Starting phenix.real_space_refine on Sat Sep 12 14:44:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22qw_68611/09_2026/22qw_68611.cif Found real_map, /net/cci-nas-00/data/ceres_data/22qw_68611/09_2026/22qw_68611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22qw_68611/09_2026/22qw_68611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22qw_68611/09_2026/22qw_68611.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22qw_68611/09_2026/22qw_68611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22qw_68611/09_2026/22qw_68611.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.081 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 80 5.16 5 C 10516 2.51 5 N 2560 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16091 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3206 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3061 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 356} Chain breaks: 1 Chain: "B" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3206 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3061 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 356} Chain breaks: 1 Chain: "C" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3206 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {'CHT': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'CHT': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'CHT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.21, per 1000 atoms: 0.26 Number of scatterers: 16091 At special positions: 0 Unit cell: (101.28, 94.95, 142.425, 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 80 16.00 O 2935 8.00 N 2560 7.00 C 10516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 156 " - pdb=" SG CYS C 170 " 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG A 602 " - " ASN A 224 " " NAG A 603 " - " ASN A 96 " " NAG B 602 " - " ASN B 96 " " NAG C 602 " - " ASN C 96 " " NAG C 603 " - " ASN C 224 " " NAG F 1 " - " ASN A 52 " " NAG G 1 " - " ASN D 125 " " NAG H 1 " - " ASN D 198 " " NAG I 1 " - " ASN B 224 " " NAG J 1 " - " ASN B 52 " " NAG K 1 " - " ASN E 125 " " NAG L 1 " - " ASN E 198 " " NAG M 1 " - " ASN C 52 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 909.5 milliseconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3718 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 43.2% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 245 through 261 Processing helix chain 'A' and resid 273 through 295 removed outlier: 3.746A pdb=" N GLN A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 332 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 340 through 355 Processing helix chain 'A' and resid 496 through 547 Processing helix chain 'D' and resid 39 through 48 removed outlier: 3.920A pdb=" N ASP D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 266 through 273 Processing helix chain 'D' and resid 274 through 289 removed outlier: 3.521A pdb=" N PHE D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 322 Processing helix chain 'D' and resid 331 through 359 Processing helix chain 'D' and resid 511 through 556 removed outlier: 3.822A pdb=" N ASP D 555 " --> pdb=" O GLN D 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.750A pdb=" N THR B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 245 through 261 Processing helix chain 'B' and resid 273 through 294 Processing helix chain 'B' and resid 303 through 332 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 340 through 355 Processing helix chain 'B' and resid 496 through 548 Processing helix chain 'E' and resid 38 through 48 removed outlier: 3.504A pdb=" N ASN E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 132 through 134 No H-bonds generated for 'chain 'E' and resid 132 through 134' Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 164 through 167 Processing helix chain 'E' and resid 267 through 289 removed outlier: 4.441A pdb=" N ILE E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) Proline residue: E 276 - end of helix Processing helix chain 'E' and resid 301 through 322 removed outlier: 3.672A pdb=" N MET E 318 " --> pdb=" O ILE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 360 removed outlier: 3.525A pdb=" N ARG E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 556 removed outlier: 3.569A pdb=" N ASP E 555 " --> pdb=" O GLN E 551 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS E 556 " --> pdb=" O TYR E 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 35 Processing helix chain 'C' and resid 85 through 88 removed outlier: 4.090A pdb=" N TYR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.904A pdb=" N GLU C 95 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 245 through 261 Processing helix chain 'C' and resid 273 through 294 Processing helix chain 'C' and resid 303 through 332 Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 340 through 355 Processing helix chain 'C' and resid 496 through 547 Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 103 removed outlier: 5.016A pdb=" N ASN A 130 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A 147 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TRP