Starting phenix.real_space_refine on Sat Jun 14 05:40:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9krg_62526/06_2025/9krg_62526.cif Found real_map, /net/cci-nas-00/data/ceres_data/9krg_62526/06_2025/9krg_62526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9krg_62526/06_2025/9krg_62526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9krg_62526/06_2025/9krg_62526.map" model { file = "/net/cci-nas-00/data/ceres_data/9krg_62526/06_2025/9krg_62526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9krg_62526/06_2025/9krg_62526.cif" } resolution = 2.9 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= 0.007 sd= 0.237 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 10395 2.51 5 N 2639 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15876 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2268 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 6.11, per 1000 atoms: 0.38 Number of scatterers: 15876 At special positions: 0 Unit cell: (117.18, 117.18, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2772 8.00 N 2639 7.00 C 10395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 261 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 261 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 261 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 261 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 242 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 2.1 seconds 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 7 sheets defined 69.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix removed outlier: 4.291A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.442A pdb=" N LYS A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.545A pdb=" N ALA A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 132 through 159 removed outlier: 3.825A pdb=" N ARG A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.991A pdb=" N LEU A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 231 removed outlier: 3.809A pdb=" N ASN A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 removed outlier: 3.592A pdb=" N PHE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 265 through 294 removed outlier: 3.966A pdb=" N VAL A 284 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 4.574A pdb=" N LEU A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.634A pdb=" N LYS A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.295A pdb=" N GLY A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 61 Proline residue: B 46 - end of helix removed outlier: 4.291A pdb=" N GLN B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 104 through 109 removed outlier: 4.442A pdb=" N LYS B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.545A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 132 through 159 removed outlier: 3.824A pdb=" N ARG B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 159 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.991A pdb=" N LEU B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 231 removed outlier: 3.809A pdb=" N ASN B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 removed outlier: 3.592A pdb=" N PHE B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 265 through 294 removed outlier: 3.966A pdb=" N VAL B 284 " --> pdb=" O TYR B 280 " (cutoff:3.500A) Proline residue: B 285 - end of helix removed outlier: 4.574A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.634A pdb=" N LYS B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.295A pdb=" N GLY B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 61 Proline residue: C 46 - end of helix removed outlier: 4.292A pdb=" N GLN C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 104 through 109 removed outlier: 4.442A pdb=" N LYS C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 132 removed outlier: 3.545A pdb=" N ALA C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 132 through 159 removed outlier: 3.825A pdb=" N ARG C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 159 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 201 removed outlier: 3.991A pdb=" N LEU C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 231 removed outlier: 3.809A pdb=" N ASN C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 removed outlier: 3.592A pdb=" N PHE C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 265 through 294 removed outlier: 3.966A pdb=" N VAL C 284 " --> pdb=" O TYR C 280 " (cutoff:3.500A) Proline residue: C 285 - end of helix removed outlier: 4.574A pdb=" N LEU C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 317 removed outlier: 3.633A pdb=" N LYS C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.296A pdb=" N GLY C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 61 Proline residue: D 46 - end of helix removed outlier: 4.292A pdb=" N GLN D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 104 through 109 removed outlier: 4.443A pdb=" N LYS D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.545A pdb=" N ALA D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 132 through 159 removed outlier: 3.824A pdb=" N ARG D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN D 159 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 201 removed outlier: 3.991A pdb=" N LEU D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 231 removed outlier: 3.809A pdb=" N ASN D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 removed outlier: 3.592A pdb=" N PHE D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 232 through 235' Processing helix chain 'D' and resid 265 through 294 removed outlier: 3.966A pdb=" N VAL D 284 " --> pdb=" O TYR D 280 " (cutoff:3.500A) Proline residue: D 285 - end of helix removed outlier: 4.574A pdb=" N LEU D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.634A pdb=" N LYS D 317 " --> pdb=" O LEU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.296A pdb=" N GLY D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 61 Proline residue: E 46 - end of helix removed outlier: 4.291A pdb=" N GLN E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 104 through 109 removed outlier: 4.442A pdb=" N LYS E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 132 removed outlier: 3.545A pdb=" N ALA E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 132 through 159 removed outlier: 3.824A pdb=" N ARG E 156 " --> pdb=" O ASN E 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU E 157 " --> pdb=" O ARG E 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.991A pdb=" N LEU E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 231 removed outlier: 3.809A pdb=" N ASN E 213 " --> pdb=" O TYR E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 removed outlier: 3.592A pdb=" N PHE E 235 " --> pdb=" O LEU E 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 232 through 235' Processing helix chain 'E' and resid 265 through 294 removed outlier: 3.966A pdb=" N VAL E 284 " --> pdb=" O TYR E 280 " (cutoff:3.500A) Proline residue: E 285 - end of helix removed outlier: 4.574A pdb=" N LEU E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 317 removed outlier: 3.633A pdb=" N LYS E 317 " --> pdb=" O LEU E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 336 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.295A pdb=" N GLY E 374 " --> pdb=" O THR