: 0.6254 (mtm-85) cc_final: 0.5865 (mtm110) REVERT: K 365 ARG cc_start: 0.7590 (ptm-80) cc_final: 0.7252 (ptm160) REVERT: K 377 PHE cc_start: 0.7361 (t80) cc_final: 0.6946 (t80) REVERT: K 463 ASN cc_start: 0.7331 (t0) cc_final: 0.7011 (t0) REVERT: K 593 GLN cc_start: 0.6711 (mm110) cc_final: 0.6463 (mm110) REVERT: K 695 ARG cc_start: 0.3949 (OUTLIER) cc_final: 0.2215 (mtp180) REVERT: L 24 LEU cc_start: 0.5537 (mt) cc_final: 0.5318 (mp) REVERT: M 74 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7080 (mptp) REVERT: N 17 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5702 (ptmm) REVERT: N 131 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6662 (tp-100) REVERT: N 134 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6456 (tttt) REVERT: N 135 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6823 (mm-30) REVERT: O 24 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.4892 (tpm170) REVERT: O 29 PHE cc_start: 0.6547 (t80) cc_final: 0.6326 (t80) REVERT: O 48 GLU cc_start: 0.5627 (OUTLIER) cc_final: 0.5249 (mp0) REVERT: O 68 ASN cc_start: 0.4915 (OUTLIER) cc_final: 0.4442 (p0) REVERT: O 127 MET cc_start: 0.5791 (mmm) cc_final: 0.5468 (mpm) REVERT: O 133 GLU cc_start: 0.4121 (OUTLIER) cc_final: 0.3573 (OUTLIER) REVERT: O 152 LEU cc_start: 0.5574 (OUTLIER) cc_final: 0.5248 (mt) REVERT: P 1 MET cc_start: 0.4153 (tmt) cc_final: 0.3098 (tmt) REVERT: P 54 LYS cc_start: 0.6922 (ptpp) cc_final: 0.6707 (ptpp) REVERT: P 85 MET cc_start: 0.6744 (mmp) cc_final: 0.5974 (mtt) REVERT: Q 35 GLN cc_start: 0.6743 (tt0) cc_final: 0.5799 (tm-30) REVERT: R 15 GLN cc_start: 0.6950 (mt0) cc_final: 0.6608 (mp10) REVERT: R 76 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5808 (ptt90) REVERT: R 96 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6946 (ttp) REVERT: S 46 MET cc_start: 0.6340 (mtm) cc_final: 0.5953 (ptt) REVERT: S 54 GLU cc_start: 0.6459 (mm-30) cc_final: 0.5996 (tp30) outliers start: 132 outliers final: 54 residues processed: 641 average time/residue: 1.6001 time to fit residues: 1200.1561 Evaluate side-chains 595 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 519 time to evaluate : 2.756 ------------------------------------------------------------------------------- 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 B residue 27 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 60 GLU 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 F residue 36 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG 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 50 ILE 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 97 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 443 VAL Chi-restraints excluded: chain K residue 554 PHE Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 44 ILE 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 M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 17 LYS 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 24 ARG Chi-restraints excluded: chain O residue 48 GLU 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 152 LEU 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 P residue 112 LEU Chi-restraints excluded: chain Q residue 79 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 96 MET Chi-restraints excluded: chain R residue 149 VAL 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 250 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 299 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 272 optimal weight: 0.6980 chunk 146 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN F 2 GLN ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 79 GLN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN J 101 ASN K 26 ASN K 29 HIS N 47 ASN O 35 GLN O 68 ASN P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN 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 = 0.4581 r_free = 0.4581 target = 0.229151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.209764 restraints weight = 31349.446| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 1.52 r_work: 0.4285 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27538 Z= 0.138 