Starting phenix.real_space_refine on Sat May 17 15:07:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9krg_62526/05_2025/9krg_62526.cif Found real_map, /net/cci-nas-00/data/ceres_data/9krg_62526/05_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_62526/05_2025/9krg_62526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9krg_62526/05_2025/9krg_62526.map" model { file = "/net/cci-nas-00/data/ceres_data/9krg_62526/05_2025/9krg_62526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9krg_62526/05_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-5687/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: 5.20, per 1000 atoms: 0.33 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: 3.47 Conformation dependent library (CDL) restraints added in 1.8 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: 1.55 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: 4.25 Time building geometry restraints manager: 4.11 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: 0.13 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 29.390 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.730 ------------------------------------------------------------------------------- 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 : 1.829 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: 1.1785 time to fit residues: 398.1496 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 : 1.699 ------------------------------------------------------------------------------- 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 = 67)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137494 restraints weight = 16738.226| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.99 r_work: 0.3416 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 2.001 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: 0.6914 (ttt90) cc_final: 0.6646 (ttt-90) REVERT: A 37 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6334 (tp) REVERT: A 72 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: A 75 ARG cc_start: 0.7276 (mmm-85) cc_final: 0.6739 (mmp-170) REVERT: A 81 ASP cc_start: 0.8364 (m-30) cc_final: 0.8159 (m-30) REVERT: A 218 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7985 (mt) REVERT: A 229 HIS cc_start: 0.7486 (t-90) cc_final: 0.7230 (t-90) REVERT: A 254 HIS cc_start: 0.7383 (t-170) cc_final: 0.6710 (t-90) REVERT: A 257 ASN cc_start: 0.8151 (t0) cc_final: 0.7773 (m-40) REVERT: A 281 THR cc_start: 0.8273 (m) cc_final: 0.7898 (m) REVERT: B 36 ARG cc_start: 0.6833 (ttt90) cc_final: 0.6591 (ttt-90) REVERT: B 75 ARG cc_start: 0.7608 (mmm-85) cc_final: 0.7127 (mmp-170) REVERT: B 229 HIS cc_start: 0.7211 (t-90) cc_final: 0.6936 (t-90) REVERT: B 238 GLU cc_start: 0.8271 (pm20) cc_final: 0.8063 (pm20) REVERT: B 248 LEU cc_start: 0.7450 (mp) cc_final: 0.7119 (mt) REVERT: B 257 ASN cc_start: 0.8327 (t0) cc_final: 0.7780 (m110) REVERT: B 262 ARG cc_start: 0.8335 (ttt90) cc_final: 0.7735 (ttt-90) REVERT: C 75 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.6991 (mmp-170) REVERT: C 201 ARG cc_start: 0.6649 (mmm-85) cc_final: 0.6284 (mtm180) REVERT: C 218 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7581 (mt) REVERT: C 238 GLU cc_start: 0.8481 (pm20) cc_final: 0.8104 (pt0) REVERT: D 75 ARG cc_start: 0.7392 (mmm-85) cc_final: 0.6874 (mmp-170) REVERT: D 108 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8365 (mtpt) REVERT: D 201 ARG cc_start: 0.6770 (mmm-85) cc_final: 0.6422 (ttm-80) REVERT: D 218 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7272 (mp) REVERT: D 229 HIS cc_start: 0.7778 (t-90) cc_final: 0.7197 (t70) REVERT: D 238 GLU cc_start: 0.8455 (pm20) cc_final: 0.8222 (pm20) REVERT: D 281 THR cc_start: 0.8315 (m) cc_final: 0.7939 (m) REVERT: E 36 ARG cc_start: 0.6985 (ttt90) cc_final: 0.6581 (ttt-90) REVERT: E 75 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.6935 (mmp-170) REVERT: E 81 ASP cc_start: 0.8350 (m-30) cc_final: 0.8042 (m-30) REVERT: E 201 ARG cc_start: 0.6755 (ttt-90) cc_final: 0.6486 (mpp80) REVERT: E 229 HIS cc_start: 0.7309 (t-90) cc_final: 0.6736 (t-90) REVERT: E 262 ARG cc_start: 0.8383 (ttt90) cc_final: 0.7744 (ttm-80) REVERT: F 75 ARG cc_start: 0.7478 (mmm-85) cc_final: 0.7089 (mmp-170) REVERT: F 218 ILE cc_start: 0.8157 (mm) cc_final: 0.7907 (mt) REVERT: F 229 HIS cc_start: 0.7708 (t-90) cc_final: 0.7048 (t70) REVERT: F 257 ASN cc_start: 0.8335 (t0) cc_final: 0.8110 (m-40) REVERT: F 281 THR cc_start: 0.8271 (m) cc_final: 0.7991 (m) REVERT: G 36 ARG cc_start: 0.7170 (ttt90) cc_final: 0.6776 (ttt-90) REVERT: G 75 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7246 (mmp-170) REVERT: G 120 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8066 (mp) REVERT: G 121 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8179 (mmt) REVERT: G 201 ARG cc_start: 0.6496 (mmm-85) cc_final: 0.5943 (mpp80) REVERT: G 218 ILE cc_start: 0.8157 (mm) cc_final: 0.7867 (mt) REVERT: G 229 HIS cc_start: 0.7488 (t-90) cc_final: 0.6868 (t-90) REVERT: G 262 ARG cc_start: 0.8283 (ttt90) cc_final: 0.8007 (ttt-90) outliers start: 135 outliers final: 28 residues processed: 354 average time/residue: 0.9714 time to fit residues: 387.9477 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 : 1.866 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.199027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137662 restraints weight = 16618.757| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.97 r_work: 0.3384 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16240 