E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 Proline residue: F 46 - end of helix removed outlier: 4.292A pdb=" N GLN F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 104 through 109 removed outlier: 4.442A pdb=" N LYS F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 132 removed outlier: 3.545A pdb=" N ALA F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 132 through 159 removed outlier: 3.825A pdb=" N ARG F 156 " --> pdb=" O ASN F 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN F 159 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 201 removed outlier: 3.991A pdb=" N LEU F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 231 removed outlier: 3.809A pdb=" N ASN F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 235 removed outlier: 3.592A pdb=" N PHE F 235 " --> pdb=" O LEU F 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 232 through 235' Processing helix chain 'F' and resid 265 through 294 removed outlier: 3.966A pdb=" N VAL F 284 " --> pdb=" O TYR F 280 " (cutoff:3.500A) Proline residue: F 285 - end of helix removed outlier: 4.574A pdb=" N LEU F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 317 removed outlier: 3.634A pdb=" N LYS F 317 " --> pdb=" O LEU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 336 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.296A pdb=" N GLY F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 61 Proline residue: G 46 - end of helix removed outlier: 4.291A pdb=" N GLN G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 104 through 109 removed outlier: 4.442A pdb=" N LYS G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 132 removed outlier: 3.545A pdb=" N ALA G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 132 through 159 removed outlier: 3.824A pdb=" N ARG G 156 " --> pdb=" O ASN G 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU G 157 " --> pdb=" O ARG G 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 201 removed outlier: 3.991A pdb=" N LEU G 196 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 231 removed outlier: 3.809A pdb=" N ASN G 213 " --> pdb=" O TYR G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 235 removed outlier: 3.592A pdb=" N PHE G 235 " --> pdb=" O LEU G 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 232 through 235' Processing helix chain 'G' and resid 265 through 294 removed outlier: 3.966A pdb=" N VAL G 284 " --> pdb=" O TYR G 280 " (cutoff:3.500A) Proline residue: G 285 - end of helix removed outlier: 4.574A pdb=" N LEU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 317 removed outlier: 3.634A pdb=" N LYS G 317 " --> pdb=" O LEU G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 336 Processing helix chain 'G' and resid 368 through 374 removed outlier: 4.295A pdb=" N GLY G 374 " --> pdb=" O THR G 370 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=7, first strand: chain 'G' and resid 64 through 66 959 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4881 1.34 - 1.46: 3905 1.46 - 1.58: 7349 1.58 - 1.70: 0 1.70 - 1.81: 91 Bond restraints: 16226 Sorted by residual: bond pdb=" CB GLU C 193 " pdb=" CG GLU C 193 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB GLU D 193 " pdb=" CG GLU D 193 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CB GLU B 193 " pdb=" CG GLU B 193 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CB GLU E 193 " pdb=" CG GLU E 193 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CB GLU A 193 " pdb=" CG GLU A 193 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.60e+00 ... (remaining 16221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 21452 1.83 - 3.66: 395 3.66 - 5.49: 98 5.49 - 7.31: 98 7.31 - 9.14: 14 Bond angle restraints: 22057 Sorted by residual: angle pdb=" CA GLU B 193 " pdb=" CB GLU B 193 " pdb=" CG GLU B 193 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU G 193 " pdb=" CB GLU G 193 " pdb=" CG GLU G 193 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU D 193 " pdb=" CB GLU D 193 " pdb=" CG GLU D 193 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU A 193 " pdb=" CB GLU A 193 " pdb=" CG GLU A 193 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU F 193 " pdb=" CB GLU F 193 " pdb=" CG GLU F 193 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 ... (remaining 22052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 7945 15.99 - 31.99: 1295 31.99 - 47.98: 420 47.98 - 63.97: 70 63.97 - 79.97: 21 Dihedral angle restraints: 9751 sinusoidal: 3696 harmonic: 6055 Sorted by residual: dihedral pdb=" CA GLU G 252 " pdb=" C GLU G 252 " pdb=" N THR G 253 " pdb=" CA THR G 253 " ideal model delta harmonic sigma weight residual -180.00 -164.64 -15.36 0 5.00e+00 4.00e-02 9.44e+00 dihedral pdb=" N ASN C 152 " pdb=" CA ASN C 152 " pdb=" CB ASN C 152 " pdb=" CG ASN C 152 " ideal model delta sinusoidal sigma weight residual -60.00 -117.00 57.00 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N ASN A 152 " pdb=" CA ASN A 152 " pdb=" CB ASN A 152 " pdb=" CG ASN A 152 " ideal model delta sinusoidal sigma weight residual -60.00 -116.98 56.98 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 9748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1641 0.030 - 0.061: 641 0.061 - 0.091: 252 0.091 - 0.121: 105 0.121 - 0.152: 28 Chirality restraints: 2667 Sorted by residual: chirality pdb=" CA SER B 45 " pdb=" N SER B 45 " pdb=" C SER B 45 " pdb=" CB SER B 45 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA SER D 45 " pdb=" N SER D 45 " pdb=" C SER D 45 " pdb=" CB SER D 45 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA SER C 45 " pdb=" N SER C 45 " pdb=" C SER C 45 " pdb=" CB SER C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2664 not shown) Planarity restraints: 2681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 193 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" CD GLU D 193 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU D 193 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU D 193 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 193 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" CD GLU B 193 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU B 193 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 193 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 193 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" CD GLU F 193 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU F 193 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU F 193 " 0.013 2.00e-02 2.50e+03 ... (remaining 2678 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3559 2.78 - 3.31: 14888 3.31 - 3.84: 25882 3.84 - 4.37: 25205 4.37 - 4.90: 46288 Nonbonded interactions: 115822 Sorted by model distance: nonbonded pdb=" OH TYR D 224 " pdb=" OG1 THR D 281 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR G 224 " pdb=" OG1 THR G 281 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR F 224 " pdb=" OG1 THR F 281 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR B 224 " pdb=" OG1 THR B 281 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR C 224 " pdb=" OG1 THR C 281 " model vdw 2.245 3.040 ... (remaining 115817 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 33.880 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5216 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 : 0.004 0.042 16240 Z= 0.168 Angle : 0.787 9.144 22085 Z= 0.400 Chirality : 0.042 0.152 2667 Planarity : 0.004 0.040 2681 Dihedral : 17.936 79.968 5733 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.81 % Allowed : 41.07 % Favored : 58.