A 77 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE A 79 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP A 58 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ARG A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER A 56 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N PHE A 83 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N SER A 54 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE A 51 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE A 187 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 53 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 removed outlier: 5.209A pdb=" N SER A 176 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 226 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 208 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG A 235 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE A 206 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 126 through 130 removed outlier: 5.134A pdb=" N ASN D 157 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D 176 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN D 98 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU D 91 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS D 100 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE D 89 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN D 102 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG D 110 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS D 79 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 139 through 141 removed outlier: 5.025A pdb=" N SER D 205 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL D 254 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER D 236 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN D 263 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL D 234 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 103 removed outlier: 5.311A pdb=" N ASN B 130 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B 147 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 141 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TRP B 77 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE B 79 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASP B 58 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ARG B 81 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B 56 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N PHE B 83 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N SER B 54 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE B 51 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B 187 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 53 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.588A pdb=" N CYS B 170 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER B 176 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 226 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 208 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG B 235 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE B 206 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 127 through 130 removed outlier: 5.115A pdb=" N ASN E 157 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU E 176 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN E 98 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU E 91 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS E 100 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE E 89 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN E 102 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG E 110 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS E 79 " --> pdb=" O ARG E 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 139 through 141 removed outlier: 4.966A pdb=" N SER E 205 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL E 254 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER E 236 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN E 263 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL E 234 " --> pdb=" O GLN E 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 103 removed outlier: 5.261A pdb=" N ASN C 130 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU C 147 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE C 62 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TRP C 77 " --> pdb=" O TYR C 60 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR C 60 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE C 79 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP C 58 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ARG C 81 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N SER C 56 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N PHE C 83 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 9.550A pdb=" N SER C 54 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE C 51 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N PHE C 187 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL C 53 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.962A pdb=" N SER C 176 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 226 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 208 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG C 235 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE C 206 " --> pdb=" O ARG C 235 " (cutoff:3.500A) 869 hydrogen bonds defined for protein. 