Z= 0.135 Angle : 0.583 8.771 22085 Z= 0.285 Chirality : 0.038 0.133 2667 Planarity : 0.004 0.039 2681 Dihedral : 3.664 15.338 2177 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 7.37 % Allowed : 33.58 % Favored : 59.04 % 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: 0.95 (0.19), residues: 1967 helix: 1.73 (0.14), residues: 1344 sheet: -1.24 (0.46), residues: 119 loop : -1.95 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 297 HIS 0.006 0.001 HIS F 254 PHE 0.015 0.001 PHE A 269 TYR 0.014 0.002 TYR G 112 ARG 0.005 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 959) hydrogen bonds : angle 3.94161 ( 2856) SS BOND : bond 0.00190 ( 14) SS BOND : angle 0.73378 ( 28) covalent geometry : bond 0.00314 (16226) covalent geometry : angle 0.58270 (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 355 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 227 time to evaluate : 1.708 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: 0.7459 (ttt90) cc_final: 0.7173 (ttt-90) REVERT: A 37 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.6771 (tp) REVERT: A 72 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: A 235 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: A 238 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: A 254 HIS cc_start: 0.8243 (t-170) cc_final: 0.7943 (t-90) REVERT: A 281 THR cc_start: 0.8493 (m) cc_final: 0.8103 (m) REVERT: B 52 LEU cc_start: 0.7128 (tp) cc_final: 0.6825 (tm) REVERT: B 75 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7433 (mmp-170) REVERT: B 238 GLU cc_start: 0.8449 (pm20) cc_final: 0.8195 (pt0) REVERT: C 75 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7681 (mmp-170) REVERT: C 218 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (mt) REVERT: D 75 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7248 (mmp-170) REVERT: D 229 HIS cc_start: 0.7866 (t-90) cc_final: 0.7557 (t70) REVERT: D 235 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: D 238 GLU cc_start: 0.8578 (pm20) cc_final: 0.8322 (pt0) REVERT: D 257 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7989 (m-40) REVERT: D 281 THR cc_start: 0.8657 (m) cc_final: 0.8279 (m) REVERT: E 36 ARG cc_start: 0.7441 (ttt90) cc_final: 0.7056 (ttt-90) REVERT: E 37 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6696 (tp) REVERT: E 75 ARG cc_start: 0.7676 (mmm-85) cc_final: 0.7340 (mmp-170) REVERT: E 81 ASP cc_start: 0.8426 (m-30) cc_final: 0.8205 (m-30) REVERT: E 201 ARG cc_start: 0.7118 (ttt-90) cc_final: 0.6861 (mpp80) REVERT: E 229 HIS cc_start: 0.7517 (t-90) cc_final: 0.7002 (t-90) REVERT: E 257 ASN cc_start: 0.8662 (t0) cc_final: 0.8338 (m-40) REVERT: E 285 PRO cc_start: 0.7455 (Cg_exo) cc_final: 0.7037 (Cg_endo) REVERT: F 51 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7859 (m) REVERT: F 75 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.7423 (mmp-170) REVERT: F 218 ILE cc_start: 0.8597 (mm) cc_final: 0.8279 (mt) REVERT: F 229 HIS cc_start: 0.7886 (t-90) cc_final: 0.7357 (t70) REVERT: F 281 THR cc_start: 0.8448 (m) cc_final: 0.8178 (m) REVERT: G 218 ILE cc_start: 0.8636 (mm) cc_final: 0.8388 (mt) REVERT: G 229 HIS cc_start: 0.7623 (t-90) cc_final: 0.7087 (t-90) REVERT: G 238 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8066 (pt0) REVERT: G 257 ASN cc_start: 0.8392 (t0) cc_final: 0.8183 (m-40) outliers start: 128 outliers final: 38 residues processed: 330 average time/residue: 0.8475 time to fit residues: 320.8163 Evaluate side-chains 257 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 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 51 SER 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 52 LEU 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 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 52 LEU Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 72 PHE 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 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 72 PHE 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: 2.9990 chunk 5 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 152 optimal weight: 0.3980 chunk 165 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN D 254 HIS E 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.199704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138967 restraints weight = 16597.442| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.94 r_work: 0.3416 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4194 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= 0.104 Angle : 0.532 9.726 22085 Z= 0.256 Chirality : 0.036 0.127 2667 Planarity : 0.004 0.041 2681 Dihedral : 3.433 15.886 2177 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.30 % Allowed : 34.62 % 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: 1.47 (0.19), residues: 1967 helix: 2.10 (0.15), residues: 1351 sheet: -1.31 (0.56), residues: 84 loop : -1.71 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 297 HIS 0.005 0.001 HIS B 254 PHE 0.013 0.001 PHE F 269 TYR 0.011 0.001 TYR G 112 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 959) hydrogen bonds : angle 3.71737 ( 2856) SS BOND : bond 0.00148 ( 14) SS BOND : angle 0.60560 ( 28) covalent geometry : bond 0.00221 (16226) covalent geometry : angle 0.53221 (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 317 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 225 time to evaluate : 1.598 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: 0.6679 (OUTLIER) cc_final: 