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.33 (0.20), residues: 1967 helix: 1.06 (0.15), residues: 1323 sheet: -1.11 (0.50), residues: 126 loop : -1.55 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 297 HIS 0.002 0.001 HIS F 229 PHE 0.018 0.002 PHE E 189 TYR 0.010 0.001 TYR D 280 ARG 0.001 0.000 ARG E 296 Details of bonding type rmsd hydrogen bonds : bond 0.17097 ( 959) hydrogen bonds : angle 5.48455 ( 2856) SS BOND : bond 0.00186 ( 14) SS BOND : angle 0.35091 ( 28) covalent geometry : bond 0.00371 (16226) covalent geometry : angle 0.78727 (22057) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 291 time to evaluate : 1.574 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 36 ARG cc_start: 0.5371 (ttt90) cc_final: 0.5080 (ttt-90) REVERT: A 39 LYS cc_start: 0.5801 (tttt) cc_final: 0.5593 (pttt) REVERT: A 75 ARG cc_start: 0.5739 (mmm-85) cc_final: 0.5188 (mmp-170) REVERT: A 201 ARG cc_start: 0.6365 (mmm-85) cc_final: 0.6039 (mtm-85) REVERT: A 229 HIS cc_start: 0.5663 (t-90) cc_final: 0.5369 (t-90) REVERT: A 281 THR cc_start: 0.6518 (m) cc_final: 0.6274 (m) REVERT: B 229 HIS cc_start: 0.5173 (t-90) cc_final: 0.4705 (t-90) REVERT: B 281 THR cc_start: 0.6767 (m) cc_final: 0.6504 (m) REVERT: B 296 ARG cc_start: 0.4562 (tpp-160) cc_final: 0.4037 (ptt-90) REVERT: C 201 ARG cc_start: 0.6671 (mmm-85) cc_final: 0.6160 (mpp80) REVERT: C 229 HIS cc_start: 0.5705 (t-90) cc_final: 0.5476 (t-90) REVERT: D 75 ARG cc_start: 0.5157 (mmm-85) cc_final: 0.4767 (mmm160) REVERT: D 201 ARG cc_start: 0.6475 (mmm-85) cc_final: 0.6168 (ttt-90) REVERT: D 229 HIS cc_start: 0.5512 (t-90) cc_final: 0.4998 (t70) REVERT: E 36 ARG cc_start: 0.5429 (ttt90) cc_final: 0.5205 (ttt-90) REVERT: E 75 ARG cc_start: 0.5041 (mmm-85) cc_final: 0.4306 (mmm160) REVERT: E 229 HIS cc_start: 0.5137 (t-90) cc_final: 0.4540 (t70) REVERT: E 233 ASP cc_start: 0.6388 (m-30) cc_final: 0.6153 (m-30) REVERT: F 218 ILE cc_start: 0.6481 (mm) cc_final: 0.6241 (mt) REVERT: F 229 HIS cc_start: 0.5267 (t-90) cc_final: 0.4548 (t70) REVERT: F 238 GLU cc_start: 0.6427 (pm20) cc_final: 0.6130 (pm20) REVERT: G 201 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6679 (tpp-160) REVERT: G 229 HIS cc_start: 0.5710 (t-90) cc_final: 0.5094 (t70) REVERT: G 233 ASP cc_start: 0.6419 (m-30) cc_final: 0.6190 (m-30) outliers start: 14 outliers final: 0 residues processed: 305 average time/residue: 1.2566 time to fit residues: 423.5859 Evaluate side-chains 197 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 118 optimal weight: 0.2980 chunk 184 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN C 336 ASN D 336 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.198940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137493 restraints weight = 16738.227| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.00 r_work: 0.3416 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16240 Z= 0.183 Angle : 0.682 9.760 22085 Z= 0.340 Chirality : 0.042 0.142 2667 Planarity : 0.005 0.043 2681 Dihedral : 4.017 18.690 2177 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 7.78 % Allowed : 34.16 % Favored : 58.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.40 (0.19), residues: 1967 helix: 1.31 (0.14), residues: 1337 sheet: -1.13 (0.50), residues: 126 loop : -2.23 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 297 HIS 0.004 0.001 HIS F 90 PHE 0.019 0.002 PHE C 230 TYR 0.021 0.003 TYR B 112 ARG 0.007 0.001 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 959) hydrogen bonds : angle 4.32150 ( 2856) SS BOND : bond 0.00325 ( 14) SS BOND : angle 1.11817 ( 28) covalent geometry : bond 0.00442 (16226) covalent geometry : angle 0.68098 (22057) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 242 time to evaluate : 1.752 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 36 ARG cc_start: 0.6877 (ttt90) cc_final: 0.6610 (ttt-90) REVERT: A 37 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6292 (tp) REVERT: A 72 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: A 75 ARG cc_start: 0.7246 (mmm-85) cc_final: 0.6700 (mmp-170) REVERT: A 81 ASP cc_start: 0.8347 (m-30) cc_final: 0.8134 (m-30) REVERT: A 218 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7950 (mt) REVERT: A 229 HIS cc_start: 0.7463 (t-90) cc_final: 0.7200 (t-90) REVERT: A 254 HIS cc_start: 0.7363 (t-170) cc_final: 0.6695 (t-90) REVERT: A 257 ASN cc_start: 0.8138 (t0) cc_final: 0.7755 (m-40) REVERT: A 281 THR cc_start: 0.8243 (m) cc_final: 0.7866 (m) REVERT: B 36 ARG cc_start: 0.6794 (ttt90) cc_final: 0.6557 (ttt-90) REVERT: B 75 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7090 (mmp-170) REVERT: B 229 HIS cc_start: 0.7180 (t-90) cc_final: 0.6901 (t-90) REVERT: B 238 GLU cc_start: 0.8255 (pm20) cc_final: 0.8042 (pm20) REVERT: B 248 LEU cc_start: 0.7429 (mp) cc_final: 0.7100 (mt) REVERT: B 257 ASN cc_start: 0.8312 (t0) cc_final: 0.7761 (m110) REVERT: B 262 ARG cc_start: 0.8312 (ttt90) cc_final: 0.7703 (ttt-90) REVERT: C 75 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.6953 (mmp-170) REVERT: C 201 ARG cc_start: 0.6636 (mmm-85) cc_final: 0.6271 (mtm180) REVERT: C 218 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7538 (mt) REVERT: C 238 GLU cc_start: 0.8465 (pm20) cc_final: 0.8078 (pt0) REVERT: D 75 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.6842 (mmp-170) REVERT: D 108 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8331 (mtpt) REVERT: D 201 ARG cc_start: 0.6755 (mmm-85) cc_final: 0.6407 (ttm-80) REVERT: D 218 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7229 (mp) REVERT: D 229 HIS cc_start: 0.7762 (t-90) cc_final: 0.7173 (t70) REVERT: D 238 GLU cc_start: 0.8441 (pm20) cc_final: 0.8204 (pm20) REVERT: D 281 THR cc_start: 0.8288 (m) cc_final: 0.7911 (m) REVERT: E 36 ARG cc_start: 0.6944 (ttt90) cc_final: 0.6542 (ttt-90) REVERT: E 75 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.6902 (mmp-170) REVERT: E 81 ASP cc_start: 0.8334 (m-30) cc_final: 0.8021 (m-30) REVERT: E 201 ARG cc_start: 0.6744 (ttt-90) cc_final: 0.6475 (mpp80) REVERT: E 229 HIS cc_start: 0.7279 (t-90) cc_final: 0.6702 (t-90) REVERT: E 262 ARG cc_start: 0.8360 (ttt90) cc_final: 0.7708 (ttm-80) REVERT: F 75 ARG cc_start: 0.7455 (mmm-85) cc_final: 0.7059 (mmp-170) REVERT: F 218 ILE cc_start: 0.8119 (mm) cc_final: 0.7869 (mt) REVERT: F 229 HIS cc_start: 0.7682 (t-90) cc_final: 0.7015 (t70) REVERT: F 257 ASN cc_start: 0.8328 (t0) cc_final: 0.8099 (m-40) REVERT: F 281 THR cc_start: 0.8247 (m) cc_final: 0.7966 (m) REVERT: G 36 ARG cc_start: 0.7132 (ttt90) cc_final: 0.6740 (ttt-90) REVERT: G 75 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7214 (mmp-170) REVERT: G 120 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8031 (mp) REVERT: G 121 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8155 (mmt) REVERT: G 201 ARG cc_start: 0.6483 (mmm-85) cc_final: 0.5931 (mpp80) REVERT: G 218 ILE cc_start: 0.8118 (mm) cc_final: 0.7828 (mt) REVERT: G 229 HIS cc_start: 0.7459 (t-90) cc_final: 0.6833 (t-90) REVERT: G 262 ARG cc_start: 0.8259 (ttt90) cc_final: 0.7973 (ttt-90) outliers start: 135 outliers final: 28 residues processed: 354 average time/residue: 1.0195 time to fit residues: 407.7696 Evaluate side-chains 264 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 72 PHE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 292 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 13 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN F 336 ASN G 336 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.197906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136644 restraints weight = 16627.911| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.96 r_work: 0.3366 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16240 Z= 0.146 Angle : 0.599 9.116 22085 Z= 0.293 Chirality : 0.039 0.136 2667 Planarity : 0.004 0.041 2681 Dihedral : 3.730 15.480 2177 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 7.95 % Allowed : 33.24 % Favored : 58.