Angle : 0.705 11.494 37298 Z= 0.350 Chirality : 0.042 0.283 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.111 90.313 4555 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.79 % Rotamer: Outliers : 4.30 % Allowed : 31.18 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.15), residues: 3300 helix: 1.54 (0.10), residues: 2608 sheet: 0.17 (1.28), residues: 19 loop : -1.88 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 84 HIS 0.008 0.001 HIS K 29 PHE 0.021 0.001 PHE A 150 TYR 0.027 0.002 TYR L 152 ARG 0.011 0.001 ARG O 128 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 1998) hydrogen bonds : angle 4.71135 ( 5952) covalent geometry : bond 0.00306 (27522) covalent geometry : angle 0.70542 (37298) Misc. bond : bond 0.00036 ( 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 662 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 542 time to evaluate : 3.079 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: A 22 GLU cc_start: 0.5625 (mp0) cc_final: 0.5306 (pm20) REVERT: A 50 ILE cc_start: 0.6217 (mt) cc_final: 0.5968 (tt) REVERT: A 88 LEU cc_start: 0.6232 (mt) cc_final: 0.5919 (mp) REVERT: A 98 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: B 2 GLN cc_start: 0.5647 (mm-40) cc_final: 0.5330 (mm-40) REVERT: B 6 THR cc_start: 0.6549 (m) cc_final: 0.5931 (p) REVERT: B 27 LEU cc_start: 0.4608 (OUTLIER) cc_final: 0.4374 (pp) REVERT: B 85 MET cc_start: 0.4578 (mmm) cc_final: 0.4157 (mmt) REVERT: B 105 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6591 (t0) REVERT: B 140 MET cc_start: 0.4051 (ptt) cc_final: 0.3671 (ptt) REVERT: B 151 TYR cc_start: 0.5384 (t80) cc_final: 0.4810 (t80) REVERT: B 152 TYR cc_start: 0.6174 (m-80) cc_final: 0.5481 (m-80) REVERT: C 5 LYS cc_start: 0.4050 (OUTLIER) cc_final: 0.3751 (mmtt) REVERT: C 24 GLU cc_start: 0.6737 (tp30) cc_final: 0.6466 (tp30) REVERT: C 25 MET cc_start: 0.6067 (mpt) cc_final: 0.5758 (tpt) REVERT: C 26 ILE cc_start: 0.6983 (mt) cc_final: 0.6754 (tp) REVERT: C 53 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.6080 (mtm-85) REVERT: C 79 GLN cc_start: 0.6115 (OUTLIER) cc_final: 0.5849 (mm110) REVERT: C 109 MET cc_start: 0.6044 (tpp) cc_final: 0.5825 (tpt) REVERT: C 146 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6057 (pp) REVERT: C 154 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6429 (mp) REVERT: D 58 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6878 (ptmt) REVERT: D 100 ASP cc_start: 0.6172 (t70) cc_final: 0.5447 (m-30) REVERT: E 121 ARG cc_start: 0.5719 (OUTLIER) cc_final: 0.5453 (ppp80) REVERT: E 135 MET cc_start: 0.5103 (mmm) cc_final: 0.4823 (tpp) REVERT: E 142 ASP cc_start: 0.6171 (m-30) cc_final: 0.5631 (m-30) REVERT: F 58 LYS cc_start: 0.6828 (ptmt) cc_final: 0.6535 (ptpt) REVERT: G 24 ARG cc_start: 0.6068 (ttp-170) cc_final: 0.5614 (ttm170) REVERT: G 28 ASP cc_start: 0.5613 (m-30) cc_final: 0.5346 (m-30) REVERT: G 73 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5637 (ppp80) REVERT: G 98 GLU cc_start: 0.6135 (pm20) cc_final: 0.5618 (pm20) REVERT: G 127 MET cc_start: 0.6894 (tpp) cc_final: 0.6463 (mpm) REVERT: G 133 GLU cc_start: 0.5180 (mm-30) cc_final: 0.4793 (mm-30) REVERT: G 135 MET cc_start: 0.5902 (mmp) cc_final: 0.5654 (mmp) REVERT: H 28 GLN cc_start: 0.5591 (mm110) cc_final: 0.5142 (mm110) REVERT: H 54 LYS cc_start: 0.6861 (mmtt) cc_final: 0.6652 (ttmm) REVERT: H 100 ASP cc_start: 0.5993 (t70) cc_final: 0.5477 (t0) REVERT: I 158 MET cc_start: 0.5659 (tpp) cc_final: 0.4967 (ptm) REVERT: J 21 ARG cc_start: 0.1950 (OUTLIER) cc_final: 0.0889 (tpt170) REVERT: J 29 SER cc_start: 0.7861 (t) cc_final: 0.7642 (p) REVERT: J 39 LYS cc_start: 0.7301 (mtmt) cc_final: 0.7045 (mtmm) REVERT: J 141 ARG cc_start: 0.6726 (mtp85) cc_final: 0.6370 (ttm170) REVERT: K 174 ARG cc_start: 0.6639 (mtm110) cc_final: 0.5707 (mtm110) REVERT: K 214 MET cc_start: 0.6830 (mtp) cc_final: 0.6305 (mtp) REVERT: K 295 ARG cc_start: 0.6221 (mtm-85) cc_final: 0.5845 (mtm110) REVERT: K 377 PHE cc_start: 0.7396 (t80) cc_final: 0.6979 (t80) REVERT: K 463 ASN cc_start: 0.7363 (t0) cc_final: 0.7064 (t0) REVERT: K 593 GLN cc_start: 0.6727 (mm110) cc_final: 0.6467 (mm110) REVERT: K 695 ARG cc_start: 0.3826 (OUTLIER) cc_final: 0.3470 (mpt-90) REVERT: M 73 ARG cc_start: 0.6601 (tmm160) cc_final: 0.6273 (tmm160) REVERT: M 74 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6858 (mptp) REVERT: N 17 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5640 (ptmm) REVERT: N 131 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6676 (tp-100) REVERT: N 134 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6379 (tttt) REVERT: N 135 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6831 (mm-30) REVERT: N 140 MET cc_start: 0.3641 (pmt) cc_final: 0.2731 (pmm) REVERT: O 24 ARG cc_start: 0.6070 (OUTLIER) cc_final: 0.4857 (tpm170) REVERT: O 29 PHE cc_start: 0.6613 (t80) cc_final: 0.6041 (t80) REVERT: O 48 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.5266 (mp0) REVERT: O 64 ASN cc_start: 0.5027 (OUTLIER) cc_final: 0.4752 (t0) REVERT: O 68 ASN cc_start: 0.4793 (OUTLIER) cc_final: 0.4371 (p0) REVERT: O 133 GLU cc_start: 0.4157 (OUTLIER) cc_final: 0.3608 (OUTLIER) REVERT: P 54 LYS cc_start: 0.6902 (ptpp) cc_final: 0.6699 (ptpp) REVERT: P 85 MET cc_start: 0.6704 (mmp) cc_final: 0.5926 (mtt) REVERT: Q 23 LEU cc_start: 0.5116 (OUTLIER) cc_final: 0.4557 (tp) REVERT: Q 35 GLN cc_start: 0.6686 (tt0) cc_final: 0.5833 (tm-30) REVERT: Q 145 GLU cc_start: 0.4400 (pt0) cc_final: 0.4077 (pt0) REVERT: Q 152 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5752 (tp) REVERT: R 15 GLN cc_start: 0.6880 (mt0) cc_final: 0.6538 (mp10) REVERT: R 96 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6768 (ttp) REVERT: S 46 MET cc_start: 0.6433 (mtm) cc_final: 0.6036 (ptt) REVERT: S 63 ASN cc_start: 0.7090 (OUTLIER) cc_final: 0.6871 (m-40) outliers start: 120 outliers final: 51 residues processed: 620 average time/residue: 1.5283 time to fit residues: 1086.5830 Evaluate side-chains 590 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 515 time to evaluate : 2.654 ------------------------------------------------------------------------------- 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 B residue 27 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 165 PHE 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 60 GLU Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain H residue 36 LEU 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 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 153 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 554 PHE Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 118 SER 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 M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 17 LYS 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 24 ARG Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 68 ASN Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 35 ASN Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 63 ASN 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 217 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 249 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 2 GLN D 10 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 79 GLN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN J 101 ASN J 102 ASN K 26 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN R 138 ASN S 41 GLN S 63 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.228747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.209161 restraints weight = 31111.184| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 1.53 r_work: 0.4276 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27538 Z= 0.149 Angle : 0.729 11.172 37298 Z= 0.362 Chirality : 0.043 0.282 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.055 89.936 4549 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.09 % Favored : 96.76 % Rotamer: Outliers : 3.73 % Allowed : 32.15 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3300 helix: 1.50 (0.10), residues: 2605 sheet: 0.05 (1.28), residues: 19 loop : -1.86 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 84 HIS 0.014 0.001 HIS K 29 PHE 0.019 0.001 PHE K 221 TYR 0.026 0.002 TYR L 152 ARG 