0.6195 (tp) REVERT: A 72 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: A 235 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6708 (m-80) REVERT: A 238 GLU cc_start: 0.8407 (pm20) cc_final: 0.8105 (pt0) REVERT: A 254 HIS cc_start: 0.8168 (t-170) cc_final: 0.7865 (t-90) REVERT: A 281 THR cc_start: 0.8183 (m) cc_final: 0.7789 (m) REVERT: A 285 PRO cc_start: 0.7230 (Cg_exo) cc_final: 0.6986 (Cg_endo) REVERT: A 325 ASP cc_start: 0.7306 (m-30) cc_final: 0.6767 (t0) REVERT: B 52 LEU cc_start: 0.6568 (tp) cc_final: 0.6252 (tp) REVERT: B 75 ARG cc_start: 0.7478 (mmm-85) cc_final: 0.6961 (mmp-170) REVERT: B 235 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: B 238 GLU cc_start: 0.8334 (pm20) cc_final: 0.7975 (pt0) REVERT: C 75 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7044 (mmp-170) REVERT: C 218 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7461 (mt) REVERT: D 75 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.6918 (mmp-170) REVERT: D 229 HIS cc_start: 0.7546 (t-90) cc_final: 0.6944 (t-90) REVERT: D 235 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: D 238 GLU cc_start: 0.8377 (pm20) cc_final: 0.7942 (pt0) REVERT: D 257 ASN cc_start: 0.8317 (t0) cc_final: 0.7734 (m-40) REVERT: D 281 THR cc_start: 0.8313 (m) cc_final: 0.8055 (m) REVERT: E 36 ARG cc_start: 0.6964 (ttt90) cc_final: 0.6666 (ttt-90) REVERT: E 37 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6203 (tp) REVERT: E 52 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6148 (tp) REVERT: E 54 PHE cc_start: 0.6418 (OUTLIER) cc_final: 0.5200 (m-10) REVERT: E 75 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7177 (mmp-170) REVERT: E 81 ASP cc_start: 0.8192 (m-30) cc_final: 0.7923 (m-30) REVERT: E 201 ARG cc_start: 0.6998 (ttt-90) cc_final: 0.6687 (mpp80) REVERT: E 229 HIS cc_start: 0.7136 (t-90) cc_final: 0.6515 (t-90) REVERT: E 257 ASN cc_start: 0.8405 (t0) cc_final: 0.8002 (m-40) REVERT: F 75 ARG cc_start: 0.7432 (mmm-85) cc_final: 0.7019 (mmp-170) REVERT: F 218 ILE cc_start: 0.8218 (mm) cc_final: 0.7885 (mt) REVERT: F 229 HIS cc_start: 0.7668 (t-90) cc_final: 0.7005 (t70) REVERT: F 235 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6269 (m-80) REVERT: F 281 THR cc_start: 0.8270 (m) cc_final: 0.7987 (m) REVERT: F 285 PRO cc_start: 0.7248 (Cg_exo) cc_final: 0.7009 (Cg_endo) REVERT: G 37 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6063 (tp) REVERT: G 218 ILE cc_start: 0.8143 (mm) cc_final: 0.7858 (mt) REVERT: G 229 HIS cc_start: 0.7328 (t-90) cc_final: 0.6659 (t-90) REVERT: G 235 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: G 238 GLU cc_start: 0.8255 (pm20) cc_final: 0.7862 (pt0) REVERT: G 257 ASN cc_start: 0.8273 (t0) cc_final: 0.8061 (m-40) REVERT: G 285 PRO cc_start: 0.6897 (Cg_exo) cc_final: 0.6582 (Cg_endo) outliers start: 92 outliers final: 34 residues processed: 303 average time/residue: 0.9038 time to fit residues: 312.7093 Evaluate side-chains 264 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 235 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 38 VAL 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 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 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 39 LYS 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 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 72 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: 3.9990 chunk 158 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 27 optimal weight: 0.0010 chunk 13 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS B 324 ASN C 254 HIS C 324 ASN D 254 HIS E 254 HIS G 254 HIS G 324 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.199232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138354 restraints weight = 16818.129| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.94 r_work: 0.3419 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4468 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= 0.103 Angle : 0.529 9.346 22085 Z= 0.253 Chirality : 0.036 0.126 2667 Planarity : 0.004 0.041 2681 Dihedral : 3.329 14.958 2177 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.30 % Allowed : 35.43 % Favored : 59.27 % 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: 1.60 (0.19), residues: 1967 helix: 2.22 (0.15), residues: 1351 sheet: -1.27 (0.57), residues: 84 loop : -1.70 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 297 HIS 0.005 0.001 HIS B 254 PHE 0.019 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 0.03664 ( 959) hydrogen bonds : angle 3.61750 ( 2856) SS BOND : bond 0.00158 ( 14) SS BOND : angle 0.67195 ( 28) covalent geometry : bond 0.00222 (16226) covalent geometry : angle 0.52893 (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 319 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 227 time to evaluate : 1.628 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: 0.6656 (OUTLIER) cc_final: 0.6176 (tp) REVERT: A 72 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7584 (m-10) REVERT: A 238 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: A 254 HIS cc_start: 0.8199 (t-170) cc_final: 0.7877 (t-90) REVERT: A 281 THR cc_start: 0.8219 (m) cc_final: 0.7852 (m) REVERT: A 285 PRO cc_start: 0.7301 (Cg_exo) cc_final: 0.7028 (Cg_endo) REVERT: B 52 LEU cc_start: 0.6493 (tp) cc_final: 0.6185 (tp) REVERT: B 75 ARG cc_start: 0.7564 (mmm-85) cc_final: 0.7084 (mmp-170) REVERT: B 235 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6071 (m-80) REVERT: B 238 GLU