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.89 (0.19), residues: 1967 helix: 1.68 (0.14), residues: 1344 sheet: -1.25 (0.46), residues: 119 loop : -1.98 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 297 HIS 0.006 0.001 HIS F 254 PHE 0.016 0.002 PHE A 269 TYR 0.015 0.002 TYR G 112 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 959) hydrogen bonds : angle 3.97820 ( 2856) SS BOND : bond 0.00205 ( 14) SS BOND : angle 0.83136 ( 28) covalent geometry : bond 0.00351 (16226) covalent geometry : angle 0.59858 (22057) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 222 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7472 (ttt90) cc_final: 0.7181 (ttt-90) REVERT: A 37 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.6889 (tp) REVERT: A 72 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: A 235 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: A 238 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: A 248 LEU cc_start: 0.8289 (mp) cc_final: 0.8033 (mt) REVERT: A 254 HIS cc_start: 0.8387 (t-170) cc_final: 0.8048 (t-90) REVERT: A 281 THR cc_start: 0.8463 (m) cc_final: 0.8074 (m) REVERT: B 52 LEU cc_start: 0.7147 (tp) cc_final: 0.6854 (tm) REVERT: B 75 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7454 (mmp-170) REVERT: B 238 GLU cc_start: 0.8466 (pm20) cc_final: 0.8199 (pt0) REVERT: C 75 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7680 (mmp-170) REVERT: C 218 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8039 (mt) REVERT: C 238 GLU cc_start: 0.8443 (pm20) cc_final: 0.8239 (pt0) REVERT: D 75 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7284 (mmp-170) REVERT: D 218 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7884 (mp) REVERT: D 229 HIS cc_start: 0.7925 (t-90) cc_final: 0.7616 (t70) REVERT: D 235 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: D 238 GLU cc_start: 0.8610 (pm20) cc_final: 0.8347 (pt0) REVERT: D 257 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.7990 (m-40) REVERT: D 281 THR cc_start: 0.8628 (m) cc_final: 0.8227 (m) REVERT: E 36 ARG cc_start: 0.7461 (ttt90) cc_final: 0.7064 (ttt-90) REVERT: E 75 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7360 (mmp-170) REVERT: E 81 ASP cc_start: 0.8449 (m-30) cc_final: 0.8232 (m-30) REVERT: E 201 ARG cc_start: 0.7173 (ttt-90) cc_final: 0.6915 (mpp80) REVERT: E 229 HIS cc_start: 0.7570 (t-90) cc_final: 0.7047 (t-90) REVERT: E 257 ASN cc_start: 0.8674 (t0) cc_final: 0.8362 (m-40) REVERT: E 285 PRO cc_start: 0.7532 (Cg_exo) cc_final: 0.7102 (Cg_endo) REVERT: E 334 ARG cc_start: 0.6751 (tmm-80) cc_final: 0.6369 (ttm110) REVERT: F 51 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7844 (m) REVERT: F 75 ARG cc_start: 0.7734 (mmm-85) cc_final: 0.7403 (mmp-170) REVERT: F 218 ILE cc_start: 0.8577 (mm) cc_final: 0.8252 (mt) REVERT: F 229 HIS cc_start: 0.7915 (t-90) cc_final: 0.7379 (t70) REVERT: F 281 THR cc_start: 0.8467 (m) cc_final: 0.8200 (m) REVERT: G 218 ILE cc_start: 0.8581 (mm) cc_final: 0.8341 (mt) REVERT: G 229 HIS cc_start: 0.7663 (t-90) cc_final: 0.7119 (t-90) REVERT: G 238 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: G 257 ASN cc_start: 0.8404 (t0) cc_final: 0.8189 (m-40) outliers start: 138 outliers final: 42 residues processed: 332 average time/residue: 0.9487 time to fit residues: 362.3221 Evaluate side-chains 265 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 263 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 152 optimal weight: 0.0370 chunk 165 optimal weight: 0.9980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN C 254 HIS D 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.198490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137795 restraints weight = 16614.285| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.94 r_work: 0.3401 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16240 Z= 0.108 Angle : 0.541 9.845 22085 Z= 0.260 Chirality : 0.036 0.127 2667 Planarity : 0.004 0.042 2681 Dihedral : 3.478 15.734 2177 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.47 % Allowed : 34.45 % Favored : 60.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.40 (0.19), residues: 1967 helix: 2.07 (0.15), residues: 1351 sheet: -1.30 (0.57), residues: 84 loop : -1.79 (0.22), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 105 HIS 0.006 0.001 HIS G 254 PHE 0.013 0.001 PHE F 269 TYR 0.012 0.001 TYR G 112 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 959) hydrogen bonds : angle 3.72157 ( 2856) SS BOND : bond 0.00163 ( 14) SS BOND : angle 0.68282 ( 28) covalent geometry : bond 0.00235 (16226) covalent geometry : angle 0.54038 (22057) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 224 time to evaluate : 1.637 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 37 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6220 (tp) REVERT: A 72 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: A 235 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6424 (m-80) REVERT: A 238 GLU cc_start: 0.8419 (pm20) cc_final: 0.8106 (pt0) REVERT: A 248 LEU cc_start: 0.7863 (mp) cc_final: 0.7625 (mt) REVERT: A 254 HIS cc_start: 0.8251 (t-170) cc_final: 0.7935 (t-90) REVERT: A 281 THR cc_start: 0.8134 (m) cc_final: 0.7762 (m) REVERT: A 285 PRO cc_start: 0.7241 (Cg_exo) cc_final: 0.6971 (Cg_endo) REVERT: B 52 LEU cc_start: 0.6583 (tp) cc_final: 0.6265 (tp) REVERT: B 75 ARG cc_start: 0.7458 (mmm-85) cc_final: 0.6974 (mmp-170) REVERT: B 235 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: B 238 GLU cc_start: 0.8343 (pm20) cc_final: 0.7976 (pt0) REVERT: C 75 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7112 (mmp-170) REVERT: C 218 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7456 (mt) REVERT: C 238 GLU cc_start: 0.8428 (pm20) cc_final: 0.8119 (pt0) REVERT: D 75 ARG cc_start: 0.7352 (mmm-85) cc_final: 0.6924 (mmp-170) REVERT: D 229 HIS cc_start: 0.7567 (t-90) cc_final: 0.6951 (t-90) REVERT: D 235 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6696 (m-80) REVERT: D 238 GLU cc_start: 0.8389 (pm20) cc_final: 0.7917 (pt0) REVERT: D 257 ASN cc_start: 0.8321 (t0) cc_final: 0.7764 (m-40) REVERT: D 281 THR cc_start: 0.8373 (m) cc_final: 0.8122 (m) REVERT: E 36 ARG cc_start: 0.6907 (ttt90) cc_final: 0.6603 (ttt-90) REVERT: E 52 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6155 (tp) REVERT: E 54 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5098 (m-10) REVERT: E 75 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7207 (mmp-170) REVERT: E 81 ASP cc_start: 0.8220 (m-30) cc_final: 0.7954 (m-30) REVERT: E 201 ARG cc_start: 0.7023 (ttt-90) cc_final: 0.6702 (mpp80) REVERT: E 229 HIS cc_start: 0.7138 (t-90) cc_final: 0.6531 (t-90) REVERT: E 257 ASN cc_start: 0.8516 (t0) cc_final: 0.8128 (m-40) REVERT: F 75 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.7054 (mmp-170) REVERT: F 218 ILE cc_start: 0.8094 (mm) cc_final: 0.7754 (mt) REVERT: F 229 HIS cc_start: 0.7703 (t-90) cc_final: 0.7044 (t70) REVERT: F 235 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6275 (m-80) REVERT: F 281 THR cc_start: 0.8221 (m) cc_final: 0.7964 (m) REVERT: F 285 PRO cc_start: 0.7266 (Cg_exo) cc_final: 0.7011 (Cg_endo) REVERT: G 37 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6062 (tp) REVERT: G 218 ILE cc_start: 0.8145 (mm) cc_final: 0.7866 (mt) REVERT: G 229 HIS cc_start: 0.7354 (t-90) cc_final: 0.6700 (t-90) REVERT: G 235 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: G 238 GLU cc_start: 0.8307 (pm20) cc_final: 0.7919 (pt0) REVERT: G 257 ASN cc_start: 0.8284 (t0) cc_final: 0.8064 (m-40) REVERT: G 285 PRO cc_start: 0.6974 (Cg_exo) cc_final: 0.6637 (Cg_endo) outliers start: 95 outliers final: 36 residues processed: 304 average time/residue: 0.8786 time to fit residues: 306.2013 Evaluate side-chains 262 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 PHE Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 235 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 49 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 24 optimal weight: 0.0020 chunk 99 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN C 254 HIS C 324 ASN D 254 HIS F 324 ASN G 254 HIS G 324 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.197355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136505 restraints weight = 16803.649| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.93 r_work: 0.3407 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16240 Z= 0.113 Angle : 0.543 9.510 22085 Z= 0.261 Chirality : 0.037 0.128 2667 Planarity : 0.004 0.042 2681 Dihedral : 3.424 15.194 2177 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 6.16 % Allowed : 34.27 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.44 (0.19), residues: 1967 helix: 2.14 (0.15), residues: 1344 sheet: -1.25 (0.58), residues: 84 loop : -1.85 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 297 HIS 0.006 0.001 HIS G 254 PHE 0.017 0.001 PHE D 189 TYR 0.012 0.001 TYR G 112 ARG 0.003 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 959) hydrogen bonds : angle 3.65806 ( 2856) SS BOND : bond 0.00174 ( 14) SS BOND : angle 0.74748 ( 28) covalent geometry : bond 0.00255 (16226) covalent geometry : angle 0.54289 (22057) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 225 time to evaluate : 1.614 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 37 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6331 (tp) REVERT: A 72 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: A 238 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: A 254 HIS cc_start: 0.8348 (t-170) cc_final: 0.8035 (t-90) REVERT: A 281 THR cc_start: 0.8225 (m) cc_final: 0.7854 (m) REVERT: A 285 PRO cc_start: 0.7361 (Cg_exo) cc_final: 0.7071 (Cg_endo) REVERT: A 325 ASP cc_start: 0.7830 (t0) cc_final: 0.7202 (m-30) REVERT: B 52 LEU cc_start: 0.6555 (tp) cc_final: 0.6225 (tp) REVERT: B 75 ARG cc_start: 0.7494 (mmm-85) cc_final: 0.7019 (mmp-170) REVERT: B 235 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6266 (m-80) REVERT: B 238 GLU cc_start: 0.8452 (pm20) cc_final: 0.8092 (pt0) REVERT: C 75 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7287 (mmp-170) REVERT: C 122 TYR cc_start: 0.8330 (t80) cc_final: 0.8086 (t80) REVERT: C 218 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7443 (mt) REVERT: C 238 GLU cc_start: 0.8501 (pm20) cc_final: 0.8206 (pt0) REVERT: D 75 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.7002 (mmp-170) REVERT: D 229 HIS cc_start: 0.7587 (t-90) cc_final: 0.6959 (t-90) REVERT: D 235 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6709 (m-80) REVERT: D 238 GLU cc_start: 0.8549 (pm20) cc_final: 0.8100 (pt0) REVERT: D 257 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8051 (m110) REVERT: D 281 THR cc_start: 0.8403 (m) cc_final: 0.8155 (m) REVERT: E 36 ARG cc_start: 0.7031 (ttt90) cc_final: 0.6781 (ttt-90) REVERT: E 54 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5056 (m-10) REVERT: E 75 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7176 (mmp-170) REVERT: E 81 ASP cc_start: 0.8268 (m-30) cc_final: 0.7973 (m-30) REVERT: E 201 ARG cc_start: 0.7123 (ttt-90) cc_final: 0.6767 (mpp80) REVERT: E 229 HIS cc_start: 0.7130 (t-90) cc_final: 0.6571 (t-90) REVERT: E 257 ASN cc_start: 0.8562 (t0) cc_final: 0.8225 (m-40) REVERT: F 75 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.7116 (mmp-170) REVERT: F 218 ILE cc_start: 0.8081 (mm) cc_final: 0.7733 (mt) REVERT: F 229 HIS cc_start: 0.7737 (t-90) cc_final: 0.7085 (t70) REVERT: F 235 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6319 (m-80) REVERT: F 281 THR cc_start: 0.8267 (m) cc_final: 0.8015 (m) REVERT: F 285 PRO cc_start: 0.7255 (Cg_exo) cc_final: 0.6976 (Cg_endo) REVERT: G 218 ILE cc_start: 0.8124 (mm) cc_final: 0.7862 (mt) REVERT: G 229 HIS cc_start: 0.7381 (t-90) cc_final: 0.6699 (t-90) REVERT: G 238 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: G 257 ASN cc_start: 0.8322 (t0) cc_final: 0.8100 (m-40) REVERT: G 285 PRO cc_start: 0.6947 (Cg_exo) cc_final: 0.6555 (Cg_endo) outliers start: 107 outliers final: 55 residues processed: 315 average time/residue: 0.8599 time to fit residues: 311.1420 Evaluate side-chains 283 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 263 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 153 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 197 optimal weight: 0.0870 chunk 125 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 HIS D 254 HIS F 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.191757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145051 restraints weight = 16858.626| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.36 r_work: 0.3352 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16240 Z= 0.127 Angle : 0.572 10.766 22085 Z= 0.274 Chirality : 0.038 0.139 2667 Planarity : 0.004 0.039 2681 Dihedral : 3.557 15.154 2177 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.11 % Allowed : 33.81 % Favored : 60.