0.012 0.001 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 1998) hydrogen bonds : angle 4.77510 ( 5952) covalent geometry : bond 0.00335 (27522) covalent geometry : angle 0.72901 (37298) Misc. bond : bond 0.00045 ( 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 625 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 521 time to evaluate : 3.017 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: 0.5628 (mp0) cc_final: 0.5342 (pm20) REVERT: A 26 PHE cc_start: 0.5344 (t80) cc_final: 0.5071 (t80) REVERT: A 50 ILE cc_start: 0.6150 (mt) cc_final: 0.5936 (tt) REVERT: A 98 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6584 (pm20) REVERT: B 2 GLN cc_start: 0.5681 (mm-40) cc_final: 0.5360 (mm-40) REVERT: B 6 THR cc_start: 0.6544 (m) cc_final: 0.5922 (p) REVERT: B 27 LEU cc_start: 0.4631 (OUTLIER) cc_final: 0.4354 (pp) REVERT: B 85 MET cc_start: 0.4596 (mmm) cc_final: 0.4137 (mmt) REVERT: B 105 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6583 (t0) REVERT: B 151 TYR cc_start: 0.5406 (t80) cc_final: 0.4845 (t80) REVERT: B 152 TYR cc_start: 0.6255 (m-80) cc_final: 0.5529 (m-80) REVERT: C 25 MET cc_start: 0.6076 (mpt) cc_final: 0.5732 (tpt) REVERT: C 31 LYS cc_start: 0.6555 (mtmm) cc_final: 0.6280 (mtmm) REVERT: C 53 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.5821 (mtm-85) REVERT: C 79 GLN cc_start: 0.6192 (OUTLIER) cc_final: 0.5915 (mm110) REVERT: C 82 MET cc_start: 0.4553 (mmm) cc_final: 0.4011 (mpm) REVERT: C 109 MET cc_start: 0.6060 (tpp) cc_final: 0.5859 (tpt) REVERT: C 146 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6106 (pp) REVERT: C 154 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6521 (mp) REVERT: D 1 MET cc_start: 0.4881 (pmt) cc_final: 0.4389 (ppp) REVERT: D 10 ASN cc_start: 0.6887 (m-40) cc_final: 0.6671 (m110) REVERT: D 58 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6897 (ptmt) REVERT: D 100 ASP cc_start: 0.6230 (t70) cc_final: 0.5508 (m-30) REVERT: E 121 ARG cc_start: 0.5729 (OUTLIER) cc_final: 0.5463 (ppp80) REVERT: E 135 MET cc_start: 0.5040 (mmm) cc_final: 0.4765 (tpp) REVERT: E 142 ASP cc_start: 0.6212 (m-30) cc_final: 0.5841 (m-30) REVERT: F 58 LYS cc_start: 0.6884 (ptmt) cc_final: 0.6555 (ptpt) REVERT: G 24 ARG cc_start: 0.6072 (ttp-170) cc_final: 0.5650 (ttm170) REVERT: G 28 ASP cc_start: 0.5613 (m-30) cc_final: 0.5398 (m-30) REVERT: G 73 ARG cc_start: 0.6185 (OUTLIER) cc_final: 0.5660 (ppp80) REVERT: G 98 GLU cc_start: 0.6130 (pm20) cc_final: 0.5661 (pm20) REVERT: G 127 MET cc_start: 0.6832 (tpp) cc_final: 0.6402 (mpm) REVERT: G 135 MET cc_start: 0.5924 (mmp) cc_final: 0.5631 (mmp) REVERT: H 28 GLN cc_start: 0.5556 (mm110) cc_final: 0.5241 (mm110) REVERT: H 54 LYS cc_start: 0.6855 (mmtt) cc_final: 0.6652 (ttmm) REVERT: H 76 ARG cc_start: 0.5591 (OUTLIER) cc_final: 0.5216 (ppp-140) REVERT: H 100 ASP cc_start: 0.5949 (t70) cc_final: 0.5452 (t0) REVERT: I 13 ARG cc_start: 0.6858 (mtp180) cc_final: 0.6548 (mtm180) REVERT: J 21 ARG cc_start: 0.1947 (OUTLIER) cc_final: 0.0859 (tpt170) REVERT: J 29 SER cc_start: 0.7862 (t) cc_final: 0.7646 (p) REVERT: J 39 LYS cc_start: 0.7309 (mtmt) cc_final: 0.7051 (mtmm) REVERT: J 58 LYS cc_start: 0.6201 (ttmt) cc_final: 0.5739 (mtmt) REVERT: J 78 ARG cc_start: 0.6868 (mmm-85) cc_final: 0.6535 (mtm-85) REVERT: K 174 ARG cc_start: 0.6662 (mtm110) cc_final: 0.5792 (mtm110) REVERT: K 214 MET cc_start: 0.6873 (mtp) cc_final: 0.6644 (mtp) REVERT: K 295 ARG cc_start: 0.6214 (mtm-85) cc_final: 0.5850 (mtm110) REVERT: K 377 PHE cc_start: 0.7421 (t80) cc_final: 0.7044 (t80) REVERT: K 463 ASN cc_start: 0.7354 (t0) cc_final: 0.7053 (t0) REVERT: K 691 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6115 (pp20) REVERT: K 695 ARG cc_start: 0.3748 (OUTLIER) cc_final: 0.2068 (mtp180) REVERT: L 113 LYS cc_start: 0.6451 (tmtt) cc_final: 0.6048 (tmtm) REVERT: M 73 ARG cc_start: 0.6652 (tmm160) cc_final: 0.6283 (tmm160) REVERT: M 74 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6992 (mptp) REVERT: N 17 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5541 (ptmm) REVERT: N 131 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6677 (tp-100) REVERT: N 134 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6398 (tttt) REVERT: N 135 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6844 (mm-30) REVERT: O 29 PHE cc_start: 0.6613 (t80) cc_final: 0.6005 (t80) REVERT: O 46 ASN cc_start: 0.5208 (p0) cc_final: 0.4793 (t0) REVERT: O 48 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.5265 (mp0) REVERT: O 64 ASN cc_start: 0.4952 (OUTLIER) cc_final: 0.4706 (t0) REVERT: P 28 GLN cc_start: 0.5326 (OUTLIER) cc_final: 0.4535 (mp-120) REVERT: P 54 LYS cc_start: 0.6862 (ptpp) cc_final: 0.6656 (ptpp) REVERT: P 85 MET cc_start: 0.6710 (mmp) cc_final: 0.5929 (mtt) REVERT: Q 23 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4597 (tp) REVERT: Q 35 GLN cc_start: 0.6690 (tt0) cc_final: 0.5847 (tm-30) REVERT: Q 79 GLN cc_start: 0.5631 (OUTLIER) cc_final: 0.5101 (mp-120) REVERT: Q 145 GLU cc_start: 0.4509 (pt0) cc_final: 0.4151 (pt0) REVERT: Q 152 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5742 (tp) REVERT: R 15 GLN cc_start: 0.6908 (mt0) cc_final: 0.6577 (mp10) REVERT: R 76 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5701 (ptt90) REVERT: R 96 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6855 (ttp) REVERT: S 46 MET cc_start: 0.6552 (mtm) cc_final: 0.6131 (ptt) outliers start: 104 outliers final: 53 residues processed: 591 average time/residue: 1.5918 time to fit residues: 1076.9276 Evaluate side-chains 588 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 510 time to evaluate : 2.936 ------------------------------------------------------------------------------- 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 B residue 27 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 165 PHE 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 60 GLU Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG 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 50 ILE 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 97 LEU 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 67 ILE Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 554 PHE Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 118 SER 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 M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 17 LYS 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 48 GLU Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 102 GLU 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 112 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 149 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 170 optimal weight: 3.9990 chunk 278 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 254 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 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** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN J 101 ASN K 26 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN 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 = 0.4577 r_free = 0.4577 target = 0.228696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.209186 restraints weight = 31109.067| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 1.52 r_work: 0.4276 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27538 Z= 0.169 Angle : 0.834 59.199 37298 Z= 0.438 Chirality : 0.043 0.261 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.051 89.903 4549 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.15 % Favored : 96.70 % Rotamer: Outliers : 3.44 % Allowed : 32.72 % Favored : 63.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3300 helix: 1.48 (0.10), residues: 2605 sheet: 0.07 (1.28), residues: 19 loop : -1.86 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 84 HIS 0.017 0.001 HIS K 29 PHE 0.018 0.001 PHE K 221 TYR 0.023 0.002 TYR L 152 ARG 0.022 0.001 ARG P 77 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 1998) hydrogen bonds : angle 4.77996 ( 5952) covalent geometry : bond 0.00383 (27522) covalent geometry : angle 0.83358 (37298) Misc. bond : bond 0.00083 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26295.33 seconds wall clock time: 458 minutes 46.32 seconds (27526.32 seconds total)