cc_start: 0.8371 (pm20) cc_final: 0.8016 (pt0) REVERT: C 75 ARG cc_start: 0.7603 (mmm-85) cc_final: 0.7004 (mmp-170) REVERT: C 218 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7421 (mt) REVERT: C 285 PRO cc_start: 0.6860 (Cg_exo) cc_final: 0.6574 (Cg_endo) REVERT: D 75 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.6916 (mmp-170) REVERT: D 229 HIS cc_start: 0.7565 (t-90) cc_final: 0.6924 (t-90) REVERT: D 235 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: D 238 GLU cc_start: 0.8498 (pm20) cc_final: 0.8041 (pt0) REVERT: D 257 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8065 (m110) REVERT: D 285 PRO cc_start: 0.7290 (Cg_exo) cc_final: 0.6989 (Cg_endo) REVERT: E 54 PHE cc_start: 0.6217 (OUTLIER) cc_final: 0.5160 (m-10) REVERT: E 75 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7114 (mmp-170) REVERT: E 81 ASP cc_start: 0.8175 (m-30) cc_final: 0.7907 (m-30) REVERT: E 201 ARG cc_start: 0.7017 (ttt-90) cc_final: 0.6708 (mpp80) REVERT: E 229 HIS cc_start: 0.7089 (t-90) cc_final: 0.6513 (t-90) REVERT: E 257 ASN cc_start: 0.8600 (t0) cc_final: 0.8255 (m-40) REVERT: E 334 ARG cc_start: 0.6463 (tmm-80) cc_final: 0.6047 (ttm110) REVERT: F 75 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.7069 (mmp-170) REVERT: F 218 ILE cc_start: 0.8183 (mm) cc_final: 0.7856 (mt) REVERT: F 229 HIS cc_start: 0.7695 (t-90) cc_final: 0.7052 (t70) REVERT: F 235 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: F 281 THR cc_start: 0.8246 (m) cc_final: 0.7990 (m) REVERT: F 285 PRO cc_start: 0.7203 (Cg_exo) cc_final: 0.6951 (Cg_endo) REVERT: G 37 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6033 (tp) REVERT: G 218 ILE cc_start: 0.8126 (mm) cc_final: 0.7848 (mt) REVERT: G 229 HIS cc_start: 0.7353 (t-90) cc_final: 0.6678 (t-90) REVERT: G 238 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8024 (pt0) REVERT: G 257 ASN cc_start: 0.8281 (t0) cc_final: 0.8075 (m-40) REVERT: G 285 PRO cc_start: 0.7007 (Cg_exo) cc_final: 0.6648 (Cg_endo) outliers start: 92 outliers final: 50 residues processed: 305 average time/residue: 0.8706 time to fit residues: 305.2279 Evaluate side-chains 281 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 30 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 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 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 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 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 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 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 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 54 PHE Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 198 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.192028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145648 restraints weight = 16837.439| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.38 r_work: 0.3368 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16240 Z= 0.131 Angle : 0.578 10.650 22085 Z= 0.276 Chirality : 0.038 0.132 2667 Planarity : 0.004 0.043 2681 Dihedral : 3.537 15.249 2177 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 6.39 % Allowed : 33.70 % 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: 1.52 (0.19), residues: 1967 helix: 2.17 (0.14), residues: 1344 sheet: -1.33 (0.45), residues: 119 loop : -1.71 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 297 HIS 0.006 0.001 HIS D 254 PHE 0.020 0.002 PHE G 189 TYR 0.014 0.002 TYR G 112 ARG 0.003 0.000 ARG G 293 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 959) hydrogen bonds : angle 3.67747 ( 2856) SS BOND : bond 0.00212 ( 14) SS BOND : angle 0.95232 ( 28) covalent geometry : bond 0.00310 (16226) covalent geometry : angle 0.57733 (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 326 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 215 time to evaluate : 1.644 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: 0.8574 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: A 238 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8289 (pt0) REVERT: A 281 THR cc_start: 0.8450 (m) cc_final: 0.8089 (m) REVERT: A 285 PRO cc_start: 0.7682 (Cg_exo) cc_final: 0.7363 (Cg_endo) REVERT: B 52 LEU cc_start: 0.7007 (tp) cc_final: 0.6715 (tp) REVERT: B 75 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7514 (mmp-170) REVERT: B 235 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: B 238 GLU cc_start: 0.8538 (pm20) cc_final: 0.8249 (pt0) REVERT: C 51 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8360 (p) REVERT: C 75 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7481 (mmp-170) REVERT: C 122 TYR cc_start: 0.8580 (t80) cc_final: 0.8376 (t80) REVERT: C 218 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7713 (mt) REVERT: D 75 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7307 (mmp-170) REVERT: D 120 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8363 (tp) REVERT: D 214 SER cc_start: 0.8272 (t) cc_final: 0.7682 (m) REVERT: D 218 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7612 (mp) REVERT: D 229 HIS cc_start: 0.7851 (t-90) cc_final: 0.7294 (t-90) REVERT: D 235 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: D 257 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8325 (m110) REVERT: E 36 ARG cc_start: 0.7388 (ttt90) cc_final: 0.7113 (ttt-90) REVERT: E 54 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.5365 (m-10) REVERT: E 75 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7489 (mmp-170) REVERT: E 81 ASP cc_start: 0.8441 (m-30) cc_final: 0.8196 (m-30) REVERT: E 201 ARG cc_start: 0.7263 (ttt-90) cc_final: 0.6983 (mpp80) REVERT: E 229 HIS cc_start: 0.7431 (t-90) cc_final: 0.6903 (t-90) REVERT: E 257 ASN cc_start: 0.8760 (t0) cc_final: 0.8477 (m-40) REVERT: F 75 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7450 (mmp-170) REVERT: F 218 ILE cc_start: 0.8372 (mm) cc_final: 0.8025 (mt) REVERT: F 229 HIS cc_start: 0.8103 (t-90) cc_final: 0.7512 (t70) REVERT: F 235 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: F 281 THR cc_start: 0.8459 (m) cc_final: 0.8209 (m) REVERT: F 285 PRO cc_start: 0.7418 (Cg_exo) cc_final: 0.7089 (Cg_endo) REVERT: G 72 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: G 218 ILE cc_start: 0.8386 (mm) cc_final: 0.8134 (mt) REVERT: G 229 HIS cc_start: 0.7713 (t-90) cc_final: 0.7105 (t-90) REVERT: G 238 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: G 257 ASN cc_start: 0.8471 (t0) cc_final: 0.8266 (m-40) REVERT: G 285 PRO cc_start: 0.7321 (Cg_exo) cc_final: 0.6934 (Cg_endo) outliers start: 111 outliers final: 63 residues processed: 306 average time/residue: 0.8490 time to fit residues: 297.6534 Evaluate side-chains 288 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 233 ASP Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 30 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 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 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 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 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 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 218 ILE 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 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 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 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: 0.5980 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 202 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 G 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.195436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136956 restraints weight = 16845.700| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.78 r_work: 0.3423 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4918 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= 0.101 Angle : 0.523 9.084 22085 Z= 0.249 Chirality : 0.036 0.125 2667 Planarity : 0.004 0.041 2681 Dihedral : 3.324 15.368 2177 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.92 % Allowed : 36.23 % Favored : 59.85 % 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: 1.75 (0.19), residues: 1967 helix: 2.37 (0.14), residues: 1344 sheet: -1.09 (0.59), residues: 84 loop : -1.72 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 G 112 ARG 0.003 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 959) hydrogen bonds : angle 3.55380 ( 2856) SS BOND : bond 0.00142 ( 14) SS BOND : angle 0.68745 ( 28) covalent geometry : bond 0.00212 (16226) covalent geometry : angle 0.52315 (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 300 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 232 time to evaluate : 1.716 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: 0.6901 (OUTLIER) cc_final: 0.6450 (tp) REVERT: A 72 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7590 (m-10) REVERT: A 238 GLU cc_start: 0.8393 (pm20) cc_final: 0.8137 (pt0) REVERT: A 281 THR cc_start: 0.8216 (m) cc_final: 0.7903 (m) REVERT: A 285 PRO cc_start: 0.7447 (Cg_exo) cc_final: 0.7138 (Cg_endo) REVERT: B 52 LEU cc_start: 0.6641 (tp) cc_final: 0.6427 (tp) REVERT: B 75 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7213 (mmp-170) REVERT: B 235 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6165 (m-80) REVERT: B 238 GLU cc_start: 0.8449 (pm20) cc_final: 0.8026 (pt0) REVERT: C 51 SER cc_start: 0.8511 (t) cc_final: 0.8256 (p) REVERT: C 75 ARG cc_start: 0.7689 (mmm-85) cc_final: 0.7069 (mmp-170) REVERT: C 122 TYR cc_start: 0.8378 (t80) cc_final: 0.8140 (t80) REVERT: D 75 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7172 (mmp-170) REVERT: D 218 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7879 (mt) REVERT: D 229 HIS cc_start: 0.7562 (t-90) cc_final: 0.6953 (t-90) REVERT: D 235 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: D 257 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8164 (m110) REVERT: D 285 PRO cc_start: 0.7320 (Cg_exo) cc_final: 0.7099 (Cg_endo) REVERT: E 37 ILE cc_start: 0.6595 (OUTLIER) cc_final: 0.6065 (tp) REVERT: E 52 LEU cc_start: 0.7177 (tt) cc_final: 0.6960 (tt) REVERT: E 54 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.5296 (m-10) REVERT: E 75 ARG cc_start: 0.7745 (mmm-85) cc_final: 0.7286 (mmp-170) REVERT: E 81 ASP cc_start: 0.8233 (m-30) cc_final: 0.7996 (m-30) REVERT: E 201 ARG cc_start: 0.7181 (ttt-90) cc_final: 0.6863 (mpp80) REVERT: E 229 HIS cc_start: 0.7122 (t-90) cc_final: 0.6561 (t-90) REVERT: E 257 ASN cc_start: 0.8659 (t0) cc_final: 0.8333 (m-40) REVERT: E 325 ASP cc_start: 0.7541 (t0) cc_final: 0.7298 (t0) REVERT: E 334 ARG cc_start: 0.6435 (tmm-80) cc_final: 0.6023 (ttm110) REVERT: F 75 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7301 (mmp-170) REVERT: F 218 ILE cc_start: 0.8152 (mm) cc_final: 0.7802 (mt) REVERT: F 229 HIS cc_start: 0.7818 (t-90) cc_final: 0.7171 (t70) REVERT: F 235 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: F 281 THR cc_start: 0.8388 (m) cc_final: 0.8099 (m) REVERT: F 285 PRO cc_start: 0.7158 (Cg_exo) cc_final: 