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.52 (0.19), residues: 1967 helix: 2.18 (0.14), residues: 1344 sheet: -1.40 (0.46), residues: 119 loop : -1.71 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 297 HIS 0.006 0.001 HIS D 254 PHE 0.019 0.002 PHE G 189 TYR 0.014 0.002 TYR G 112 ARG 0.003 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 959) hydrogen bonds : angle 3.67477 ( 2856) SS BOND : bond 0.00224 ( 14) SS BOND : angle 0.91438 ( 28) covalent geometry : bond 0.00298 (16226) covalent geometry : angle 0.57111 (22057) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 218 time to evaluate : 1.591 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 72 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: A 238 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: A 281 THR cc_start: 0.8405 (m) cc_final: 0.8049 (m) REVERT: A 285 PRO cc_start: 0.7623 (Cg_exo) cc_final: 0.7304 (Cg_endo) REVERT: B 52 LEU cc_start: 0.6798 (tp) cc_final: 0.6525 (tp) REVERT: B 75 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7489 (mmp-170) REVERT: B 235 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: B 238 GLU cc_start: 0.8595 (pm20) cc_final: 0.8295 (pt0) REVERT: C 51 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8385 (p) REVERT: C 75 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7514 (mmp-170) REVERT: C 122 TYR cc_start: 0.8554 (t80) cc_final: 0.8335 (t80) REVERT: C 218 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7668 (mt) REVERT: C 238 GLU cc_start: 0.8671 (pm20) cc_final: 0.8432 (pt0) REVERT: D 75 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7266 (mmp-170) REVERT: D 120 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8347 (tp) REVERT: D 229 HIS cc_start: 0.7923 (t-90) cc_final: 0.7347 (t-90) REVERT: D 235 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.6907 (m-80) REVERT: D 257 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8283 (m110) REVERT: D 281 THR cc_start: 0.8610 (m) cc_final: 0.8255 (m) REVERT: D 325 ASP cc_start: 0.7577 (m-30) cc_final: 0.7254 (t0) REVERT: E 36 ARG cc_start: 0.7375 (ttt90) cc_final: 0.7113 (ttt-90) REVERT: E 54 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5427 (m-10) REVERT: E 75 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7478 (mmp-170) REVERT: E 81 ASP cc_start: 0.8471 (m-30) cc_final: 0.8227 (m-30) REVERT: E 201 ARG cc_start: 0.7269 (ttt-90) cc_final: 0.6991 (mpp80) REVERT: E 229 HIS cc_start: 0.7463 (t-90) cc_final: 0.6972 (t-90) REVERT: E 257 ASN cc_start: 0.8756 (t0) cc_final: 0.8450 (m-40) REVERT: F 75 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7440 (mmp-170) REVERT: F 218 ILE cc_start: 0.8329 (mm) cc_final: 0.7982 (mt) REVERT: F 229 HIS cc_start: 0.8138 (t-90) cc_final: 0.7535 (t70) REVERT: F 235 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: F 281 THR cc_start: 0.8433 (m) cc_final: 0.8174 (m) REVERT: F 285 PRO cc_start: 0.7379 (Cg_exo) cc_final: 0.7035 (Cg_endo) REVERT: F 324 ASN cc_start: 0.6589 (OUTLIER) cc_final: 0.6385 (m-40) REVERT: G 72 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7981 (m-10) REVERT: G 218 ILE cc_start: 0.8365 (mm) cc_final: 0.8116 (mt) REVERT: G 229 HIS cc_start: 0.7752 (t-90) cc_final: 0.7158 (t-90) REVERT: G 238 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8191 (pt0) REVERT: G 257 ASN cc_start: 0.8514 (t0) cc_final: 0.8293 (m-40) REVERT: G 285 PRO cc_start: 0.7288 (Cg_exo) cc_final: 0.6889 (Cg_endo) outliers start: 106 outliers final: 60 residues processed: 305 average time/residue: 0.9196 time to fit residues: 320.9129 Evaluate side-chains 288 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 215 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 72 PHE Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 149 optimal weight: 0.3980 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 168 optimal weight: 0.0670 chunk 139 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 187 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 HIS F 324 ASN G 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.194985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148683 restraints weight = 16878.984| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.31 r_work: 0.3418 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16240 Z= 0.100 Angle : 0.526 9.359 22085 Z= 0.249 Chirality : 0.036 0.126 2667 Planarity : 0.004 0.040 2681 Dihedral : 3.338 15.133 2177 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.38 % Allowed : 35.37 % Favored : 60.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.87 (0.19), residues: 1967 helix: 2.44 (0.14), residues: 1351 sheet: -1.14 (0.59), residues: 84 loop : -1.68 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 105 HIS 0.006 0.001 HIS G 254 PHE 0.021 0.001 PHE D 189 TYR 0.011 0.001 TYR E 195 ARG 0.003 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 959) hydrogen bonds : angle 3.56286 ( 2856) SS BOND : bond 0.00143 ( 14) SS BOND : angle 0.68292 ( 28) covalent geometry : bond 0.00210 (16226) covalent geometry : angle 0.52565 (22057) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 228 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6339 (tp) REVERT: A 72 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: A 221 SER cc_start: 0.8233 (t) cc_final: 0.7983 (p) REVERT: A 238 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: A 281 THR cc_start: 0.8316 (m) cc_final: 0.8003 (m) REVERT: A 285 PRO cc_start: 0.7611 (Cg_exo) cc_final: 0.7298 (Cg_endo) REVERT: B 52 LEU cc_start: 0.6622 (tp) cc_final: 0.6397 (tp) REVERT: B 75 ARG cc_start: 0.7909 (mmm-85) cc_final: 0.7442 (mmp-170) REVERT: B 235 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: B 238 GLU cc_start: 0.8514 (pm20) cc_final: 0.8130 (pt0) REVERT: C 51 SER cc_start: 0.8664 (t) cc_final: 0.8426 (p) REVERT: C 122 TYR cc_start: 0.8514 (t80) cc_final: 0.8307 (t80) REVERT: C 238 GLU cc_start: 0.8618 (pm20) cc_final: 0.8416 (pt0) REVERT: D 75 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7540 (mmp-170) REVERT: D 218 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8064 (mt) REVERT: D 229 HIS cc_start: 0.7764 (t-90) cc_final: 0.7150 (t-90) REVERT: D 235 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6905 (m-80) REVERT: D 257 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8262 (m110) REVERT: D 281 THR cc_start: 0.8491 (m) cc_final: 0.8244 (m) REVERT: D 285 PRO cc_start: 0.7378 (Cg_exo) cc_final: 0.7125 (Cg_endo) REVERT: D 325 ASP cc_start: 0.7523 (m-30) cc_final: 0.7217 (t0) REVERT: E 37 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6255 (tp) REVERT: E 52 LEU cc_start: 0.7347 (tt) cc_final: 0.7105 (tt) REVERT: E 54 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.5494 (m-10) REVERT: E 75 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7486 (mmp-170) REVERT: E 81 ASP cc_start: 0.8358 (m-30) cc_final: 0.8089 (m-30) REVERT: E 201 ARG cc_start: 0.7270 (ttt-90) cc_final: 0.6948 (mpp80) REVERT: E 229 HIS cc_start: 0.7299 (t-90) cc_final: 0.6806 (t-90) REVERT: E 257 ASN cc_start: 0.8706 (t0) cc_final: 0.8396 (m-40) REVERT: E 318 MET cc_start: 0.4583 (tpt) cc_final: 0.4040 (mmt) REVERT: E 334 ARG cc_start: 0.6661 (tmm-80) cc_final: 0.6229 (ttm110) REVERT: F 75 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7459 (mmp-170) REVERT: F 218 ILE cc_start: 0.8318 (mm) cc_final: 0.7972 (mt) REVERT: F 229 HIS cc_start: 0.7988 (t-90) cc_final: 0.7371 (t70) REVERT: F 235 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: F 281 THR cc_start: 0.8400 (m) cc_final: 0.8130 (m) REVERT: F 285 PRO cc_start: 0.7299 (Cg_exo) cc_final: 0.6960 (Cg_endo) REVERT: G 37 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6307 (tp) REVERT: G 218 ILE cc_start: 0.8307 (mm) cc_final: 0.8033 (mt) REVERT: G 229 HIS cc_start: 0.7605 (t-90) cc_final: 0.6992 (t-90) REVERT: G 235 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: G 238 GLU cc_start: 0.8413 (pm20) cc_final: 0.8005 (pt0) REVERT: G 257 ASN cc_start: 0.8444 (t0) cc_final: 0.8234 (m-40) REVERT: G 285 PRO cc_start: 0.7259 (Cg_exo) cc_final: 0.6861 (Cg_endo) outliers start: 76 outliers final: 46 residues processed: 291 average time/residue: 0.8877 time to fit residues: 296.5808 Evaluate side-chains 277 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 263 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 138 optimal weight: 4.9990 chunk 168 optimal weight: 0.0870 chunk 115 optimal weight: 50.0000 chunk 3 optimal weight: 0.0770 chunk 111 optimal weight: 20.0000 chunk 196 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.8318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 HIS G 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.193593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147814 restraints weight = 16799.977| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.30 r_work: 0.3402 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16240 Z= 0.106 Angle : 0.538 10.071 22085 Z= 0.255 Chirality : 0.036 0.126 2667 Planarity : 0.004 0.041 2681 Dihedral : 3.348 14.701 2177 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.61 % Allowed : 35.43 % Favored : 59.