2538 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: 2.95 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4850 1.34 - 1.46: 3912 1.46 - 1.58: 7598 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 16492 Sorted by residual: bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.63e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.76e+00 ... (remaining 16487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 22144 2.18 - 4.36: 268 4.36 - 6.53: 36 6.53 - 8.71: 9 8.71 - 10.89: 2 Bond angle restraints: 22459 Sorted by residual: angle pdb=" N VAL D 145 " pdb=" CA VAL D 145 " pdb=" C VAL D 145 " ideal model delta sigma weight residual 112.96 109.49 3.47 1.00e+00 1.00e+00 1.20e+01 angle pdb=" CA PRO D 291 " pdb=" N PRO D 291 " pdb=" CD PRO D 291 " ideal model delta sigma weight residual 112.00 107.32 4.68 1.40e+00 5.10e-01 1.12e+01 angle pdb=" CA LEU D 350 " pdb=" CB LEU D 350 " pdb=" CG LEU D 350 " ideal model delta sigma weight residual 116.30 127.19 -10.89 3.50e+00 8.16e-02 9.68e+00 angle pdb=" CA LEU D 101 " pdb=" CB LEU D 101 " pdb=" CG LEU D 101 " ideal model delta sigma weight residual 116.30 125.96 -9.66 3.50e+00 8.16e-02 7.62e+00 angle pdb=" CB PRO D 193 " pdb=" CG PRO D 193 " pdb=" CD PRO D 193 " ideal model delta sigma weight residual 105.40 99.24 6.16 2.30e+00 1.89e-01 7.18e+00 ... (remaining 22454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 9136 21.66 - 43.33: 747 43.33 - 64.99: 141 64.99 - 86.66: 32 86.66 - 108.32: 11 Dihedral angle restraints: 10067 sinusoidal: 4338 harmonic: 5729 Sorted by residual: dihedral pdb=" CB CYS B 156 " pdb=" SG CYS B 156 " pdb=" SG CYS B 170 " pdb=" CB CYS B 170 " ideal model delta sinusoidal sigma weight residual -86.00 -8.96 -77.04 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS D 185 " pdb=" SG CYS D 185 " pdb=" SG CYS D 199 " pdb=" CB CYS D 199 " ideal model delta sinusoidal sigma weight residual 93.00 35.42 57.58 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CB CYS C 156 " pdb=" SG CYS C 156 " pdb=" SG CYS C 170 " pdb=" CB CYS C 170 " ideal model delta sinusoidal sigma weight residual 93.00 50.17 42.83 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 10064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2549 0.101 - 0.202: 98 0.202 - 0.303: 4 0.303 - 0.404: 1 0.404 - 0.505: 1 Chirality restraints: 2653 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN E 125 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 224 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2650 not shown) Planarity restraints: 2731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 247 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO C 248 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 248 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 248 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 290 " 0.048 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO D 291 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 291 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 291 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 192 " 0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO D 193 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 193 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 193 " 0.033 5.00e-02 4.00e+02 ... (remaining 2728 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2363 2.76 - 3.29: 15164 3.29 - 3.83: 28321 3.83 - 4.36: 33288 4.36 - 4.90: 57578 Nonbonded interactions: 136714 Sorted by model distance: nonbonded pdb=" OG SER E 211 " pdb=" OE2 GLU E 251 " model vdw 2.224 3.040 nonbonded pdb=" OG SER E 77 " pdb=" O LYS E 210 " model vdw 2.226 3.040 nonbonded pdb=" O LEU C 245 " pdb=" OG1 THR C 249 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU E 231 " pdb=" OH TYR E 269 " model vdw 2.233 3.040 nonbonded pdb=" O ILE C 246 " pdb=" OG SER C 250 " model vdw 2.266 3.040 ... (remaining 136709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 23 through 602) selection = chain 'B' selection = (chain 'C' and resid 23 through 602) } ncs_group { reference = (chain 'D' and resid 35 through 557) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.330 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.003 0.072 16520 Z= 0.153 Angle : 0.623 11.960 22538 Z= 0.295 Chirality : 0.045 0.505 2653 Planarity : 0.005 0.072 2718 Dihedral : 16.367 108.321 6334 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.68 % Allowed : 21.89 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 1904 helix: 2.39 (0.18), residues: 783 sheet: 0.32 (0.24), residues: 446 loop : -0.71 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 63 TYR 0.021 0.001 TYR D 155 PHE 0.015 0.001 PHE A 301 TRP 0.026 0.001 TRP A 539 HIS 0.002 0.001 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (16492) covalent geometry : angle 0.59618 / 0.29 (22459) SS BOND : bond 0.00095 / 0.05 ( 5) SS BOND : angle 1.60754 / 0.76 ( 