0.6835 (Cg_endo) REVERT: G 37 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6104 (tp) REVERT: G 218 ILE cc_start: 0.8183 (mm) cc_final: 0.7898 (mt) REVERT: G 229 HIS cc_start: 0.7419 (t-90) cc_final: 0.6757 (t-90) REVERT: G 235 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: G 238 GLU cc_start: 0.8500 (pm20) cc_final: 0.8061 (pt0) REVERT: G 257 ASN cc_start: 0.8333 (t0) cc_final: 0.8128 (m-40) REVERT: G 285 PRO cc_start: 0.7059 (Cg_exo) cc_final: 0.6677 (Cg_endo) outliers start: 68 outliers final: 44 residues processed: 291 average time/residue: 0.8796 time to fit residues: 292.7945 Evaluate side-chains 276 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain B residue 30 LEU 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 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 235 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 121 MET 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 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 51 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 72 PHE 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 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: 0.9980 chunk 115 optimal weight: 7.9990 chunk 3 optimal weight: 0.0980 chunk 111 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.194669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149093 restraints weight = 16787.305| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.32 r_work: 0.3410 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16240 Z= 0.103 Angle : 0.532 9.554 22085 Z= 0.253 Chirality : 0.036 0.126 2667 Planarity : 0.004 0.042 2681 Dihedral : 3.299 14.597 2177 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.44 % Allowed : 35.60 % 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: 1.87 (0.19), residues: 1967 helix: 2.46 (0.14), residues: 1344 sheet: -1.05 (0.59), residues: 84 loop : -1.66 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 B 293 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 959) hydrogen bonds : angle 3.50113 ( 2856) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.73612 ( 28) covalent geometry : bond 0.00225 (16226) covalent geometry : angle 0.53183 (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 303 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 226 time to evaluate : 1.794 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: 0.7062 (OUTLIER) cc_final: 0.6588 (tp) REVERT: A 72 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: A 238 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: A 281 THR cc_start: 0.8409 (m) cc_final: 0.8093 (m) REVERT: A 285 PRO cc_start: 0.7652 (Cg_exo) cc_final: 0.7335 (Cg_endo) REVERT: B 52 LEU cc_start: 0.6600 (tp) cc_final: 0.6399 (tp) REVERT: B 75 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7469 (mmp-170) REVERT: B 235 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: B 238 GLU cc_start: 0.8451 (pm20) cc_final: 0.8162 (pt0) REVERT: C 51 SER cc_start: 0.8707 (t) cc_final: 0.8444 (p) REVERT: C 75 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.7304 (mmp-170) REVERT: C 122 TYR cc_start: 0.8566 (t80) cc_final: 0.8321 (t80) REVERT: D 75 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7559 (mmp-170) REVERT: D 120 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8258 (tp) REVERT: D 147 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4743 (mp) REVERT: D 218 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8068 (mt) REVERT: D 229 HIS cc_start: 0.7782 (t-90) cc_final: 0.7172 (t-90) REVERT: D 235 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: D 257 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8071 (m110) REVERT: D 285 PRO cc_start: 0.7416 (Cg_exo) cc_final: 0.7156 (Cg_endo) REVERT: E 54 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.5470 (m-10) REVERT: E 75 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7474 (mmp-170) REVERT: E 81 ASP cc_start: 0.8337 (m-30) cc_final: 0.8125 (m-30) REVERT: E 201 ARG cc_start: 0.7343 (ttt-90) cc_final: 0.7040 (mpp80) REVERT: E 229 HIS cc_start: 0.7377 (t-90) cc_final: 0.6878 (t-90) REVERT: E 257 ASN cc_start: 0.8754 (t0) cc_final: 0.8447 (m-40) REVERT: E 325 ASP cc_start: 0.7750 (t0) cc_final: 0.7496 (t0) REVERT: F 75 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7616 (mmp-170) REVERT: F 218 ILE cc_start: 0.8357 (mm) cc_final: 0.8017 (mt) REVERT: F 229 HIS cc_start: 0.8049 (t-90) cc_final: 0.7466 (t70) REVERT: F 235 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6433 (m-80) REVERT: F 281 THR cc_start: 0.8476 (m) cc_final: 0.8219 (m) REVERT: G 37 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6331 (tp) REVERT: G 218 ILE cc_start: 0.8391 (mm) cc_final: 0.8121 (mt) REVERT: G 229 HIS cc_start: 0.7645 (t-90) cc_final: 0.7040 (t-90) REVERT: G 235 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: G 238 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: G 285 PRO cc_start: 0.7390 (Cg_exo) cc_final: 0.6990 (Cg_endo) REVERT: G 290 ASN cc_start: 0.7642 (t0) cc_final: 0.7407 (t0) outliers start: 77 outliers final: 50 residues processed: 291 average time/residue: 0.8804 time to fit residues: 294.6652 Evaluate side-chains 286 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 238 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 30 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 238 GLU Chi-restraints excluded: chain C residue 291 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 