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.97 (0.19), residues: 1967 helix: 2.52 (0.14), residues: 1351 sheet: -1.17 (0.59), residues: 84 loop : -1.63 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 105 HIS 0.006 0.001 HIS C 254 PHE 0.018 0.001 PHE D 189 TYR 0.013 0.001 TYR G 112 ARG 0.002 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 959) hydrogen bonds : angle 3.52994 ( 2856) SS BOND : bond 0.00178 ( 14) SS BOND : angle 0.77387 ( 28) covalent geometry : bond 0.00234 (16226) covalent geometry : angle 0.53741 (22057) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 227 time to evaluate : 1.964 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 37 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6598 (tp) REVERT: A 72 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: A 221 SER cc_start: 0.8264 (t) cc_final: 0.8009 (p) REVERT: A 238 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: A 281 THR cc_start: 0.8368 (m) cc_final: 0.8037 (m) REVERT: A 285 PRO cc_start: 0.7642 (Cg_exo) cc_final: 0.7315 (Cg_endo) REVERT: B 75 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7555 (mmp-170) REVERT: B 235 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: B 238 GLU cc_start: 0.8449 (pm20) cc_final: 0.8164 (pt0) REVERT: C 51 SER cc_start: 0.8681 (t) cc_final: 0.8426 (p) REVERT: C 75 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7414 (mmp-170) REVERT: C 122 TYR cc_start: 0.8537 (t80) cc_final: 0.8333 (t80) REVERT: D 75 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7554 (mmp-170) REVERT: D 147 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4809 (mp) REVERT: D 218 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8083 (mt) REVERT: D 229 HIS cc_start: 0.7904 (t-90) cc_final: 0.7301 (t-90) REVERT: D 235 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6989 (m-80) REVERT: D 257 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8042 (m110) REVERT: D 285 PRO cc_start: 0.7411 (Cg_exo) cc_final: 0.7140 (Cg_endo) REVERT: D 325 ASP cc_start: 0.7445 (m-30) cc_final: 0.7162 (t0) REVERT: E 54 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.5590 (m-10) REVERT: E 75 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7472 (mmp-170) REVERT: E 81 ASP cc_start: 0.8353 (m-30) cc_final: 0.8129 (m-30) REVERT: E 201 ARG cc_start: 0.7276 (ttt-90) cc_final: 0.6979 (mpp80) REVERT: E 229 HIS cc_start: 0.7367 (t-90) cc_final: 0.6864 (t-90) REVERT: E 257 ASN cc_start: 0.8751 (t0) cc_final: 0.8439 (m-40) REVERT: E 318 MET cc_start: 0.4448 (tpt) cc_final: 0.3961 (mmt) REVERT: E 334 ARG cc_start: 0.6686 (tmm-80) cc_final: 0.6264 (ttm110) REVERT: F 75 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7603 (mmp-170) REVERT: F 218 ILE cc_start: 0.8346 (mm) cc_final: 0.7991 (mt) REVERT: F 235 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.6418 (m-80) REVERT: F 281 THR cc_start: 0.8464 (m) cc_final: 0.8213 (m) REVERT: G 218 ILE cc_start: 0.8367 (mm) cc_final: 0.8101 (mt) REVERT: G 229 HIS cc_start: 0.7667 (t-90) cc_final: 0.7025 (t-90) REVERT: G 235 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: G 238 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: G 257 ASN cc_start: 0.8469 (t0) cc_final: 0.8263 (m-40) REVERT: G 285 PRO cc_start: 0.7390 (Cg_exo) cc_final: 0.6987 (Cg_endo) REVERT: G 290 ASN cc_start: 0.7624 (t0) cc_final: 0.7385 (t0) outliers start: 80 outliers final: 55 residues processed: 294 average time/residue: 0.9439 time to fit residues: 318.8627 Evaluate side-chains 288 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 324 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 176 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 chunk 162 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 HIS G 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.194862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.147920 restraints weight = 16913.752| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.21 r_work: 0.3406 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16240 Z= 0.100 Angle : 0.528 9.584 22085 Z= 0.248 Chirality : 0.036 0.129 2667 Planarity : 0.004 0.042 2681 Dihedral : 3.277 15.078 2177 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.61 % Allowed : 35.48 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.14 (0.19), residues: 1967 helix: 2.72 (0.14), residues: 1323 sheet: -1.14 (0.59), residues: 84 loop : -1.52 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 105 HIS 0.006 0.001 HIS C 254 PHE 0.017 0.001 PHE D 189 TYR 0.013 0.001 TYR G 112 ARG 0.002 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 959) hydrogen bonds : angle 3.47863 ( 2856) SS BOND : bond 0.00157 ( 14) SS BOND : angle 0.72500 ( 28) covalent geometry : bond 0.00214 (16226) covalent geometry : angle 0.52779 (22057) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 238 time to evaluate : 1.717 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 37 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6318 (tp) REVERT: A 72 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: A 221 SER cc_start: 0.8260 (t) cc_final: 0.8026 (p) REVERT: A 238 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: A 252 GLU cc_start: 0.7796 (tt0) cc_final: 0.7515 (tt0) REVERT: A 281 THR cc_start: 0.8345 (m) cc_final: 0.8051 (m) REVERT: A 285 PRO cc_start: 0.7614 (Cg_exo) cc_final: 0.7284 (Cg_endo) REVERT: B 75 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7434 (mmp-170) REVERT: B 235 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: B 238 GLU cc_start: 0.8420 (pm20) cc_final: 0.8124 (pt0) REVERT: C 51 SER cc_start: 0.8680 (t) cc_final: 0.8442 (p) REVERT: C 75 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7181 (mmp-170) REVERT: C 122 TYR cc_start: 0.8518 (t80) cc_final: 0.8283 (t80) REVERT: C 218 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7684 (mt) REVERT: D 75 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7508 (mmp-170) REVERT: D 218 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8086 (mt) REVERT: D 229 HIS cc_start: 0.7874 (t-90) cc_final: 0.7267 (t-90) REVERT: D 235 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: D 257 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8264 (m110) REVERT: E 54 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.5543 (m-10) REVERT: E 75 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.7571 (mmp-170) REVERT: E 81 ASP cc_start: 0.8331 (m-30) cc_final: 0.8094 (m-30) REVERT: E 201 ARG cc_start: 0.7264 (ttt-90) cc_final: 0.6938 (mpp80) REVERT: E 229 HIS cc_start: 0.7324 (t-90) cc_final: 0.6794 (t-90) REVERT: E 238 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: E 257 ASN cc_start: 0.8740 (t0) cc_final: 0.8423 (m-40) REVERT: E 318 MET cc_start: 0.4445 (tpt) cc_final: 0.3967 (mmt) REVERT: E 334 ARG cc_start: 0.6654 (tmm-80) cc_final: 0.6240 (ttm110) REVERT: F 75 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7533 (mmp-170) REVERT: F 218 ILE cc_start: 0.8348 (mm) cc_final: 0.8008 (mt) REVERT: F 235 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: F 281 THR cc_start: 0.8455 (m) cc_final: 0.8183 (m) REVERT: G 37 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6261 (tp) REVERT: G 218 ILE cc_start: 0.8367 (mm) cc_final: 0.8088 (mt) REVERT: G 229 HIS cc_start: 0.7607 (t-90) cc_final: 0.6961 (t-90) REVERT: G 238 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: G 257 ASN cc_start: 0.8476 (t0) cc_final: 0.8264 (m-40) REVERT: G 285 PRO cc_start: 0.7521 (Cg_exo) cc_final: 0.7095 (Cg_endo) REVERT: G 290 ASN cc_start: 0.7609 (t0) cc_final: 0.7385 (t0) outliers start: 80 outliers final: 54 residues processed: 304 average time/residue: 0.8744 time to fit residues: 305.4191 Evaluate side-chains 296 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 229 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 324 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 125 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 97 optimal weight: 0.3980 chunk 99 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 HIS F 324 ASN G 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.146041 restraints weight = 17039.831| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.41 r_work: 0.3366 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16240 Z= 0.113 Angle : 0.552 9.835 22085 Z= 0.260 Chirality : 0.037 0.130 2667 Planarity : 0.004 0.039 2681 Dihedral : 3.380 15.213 2177 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.21 % Allowed : 36.18 % Favored : 59.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.20 (0.19), residues: 1967 helix: 2.71 (0.14), residues: 1323 sheet: -0.87 (0.47), residues: 119 loop : -1.42 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 297 HIS 0.006 0.001 HIS C 254 PHE 0.024 0.002 PHE A 189 TYR 0.013 0.002 TYR B 112 ARG 0.002 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 959) hydrogen bonds : angle 3.52579 ( 2856) SS BOND : bond 0.00196 ( 14) SS BOND : angle 0.86647 ( 28) covalent geometry : bond 0.00256 (16226) covalent geometry : angle 0.55105 (22057) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 230 time to evaluate : 1.858 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 37 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6612 (tp) REVERT: A 72 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: A 221 SER cc_start: 0.8288 (t) cc_final: 0.8038 (p) REVERT: A 238 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8271 (pt0) REVERT: A 252 GLU cc_start: 0.8009 (tt0) cc_final: 0.7712 (tt0) REVERT: A 281 THR cc_start: 0.8383 (m) cc_final: 0.8061 (m) REVERT: A 285 PRO cc_start: 0.7661 (Cg_exo) cc_final: 0.7317 (Cg_endo) REVERT: B 75 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7569 (mmp-170) REVERT: B 194 ARG cc_start: 0.4244 (mmm160) cc_final: 0.3973 (ptm160) REVERT: B 235 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6793 (m-80) REVERT: B 238 GLU cc_start: 0.8493 (pm20) cc_final: 0.8206 (pt0) REVERT: C 75 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7427 (mmp-170) REVERT: C 122 TYR cc_start: 0.8564 (t80) cc_final: 0.8354 (t80) REVERT: C 218 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7716 (mt) REVERT: D 75 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7588 (mmp-170) REVERT: D 147 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.4850 (mp) REVERT: D 218 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8106 (mt) REVERT: D 229 HIS cc_start: 0.7968 (t-90) cc_final: 0.7351 (t-90) REVERT: D 235 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: D 257 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (m110) REVERT: E 54 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.5767 (m-10) REVERT: E 75 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7679 (mmp-170) REVERT: E 201 ARG cc_start: 0.7330 (ttt-90) cc_final: 0.7046 (mpp80) REVERT: E 229 HIS cc_start: 0.7412 (t-90) cc_final: 0.6898 (t-90) REVERT: E 238 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8343 (pt0) REVERT: E 257 ASN cc_start: 0.8798 (t0) cc_final: 0.8530 (m-40) REVERT: E 318 MET cc_start: 0.4573 (tpt) cc_final: 0.4188 (mmt) REVERT: E 334 ARG cc_start: 0.6659 (tmm-80) cc_final: 0.6245 (ttm110) REVERT: F 75 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.7615 (mmp-170) REVERT: F 218 ILE cc_start: 0.8336 (mm) cc_final: 0.7980 (mt) REVERT: F 235 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: F 281 THR cc_start: 0.8466 (m) cc_final: 0.8198 (m) REVERT: F 323 ILE cc_start: 0.7226 (mm) cc_final: 0.6788 (pp) REVERT: G 218 ILE cc_start: 0.8360 (mm) cc_final: 0.8093 (mt) REVERT: G 229 HIS cc_start: 0.7742 (t-90) cc_final: 0.7094 (t-90) REVERT: G 238 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: G 285 PRO cc_start: 0.7575 (Cg_exo) cc_final: 0.7137 (Cg_endo) REVERT: G 290 ASN cc_start: 0.7650 (t0) cc_final: 0.7399 (t0) outliers start: 73 outliers final: 57 residues processed: 291 average time/residue: 0.9162 time to fit residues: 304.4801 Evaluate side-chains 298 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 228 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 324 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 12 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 170 optimal weight: 0.0030 chunk 176 optimal weight: 0.9980 chunk 157 optimal weight: 30.0000 chunk 50 optimal weight: 0.5980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 HIS G 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.192519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145909 restraints weight = 16889.985| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.25 r_work: 0.3389 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 16240 Z= 0.138 Angle : 0.762 59.185 22085 Z= 0.418 Chirality : 0.037 0.351 2667 Planarity : 0.004 0.042 2681 Dihedral : 3.397 21.241 2177 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.55 % Allowed : 35.77 % Favored : 59.68 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.20 (0.19), residues: 1967 helix: 2.72 (0.14), residues: 1323 sheet: -0.87 (0.47), residues: 119 loop : -1.42 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 297 HIS 0.005 0.001 HIS C 254 PHE 0.034 0.001 PHE B 58 TYR 0.012 0.001 TYR B 112 ARG 0.004 0.000 ARG G 293 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 959) hydrogen bonds : angle 3.52645 ( 2856) SS BOND : bond 0.00220 ( 14) SS BOND : angle 0.82435 ( 28) covalent geometry : bond 0.00280 (16226) covalent geometry : angle 0.76227 (22057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11861.81 seconds wall clock time: 203 minutes 0.98 seconds (12180.98 seconds total)