10) hydrogen bonds : bond 0.14647 / 9.80 ( 869) hydrogen bonds : angle 6.18579 / 4.16 ( 2538) link_BETA1-4 : bond 0.00787 / 0.50 ( 10) link_BETA1-4 : angle 2.16087 / 1.50 ( 30) link_NAG-ASN : bond 0.00586 / 0.38 ( 13) link_NAG-ASN : angle 3.94610 / 3.07 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.3599 (ptp) cc_final: 0.2643 (tpt) REVERT: B 239 LEU cc_start: 0.8465 (tm) cc_final: 0.8252 (tp) outliers start: 12 outliers final: 7 residues processed: 209 average time/residue: 0.5129 time to fit residues: 121.7786 Evaluate side-chains 197 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 134 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN A 75 ASN A 330 GLN D 188 ASN D 197 GLN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 214 GLN E 88 GLN E 97 GLN E 143 ASN C 75 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127997 restraints weight = 17402.893| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.93 r_work: 0.3291 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16520 Z= 0.113 Angle : 0.584 10.249 22538 Z= 0.282 Chirality : 0.044 0.363 2653 Planarity : 0.004 0.057 2718 Dihedral : 8.302 64.597 2601 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.55 % Allowed : 17.98 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.19), residues: 1904 helix: 2.46 (0.18), residues: 804 sheet: 0.50 (0.25), residues: 413 loop : -0.74 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 186 TYR 0.014 0.001 TYR C 71 PHE 0.019 0.001 PHE E 288 TRP 0.020 0.001 TRP A 539 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (16492) covalent geometry : angle 0.56043 / 0.28 (22459) SS BOND : bond 0.00343 / 0.17 ( 5) SS BOND : angle 1.45651 / 0.67 ( 10) hydrogen bonds : bond 0.04294 / 2.87 ( 869) hydrogen bonds : angle 4.78812 / 3.20 ( 2538) link_BETA1-4 : bond 0.00556 / 0.31 ( 10) link_BETA1-4 : angle 1.85200 / 1.42 ( 30) link_NAG-ASN : bond 0.00541 / 0.40 ( 13) link_NAG-ASN : angle 3.59808 / 2.78 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.601 Fit side-chains REVERT: A 214 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: A 226 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8819 (t) REVERT: A 271 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6623 (pt0) REVERT: A 272 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6256 (tm-30) REVERT: A 332 ARG cc_start: 0.6954 (mtp85) cc_final: 0.6523 (ttm110) REVERT: A 339 MET cc_start: 0.4038 (ptp) cc_final: 0.2573 (tpt) REVERT: B 69 GLN cc_start: 0.7961 (mt0) cc_final: 0.7581 (mt0) REVERT: E 88 GLN cc_start: 0.8717 (tt0) cc_final: 0.8108 (pt0) REVERT: C 57 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8814 (ttm) REVERT: C 526 ILE cc_start: 0.8580 (mt) cc_final: 0.8363 (mm) outliers start: 45 outliers final: 19 residues processed: 229 average time/residue: 0.4954 time to fit residues: 128.6582 Evaluate side-chains 212 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 24 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN D 97 GLN D 133 HIS D 188 ASN D 197 GLN D 272 ASN D 358 GLN B 214 GLN E 97 GLN E 143 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.159042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120010 restraints weight = 17730.768| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.85 r_work: 0.3201 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16520 Z= 0.222 Angle : 0.672 12.602 22538 Z= 0.322 Chirality : 0.047 0.393 2653 Planarity : 0.005 0.058 2718 Dihedral : 7.475 59.415 2595 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.08 % Allowed : 17.87 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 1904 helix: 2.22 (0.18), residues: 804 sheet: 0.35 (0.25), residues: 422 loop : -0.73 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 186 TYR 0.020 0.002 TYR E 142 PHE 0.021 0.002 PHE A 261 TRP 0.019 0.002 TRP A 539 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (16492) covalent geometry : angle 0.64351 / 0.32 (22459) SS BOND : bond 0.00561 / 0.30 ( 5) SS BOND : angle 2.12212 / 0.97 ( 10) hydrogen bonds : bond 0.04538 / 3.04 ( 869) hydrogen bonds : angle 4.72531 / 3.15 ( 2538) link_BETA1-4 : bond 0.00595 / 0.36 ( 10) link_BETA1-4 : angle 2.00391 / 1.46 ( 30) link_NAG-ASN : bond 0.00513 / 0.33 ( 13) link_NAG-ASN : angle 4.31251 / 3.21 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 202 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: A 129 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 226 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9030 (t) REVERT: A 332 ARG cc_start: 0.7267 (mtp85) cc_final: 0.6934 (ttm110) REVERT: A 339 MET cc_start: 0.4253 (ptp) cc_final: 0.2795 (tpt) REVERT: D 76 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7410 (mmtm) REVERT: D 245 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8054 (tmtm) REVERT: E 88 GLN cc_start: 0.8607 (tt0) cc_final: 0.8068 (pt0) REVERT: E 159 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: E 268 TYR cc_start: 0.8105 (t80) cc_final: 0.7888 (t80) REVERT: C 172 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8099 (mtp) REVERT: C 221 CYS cc_start: 0.7294 (t) cc_final: 0.6883 (m) REVERT: C 284 