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 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 263 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 282 ILE 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 F residue 325 ASP 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: 0.7980 chunk 72 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 32 optimal weight: 0.0000 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.195268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148968 restraints weight = 16920.659| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.22 r_work: 0.3429 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5163 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 : 0.524 8.961 22085 Z= 0.248 Chirality : 0.036 0.125 2667 Planarity : 0.004 0.044 2681 Dihedral : 3.268 15.698 2177 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.26 % Allowed : 36.12 % 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: 2.02 (0.19), residues: 1967 helix: 2.64 (0.14), residues: 1316 sheet: -1.03 (0.59), residues: 84 loop : -1.56 (0.22), residues: 567 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 0.017 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 0.03465 ( 959) hydrogen bonds : angle 3.46308 ( 2856) SS BOND : bond 0.00168 ( 14) SS BOND : angle 0.69955 ( 28) covalent geometry : bond 0.00216 (16226) covalent geometry : angle 0.52360 (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 301 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 227 time to evaluate : 1.652 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: 0.7087 (OUTLIER) cc_final: 0.6615 (tp) REVERT: A 72 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: A 238 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: A 281 THR cc_start: 0.8382 (m) cc_final: 0.8076 (m) REVERT: A 285 PRO cc_start: 0.7660 (Cg_exo) cc_final: 0.7330 (Cg_endo) REVERT: B 75 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7556 (mmp-170) REVERT: B 235 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6445 (m-80) REVERT: B 238 GLU cc_start: 0.8422 (pm20) cc_final: 0.8139 (pt0) REVERT: C 51 SER cc_start: 0.8698 (t) cc_final: 0.8445 (p) REVERT: C 75 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7188 (mmp-170) REVERT: C 122 TYR cc_start: 0.8575 (t80) cc_final: 0.8341 (t80) REVERT: C 218 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7708 (mt) REVERT: D 75 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7520 (mmp-170) REVERT: D 120 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8243 (tp) REVERT: D 147 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4791 (mp) REVERT: D 218 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8084 (mt) REVERT: D 229 HIS cc_start: 0.7800 (t-90) cc_final: 0.7188 (t-90) REVERT: D 235 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: D 257 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8061 (m110) REVERT: D 285 PRO cc_start: 0.7341 (Cg_exo) cc_final: 0.7043 (Cg_endo) REVERT: E 54 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5497 (m-10) REVERT: E 75 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7584 (mmp-170) REVERT: E 81 ASP cc_start: 0.8319 (m-30) cc_final: 0.8101 (m-30) REVERT: E 201 ARG cc_start: 0.7386 (ttt-90) cc_final: 0.6927 (mpp80) REVERT: E 229 HIS cc_start: 0.7342 (t-90) cc_final: 0.6831 (t-90) REVERT: E 257 ASN cc_start: 0.8743 (t0) cc_final: 0.8471 (m-40) REVERT: E 318 MET cc_start: 0.4371 (tpt) cc_final: 0.3867 (mmt) REVERT: E 325 ASP cc_start: 0.7753 (t0) cc_final: 0.7499 (t0) REVERT: F 75 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7550 (mmp-170) REVERT: F 218 ILE cc_start: 0.8355 (mm) cc_final: 0.8005 (mt) REVERT: F 229 HIS cc_start: 0.8037 (t-90) cc_final: 0.7446 (t70) REVERT: F 235 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: F 281 THR cc_start: 0.8465 (m) cc_final: 0.8203 (m) REVERT: F 323 ILE cc_start: 0.7702 (mm) cc_final: 0.7245 (pp) REVERT: G 37 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6293 (tp) REVERT: G 218 ILE cc_start: 0.8398 (mm) cc_final: 0.8118 (mt) REVERT: G 229 HIS cc_start: 0.7620 (t-90) cc_final: 0.7009 (t-90) REVERT: G 235 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: G 238 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: G 285 PRO cc_start: 0.7510 (Cg_exo) cc_final: 0.7089 (Cg_endo) REVERT: G 290 ASN cc_start: 0.7648 (t0) cc_final: 0.7376 (t0) outliers start: 74 outliers final: 50 residues processed: 289 average time/residue: 0.8775 time to fit residues: 289.2866 Evaluate side-chains 288 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 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 218 ILE 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 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 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 263 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 282 ILE 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 125 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.193977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148601 restraints weight = 17037.503| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.36 r_work: 0.3399 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16240 Z= 0.106 Angle : 0.541 9.816 22085 Z= 0.255 Chirality : 0.036 0.127 2667 Planarity : 0.004 0.043 2681 Dihedral : 3.301 14.953 2177 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.09 % Allowed : 36.35 % 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: 2.05 (0.19), residues: 