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6609 (mtt) REVERT: C 288 MET cc_start: 0.6589 (ttt) cc_final: 0.6228 (ttp) outliers start: 72 outliers final: 27 residues processed: 251 average time/residue: 0.5092 time to fit residues: 144.2364 Evaluate side-chains 219 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 146 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN D 97 GLN D 188 ASN D 208 ASN D 272 ASN D 358 GLN B 214 GLN E 97 GLN E 224 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118407 restraints weight = 17502.827| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.95 r_work: 0.3176 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16520 Z= 0.222 Angle : 0.663 12.540 22538 Z= 0.318 Chirality : 0.046 0.395 2653 Planarity : 0.004 0.056 2718 Dihedral : 7.003 59.923 2595 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.86 % Allowed : 18.32 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1904 helix: 2.09 (0.17), residues: 804 sheet: 0.34 (0.25), residues: 412 loop : -0.76 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 186 TYR 0.015 0.002 TYR E 142 PHE 0.021 0.002 PHE A 261 TRP 0.018 0.002 TRP A 539 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (16492) covalent geometry : angle 0.63184 / 0.31 (22459) SS BOND : bond 0.00548 / 0.29 ( 5) SS BOND : angle 2.14492 / 0.98 ( 10) hydrogen bonds : bond 0.04454 / 2.98 ( 869) hydrogen bonds : angle 4.70645 / 3.14 ( 2538) link_BETA1-4 : bond 0.00588 / 0.38 ( 10) link_BETA1-4 : angle 2.01134 / 1.45 ( 30) link_NAG-ASN : bond 0.00512 / 0.34 ( 13) link_NAG-ASN : angle 4.44785 / 3.31 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 226 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.9005 (t) REVERT: A 272 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: A 332 ARG cc_start: 0.7282 (mtp85) cc_final: 0.7028 (ttm110) REVERT: A 337 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5699 (pt0) REVERT: A 339 MET cc_start: 0.4477 (ptp) cc_final: 0.2950 (tpt) REVERT: D 46 MET cc_start: 0.8037 (ttt) cc_final: 0.7811 (ttp) REVERT: D 76 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7476 (mmtm) REVERT: D 245 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8116 (tmtm) REVERT: B 288 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7023 (ttt) REVERT: E 159 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: E 245 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7759 (tttm) REVERT: E 268 TYR cc_start: 0.8103 (t80) cc_final: 0.7890 (t80) REVERT: C 54 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8642 (m) REVERT: C 172 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8102 (mtp) REVERT: C 221 CYS cc_start: 0.7397 (t) cc_final: 0.7017 (m) REVERT: C 246 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7329 (mm) REVERT: C 284 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7099 (mtp) REVERT: C 288 MET cc_start: 0.6638 (ttt) cc_final: 0.6296 (ttp) outliers start: 68 outliers final: 32 residues processed: 234 average time/residue: 0.4957 time to fit residues: 131.2434 Evaluate side-chains 220 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN D 97 GLN D 272 ASN D 358 GLN B 214 GLN E 143 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122237 restraints weight = 17404.466| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.90 r_work: 0.3202 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16520 Z= 0.127 Angle : 0.574 11.104 22538 Z= 0.277 Chirality : 0.043 0.375 2653 Planarity : 0.004 0.052 2718 Dihedral : 6.477 58.780 2595 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.35 % Allowed : 19.46 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 1904 helix: 2.33 (0.18), residues: 804 sheet: 0.36 (0.25), residues: 419 loop : -0.69 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 186 TYR 0.011 0.001 TYR E 268 PHE 0.011 0.001 PHE A 517 TRP 0.018 0.001 TRP A 539 HIS 0.002 0.000 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (16492) covalent geometry : angle 0.54241 / 0.27 (22459) SS BOND : bond 0.00329 / 0.17 ( 5) SS BOND : angle 1.76499 / 0.82 ( 10) hydrogen bonds : bond 0.03999 / 2.68 ( 869) hydrogen bonds : angle 4.53250 / 3.03 ( 2538) link_BETA1-4 : bond 0.00619 / 0.39 ( 10) link_BETA1-4 : angle 1.80545 / 1.29 ( 30) link_NAG-ASN : bond 0.00562 / 0.38 ( 13) link_NAG-ASN : angle 4.23633 / 3.14 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: A 226 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9015 (t) REVERT: A 272 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: A 332 ARG cc_start: 0.7205 (mtp85) cc_final: 0.6982 (ttm110) REVERT: A 337 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5709 (pt0) REVERT: A 339 MET cc_start: 0.4559 (ptp) cc_final: 0.2771 (tpt) REVERT: A 512 VAL cc_start: 0.6927 (t) cc_final: 0.6544 (p) REVERT: D 46 MET cc_start: 0.8034 (ttt) cc_final: 0.7833 (ttp) REVERT: D 245 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8099 (tmtm) REVERT: E 47 LYS cc_start: 0.7384 (ptpp) cc_final: 0.6643 (mtmt) REVERT: E 159 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: E 245 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7740 (tttm) REVERT: E 268 TYR cc_start: 0.8116 (t80) cc_final: 0.7869 (t80) REVERT: C 172 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8102 (mtp) REVERT: C 192 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8707 (ptpp) REVERT: C 221 CYS cc_start: 0.7461 (t) cc_final: 0.6911 (m) outliers start: 59 outliers final: 28 residues processed: 233 average time/residue: 0.5173 time to fit residues: 136.4399 Evaluate side-chains 219 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 122 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN D 97 GLN D 272 ASN D 358 GLN E 143 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.156945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118128 restraints weight = 17686.819| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.86 r_work: 0.3169 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16520 Z= 0.178 Angle : 0.610 11.907 22538 Z= 0.293 Chirality : 0.045 0.375 2653 Planarity : 0.004 0.053 2718 Dihedral : 6.327 58.739 2593 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.69 % Allowed : 19.80 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 1904 helix: 2.27 (0.18), residues: 804 sheet: 0.42 (0.25), residues: 409 loop : -0.72 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 186 TYR 0.013 0.001 TYR E 268 PHE 0.017 0.001 PHE A 261 TRP 0.016 0.001 TRP A 539 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (16492) covalent geometry : angle 0.57909 / 0.29 (22459) SS BOND : bond 0.00447 / 0.24 ( 5) SS BOND : angle 1.92985 / 0.88 ( 10) hydrogen bonds : bond 0.04143 / 2.78 ( 869) hydrogen bonds : angle 4.54502 / 3.03 ( 2538) link_BETA1-4 : bond 0.00601 / 0.38 ( 10) link_BETA1-4 : angle 1.83749 / 1.30 ( 30) link_NAG-ASN : bond 0.00507 / 0.33 ( 13) link_NAG-ASN : angle 4.28570 / 3.19 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: A 226 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9003 (t) REVERT: A 272 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: A 332 ARG cc_start: 0.7250 (mtp85) cc_final: 0.7040 (ttm110) REVERT: A 337 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5732 (pt0) REVERT: A 339 MET cc_start: 0.4682 (ptp) cc_final: 0.2867 (tpt) REVERT: A 512 VAL cc_start: 0.7009 (t) cc_final: 0.6624 (p) REVERT: D 46 MET cc_start: 0.8064 (ttt) cc_final: 0.7844 (ttp) REVERT: D 245 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8063 (tmtm) REVERT: E 47 LYS cc_start: 0.7433 (ptpp) cc_final: 0.7011 (mtmm) REVERT: E 159 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: E 245 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7795 (tttm) REVERT: E 268 TYR cc_start: 0.8149 (t80) cc_final: 0.7920 (t80) REVERT: C 54 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8671 (m) REVERT: C 160 LEU cc_start: 0.8804 (mp) cc_final: 0.8588 (mp) REVERT: C 172 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8057 (mtp) REVERT: C 221 CYS cc_start: 0.7387 (t) cc_final: 0.6946 (m) outliers start: 65 outliers final: 33 residues processed: 238 average time/residue: 0.5121 time to fit residues: 138.0494 Evaluate side-chains 226 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 66 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 97 GLN D 272 ASN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118122 restraints weight = 17694.534| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.88 r_work: 0.3188 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16520 Z= 0.150 Angle : 0.605 11.775 22538 Z= 0.289 Chirality : 0.044 0.368 2653 Planarity : 0.004 0.051 2718 Dihedral : 6.261 57.901 2593 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.46 % Allowed : 20.02 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 1904 helix: 2.31 (0.17), residues: 804 sheet: 0.40 (0.25), residues: 409 loop : -0.72 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 186 TYR 0.029 0.001 TYR B 104 PHE 0.017 0.001 PHE B 517 TRP 0.017 0.001 TRP A 539 HIS 0.002 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16492) covalent geometry : angle 0.57004 / 0.28 (22459) SS BOND : bond 0.00381 / 0.20 ( 5) SS BOND : angle 1.85663 / 0.85 ( 10) hydrogen bonds : bond 0.04016 / 2.69 ( 869) hydrogen bonds : angle 4.50173 / 3.00 ( 2538) link_BETA1-4 : bond 0.00600 / 0.38 ( 10) link_BETA1-4 : angle 1.79106 / 1.27 ( 30) link_NAG-ASN : bond 0.00589 / 0.41 ( 13) link_NAG-ASN : angle 4.57266 / 3.46 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: A 226 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9015 (t) REVERT: A 272 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: A 337 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5721 (pt0) REVERT: A 339 MET cc_start: 0.4754 (ptp) cc_final: 0.2987 (tpt) REVERT: A 512 VAL cc_start: 0.6926 (t) cc_final: 0.6567 (p) REVERT: D 224 GLN cc_start: 0.8185 (mm110) cc_final: 0.7635 (mp10) REVERT: D 245 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8053 (tmtm) REVERT: E 47 LYS cc_start: 0.7364 (ptpp) cc_final: 0.6980 (mtmm) REVERT: E 159 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: E 245 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7771 (tttm) REVERT: E 268 TYR cc_start: 0.8110 (t80) cc_final: 0.7820 (t80) REVERT: C 54 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8673 (m) REVERT: C 160 LEU cc_start: 0.8790 (mp) cc_final: 0.8582 (mp) REVERT: C 172 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8077 (mtp) REVERT: C 192 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8715 (ptpp) REVERT: C 221 CYS cc_start: 0.7393 (t) cc_final: 0.6938 (m) outliers start: 61 outliers final: 32 residues processed: 237 average time/residue: 0.4950 time to fit residues: 133.3645 Evaluate side-chains 224 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 132 optimal weight: 5.9990 chunk 179 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN D 97 GLN D 272 ASN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN E 143 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118393 restraints weight = 17708.414| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.86 r_work: 0.3217 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16520 Z= 0.129 Angle : 0.576 11.454 22538 Z= 0.276 Chirality : 0.043 0.358 2653 Planarity : 0.004 0.050 2718 Dihedral : 6.095 59.582 2593 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.01 % Allowed : 20.82 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 1904 helix: 2.41 (0.18), residues: 804 sheet: 0.42 (0.25), residues: 409 loop : -0.70 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 186 TYR 0.025 0.001 TYR B 104 PHE 0.016 0.001 PHE B 517 TRP 0.017 0.001 TRP A 539 HIS 0.002 0.000 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16492) covalent geometry : angle 0.54462 / 0.27 (22459) SS BOND : bond 0.00336 / 0.18 ( 5) SS BOND : angle 1.72039 / 0.79 ( 10) hydrogen bonds : bond 0.03879 / 2.60 ( 869) hydrogen bonds : angle 4.43580 / 2.96 ( 2538) link_BETA1-4 : bond 0.00624 / 0.39 ( 10) link_BETA1-4 : angle 1.73114 / 1.24 ( 30) link_NAG-ASN : bond 0.00555 / 0.37 ( 13) link_NAG-ASN : angle 4.25423 / 3.21 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: A 210 LYS cc_start: 0.8658 (mttm) cc_final: 0.8332 (mtpt) REVERT: A 226 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.8980 (t) REVERT: A 272 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: A 337 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5863 (pt0) REVERT: A 339 MET cc_start: 0.4772 (ptp) cc_final: 0.3040 (tpt) REVERT: A 512 VAL cc_start: 0.6868 (t) cc_final: 0.6532 (p) REVERT: D 76 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7472 (mmtm) REVERT: D 224 GLN cc_start: 0.8162 (mm110) cc_final: 0.7628 (mp10) REVERT: D 245 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8054 (tmtm) REVERT: E 47 LYS cc_start: 0.7323 (ptpp) cc_final: 0.7002 (mtmm) REVERT: E 159 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: E 188 ASN cc_start: 0.8012 (t0) cc_final: 0.7805 (t0) REVERT: E 245 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7730 (tttm) REVERT: E 268 TYR cc_start: 0.8111 (t80) cc_final: 0.7773 (t80) REVERT: C 54 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8655 (m) REVERT: C 160 LEU cc_start: 0.8763 (mp) cc_final: 0.8540 (mp) REVERT: C 172 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7996 (mtp) REVERT: C 221 CYS cc_start: 0.7413 (t) cc_final: 0.6879 (m) REVERT: C 284 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7186 (mmt) outliers start: 53 outliers final: 30 residues processed: 230 average time/residue: 0.5147 time to fit residues: 133.9747 Evaluate side-chains 224 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 186 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN D 97 GLN D 163 ASN D 272 ASN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN E 143 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.159980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120187 restraints weight = 17577.317| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.86 r_work: 0.3261 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16520 Z= 0.117 Angle : 0.561 11.138 22538 Z= 0.269 Chirality : 0.043 0.351 2653 Planarity : 0.004 0.049 2718 Dihedral : 5.950 58.637 2593 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.89 % Allowed : 21.10 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.19), residues: 1904 helix: 2.45 (0.18), residues: 804 sheet: 0.38 (0.25), residues: 419 loop : -0.67 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 186 TYR 0.023 0.001 TYR B 104 PHE 0.022 0.001 PHE A 517 TRP 0.017 0.001 TRP A 539 HIS 0.002 0.000 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16492) covalent geometry : angle 0.53134 / 0.26 (22459) SS BOND : bond 0.00290 / 0.15 ( 5) SS BOND : angle 1.61723 / 0.74 ( 10) hydrogen bonds : bond 0.03773 / 2.53 ( 869) hydrogen bonds : angle 4.36523 / 2.91 ( 2538) link_BETA1-4 : bond 0.00628 / 0.39 ( 10) link_BETA1-4 : angle 1.69970 / 1.22 ( 30) link_NAG-ASN : bond 0.00571 / 0.38 ( 13) link_NAG-ASN : angle 4.05710 / 3.06 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: A 210 LYS cc_start: 0.8645 (mttm) cc_final: 0.8330 (mtpt) REVERT: A 226 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.8987 (t) REVERT: A 272 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: A 337 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5783 (pt0) REVERT: A 339 MET cc_start: 0.4964 (ptp) cc_final: 0.3152 (tpt) REVERT: D 46 MET cc_start: 0.8078 (ttt) cc_final: 0.7874 (ttp) REVERT: D 224 GLN cc_start: 0.8162 (mm110) cc_final: 0.7626 (mp10) REVERT: D 245 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8085 (tmtm) REVERT: B 269 MET cc_start: 0.5012 (mmm) cc_final: 0.4746 (mmm) REVERT: E 47 LYS cc_start: 0.7315 (ptpp) cc_final: 0.7082 (mtmm) REVERT: E 159 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: E 245 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7719 (tttm) REVERT: E 268 TYR cc_start: 0.8090 (t80) cc_final: 0.7799 (t80) REVERT: E 269 TYR cc_start: 0.8378 (m-80) cc_final: 0.7360 (m-80) REVERT: C 160 LEU cc_start: 0.8759 (mp) cc_final: 0.8524 (mp) REVERT: C 284 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7235 (mmt) outliers start: 51 outliers final: 32 residues processed: 224 average time/residue: 0.4968 time to fit residues: 125.6279 Evaluate side-chains 225 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 8 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN D 272 ASN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116854 restraints weight = 17562.098| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.89 r_work: 0.3189 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16520 Z= 0.194 Angle : 0.629 12.001 22538 Z= 0.302 Chirality : 0.045 0.356 2653 Planarity : 0.004 0.050 2718 Dihedral : 6.137 58.646 2593 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.61 % Allowed : 21.72 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 1904 helix: 2.28 (0.18), residues: 804 sheet: 0.40 (0.25), residues: 409 loop : -0.72 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 186 TYR 0.021 0.002 TYR B 104 PHE 0.029 0.002 PHE A 517 TRP 0.014 0.001 TRP A 539 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (16492) covalent geometry : angle 0.59818 / 0.29 (22459) SS BOND : bond 0.00471 / 0.26 ( 5) SS BOND : angle 1.96607 / 0.89 ( 10) hydrogen bonds : bond 0.04112 / 2.76 ( 869) hydrogen bonds : angle 4.46962 / 2.98 ( 2538) link_BETA1-4 : bond 0.00561 / 0.35 ( 10) link_BETA1-4 : angle 1.82900 / 1.29 ( 30) link_NAG-ASN : bond 0.00522 / 0.34 ( 13) link_NAG-ASN : angle 4.31944 / 3.24 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: A 210 LYS cc_start: 0.8658 (mttm) cc_final: 0.8332 (mtpt) REVERT: A 226 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.8999 (t) REVERT: A 272 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: A 337 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6038 (pt0) REVERT: A 339 MET cc_start: 0.5074 (ptp) cc_final: 0.3244 (tpt) REVERT: A 512 VAL cc_start: 0.6848 (t) cc_final: 0.6447 (p) REVERT: D 46 MET cc_start: 0.8115 (ttt) cc_final: 0.7896 (ttp) REVERT: D 224 GLN cc_start: 0.8160 (mm110) cc_final: 0.7613 (mp10) REVERT: D 245 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8039 (tmtm) REVERT: D 273 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7834 (tp) REVERT: E 47 LYS cc_start: 0.7311 (ptpp) cc_final: 0.7064 (mtmm) REVERT: E 159 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: E 245 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7830 (tttm) REVERT: E 268 TYR cc_start: 0.8086 (t80) cc_final: 0.7785 (t80) REVERT: C 54 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8653 (m) REVERT: C 160 LEU cc_start: 0.8766 (mp) cc_final: 0.8497 (mp) REVERT: C 221 CYS cc_start: 0.7427 (t) cc_final: 0.6993 (m) outliers start: 46 outliers final: 30 residues processed: 225 average time/residue: 0.4987 time to fit residues: 127.5556 Evaluate side-chains 224 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 144 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 185 optimal weight: 0.0060 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN D 272 ASN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN C 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.159242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119482 restraints weight = 17584.855| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.87 r_work: 0.3222 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16520 Z= 0.113 Angle : 0.564 11.237 22538 Z= 0.272 Chirality : 0.043 0.353 2653 Planarity : 0.004 0.048 2718 Dihedral : 5.938 58.387 2593 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.38 % Allowed : 22.23 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1904 helix: 2.42 (0.18), residues: 804 sheet: 0.35 (0.25), residues: 419 loop : -0.68 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 186 TYR 0.022 0.001 TYR B 104 PHE 0.018 0.001 PHE B 524 TRP 0.019 0.001 TRP A 539 HIS 0.002 0.000 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (16492) covalent geometry : angle 0.53501 / 0.27 (22459) SS BOND : bond 0.00273 / 0.14 ( 5) SS BOND : angle 1.63625 / 0.75 ( 10) hydrogen bonds : bond 0.03783 / 2.54 ( 869) hydrogen bonds : angle 4.39484 / 2.93 ( 2538) link_BETA1-4 : bond 0.00639 / 0.40 ( 10) link_BETA1-4 : angle 1.68647 / 1.22 ( 30) link_NAG-ASN : bond 0.00591 / 0.39 ( 13) link_NAG-ASN : angle 4.02814 / 3.01 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5336.59 seconds wall clock time: 91 minutes 52.87 seconds (5512.87 seconds total)