1967 helix: 2.66 (0.14), residues: 1316 sheet: -1.04 (0.59), residues: 84 loop : -1.56 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 297 HIS 0.007 0.001 HIS G 254 PHE 0.019 0.001 PHE G 189 TYR 0.013 0.001 TYR G 112 ARG 0.002 0.000 ARG G 293 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 959) hydrogen bonds : angle 3.47352 ( 2856) SS BOND : bond 0.00180 ( 14) SS BOND : angle 0.78253 ( 28) covalent geometry : bond 0.00236 (16226) covalent geometry : angle 0.54062 (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 296 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 225 time to evaluate : 1.616 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: 0.7044 (OUTLIER) cc_final: 0.6556 (tp) REVERT: A 72 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: A 238 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: A 252 GLU cc_start: 0.7951 (tt0) cc_final: 0.7494 (tt0) REVERT: A 281 THR cc_start: 0.8403 (m) cc_final: 0.8097 (m) REVERT: A 285 PRO cc_start: 0.7633 (Cg_exo) cc_final: 0.7300 (Cg_endo) REVERT: B 75 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7576 (mmp-170) REVERT: B 235 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: C 51 SER cc_start: 0.8696 (t) cc_final: 0.8460 (p) REVERT: C 75 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7379 (mmp-170) REVERT: C 122 TYR cc_start: 0.8570 (t80) cc_final: 0.8368 (t80) REVERT: C 218 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7697 (mt) REVERT: D 75 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7573 (mmp-170) REVERT: D 120 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8255 (tp) REVERT: D 147 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4773 (mp) REVERT: D 218 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8079 (mt) REVERT: D 229 HIS cc_start: 0.7853 (t-90) cc_final: 0.7253 (t-90) REVERT: D 235 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: D 257 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8087 (m110) REVERT: D 285 PRO cc_start: 0.7553 (Cg_exo) cc_final: 0.7264 (Cg_endo) REVERT: E 54 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.5615 (m-10) REVERT: E 75 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7653 (mmp-170) REVERT: E 81 ASP cc_start: 0.8368 (m-30) cc_final: 0.8144 (m-30) REVERT: E 201 ARG cc_start: 0.7386 (ttt-90) cc_final: 0.6937 (mpp80) REVERT: E 229 HIS cc_start: 0.7371 (t-90) cc_final: 0.6849 (t-90) REVERT: E 257 ASN cc_start: 0.8765 (t0) cc_final: 0.8483 (m-40) REVERT: E 318 MET cc_start: 0.4389 (tpt) cc_final: 0.3903 (mmt) REVERT: E 325 ASP cc_start: 0.7801 (t0) cc_final: 0.7533 (t0) REVERT: F 75 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7561 (mmp-170) REVERT: F 218 ILE cc_start: 0.8325 (mm) cc_final: 0.7972 (mt) REVERT: F 235 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: F 281 THR cc_start: 0.8485 (m) cc_final: 0.8223 (m) REVERT: F 323 ILE cc_start: 0.7497 (mm) cc_final: 0.7076 (pp) REVERT: G 37 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6385 (tp) REVERT: G 218 ILE cc_start: 0.8275 (mm) cc_final: 0.7984 (mt) REVERT: G 229 HIS cc_start: 0.7650 (t-90) cc_final: 0.7031 (t-90) REVERT: G 235 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: G 238 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8217 (pt0) REVERT: G 285 PRO cc_start: 0.7535 (Cg_exo) cc_final: 0.7105 (Cg_endo) REVERT: G 290 ASN cc_start: 0.7619 (t0) cc_final: 0.7352 (t0) outliers start: 71 outliers final: 51 residues processed: 284 average time/residue: 0.9021 time to fit residues: 291.2738 Evaluate side-chains 285 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 219 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 50 MET 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 233 ASP 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 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 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 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 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 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 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 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 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: 2.9990 chunk 97 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.191179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144458 restraints weight = 16890.705| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.39 r_work: 0.3346 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5374 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= 0.126 Angle : 0.568 9.606 22085 Z= 0.270 Chirality : 0.038 0.133 2667 Planarity : 0.004 0.044 2681 Dihedral : 3.499 16.258 2177 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.55 % Allowed : 36.06 % Favored : 59.39 % 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: 2.00 (0.19), residues: 1967 helix: 2.59 (0.14), residues: 1316 sheet: -1.21 (0.47), residues: 126 loop : -1.43 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 297 HIS 0.008 0.001 HIS C 254 PHE 0.017 0.002 PHE D 189 TYR 0.015 0.002 TYR G 112 ARG 0.004 0.000 ARG G 293 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 959) hydrogen bonds : angle 3.59113 ( 2856) SS BOND : bond 0.00236 ( 14) SS BOND : angle 0.97647 ( 28) covalent geometry : bond 0.00297 (16226) covalent geometry : angle 0.56751 (22057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11444.96 seconds wall clock time: 197 minutes 12.95 seconds (11832.95 seconds total)