Starting phenix.real_space_refine on Sat Sep 12 14:48:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22qv_68610/09_2026/22qv_68610.cif Found real_map, /net/cci-nas-00/data/ceres_data/22qv_68610/09_2026/22qv_68610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22qv_68610/09_2026/22qv_68610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22qv_68610/09_2026/22qv_68610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22qv_68610/09_2026/22qv_68610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22qv_68610/09_2026/22qv_68610.map" } resolution = 2.67 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= 0.112 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 18 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: 18 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 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: 4.15, per 1000 atoms: 0.26 Number of scatterers: 16091 At special positions: 0 Unit cell: (99.17, 96.005, 144.535, 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=3, 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 601 " - " 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 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 56 helices and 11 sheets defined 43.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.605A pdb=" N GLU A 95 " --> pdb=" O ASP A 92 " (cutoff:3.500A) 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 121 through 126 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 291 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 548 removed outlier: 3.501A pdb=" N GLY A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 48 removed outlier: 3.701A 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 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.667A pdb=" N THR D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 274 Processing helix chain 'D' and resid 274 through 289 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'D' and resid 331 through 360 Processing helix chain 'D' and resid 511 through 556 Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 90 through 94 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 125 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 291 removed outlier: 3.542A pdb=" N VAL B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 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 546 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.857A pdb=" N ASP E 115 " --> pdb=" O GLU E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 115' 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 removed outlier: 3.699A pdb=" N THR E 152 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 273 Processing helix chain 'E' and resid 274 through 289 removed outlier: 3.620A pdb=" N PHE E 289 " --> pdb=" O ILE E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 319 removed outlier: 3.827A pdb=" N VAL E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 359 Processing helix chain 'E' and resid 511 through 554 Processing helix chain 'C' and resid 24 through 35 Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 85 through 88 removed outlier: 4.022A 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 94 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 121 through 126 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 291 removed outlier: 3.853A pdb=" N VAL C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 333 removed outlier: 3.696A pdb=" N GLY C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 340 through 355 Processing helix chain 'C' and resid 496 through 547 removed outlier: 3.579A pdb=" N GLY C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 103 removed outlier: 5.812A pdb=" N ASN A 130 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU A 147 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N TRP A 77 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE A 79 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP A 58 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ARG A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER A 56 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N PHE A 83 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N SER A 54 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.718A pdb=" N GLN A 208 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG A 235 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE A 206 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 127 through 130 removed outlier: 6.200A pdb=" N ASN D 157 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU D 176 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 91 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN D 102 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE D 89 " --> pdb=" O ASN D 102 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TRP D 104 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR D 87 " --> pdb=" O TRP D 104 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE D 106 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER D 85 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LYS D 108 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N SER D 83 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ARG D 110 " --> pdb=" O HIS D 81 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N HIS D 81 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU D 78 " --> pdb=" O ASP D 214 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR D 216 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 80 " --> pdb=" O TYR D 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 139 through 141 removed outlier: 4.936A pdb=" N SER D 205 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL D 254 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER D 236 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN D 263 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 5.695A 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: 5.473A pdb=" N ASN B 130 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU B 147 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TRP B 77 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE B 79 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP B 58 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ARG B 81 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER B 56 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N PHE B 83 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N SER B 54 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.907A pdb=" N SER B 176 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 226 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR B 225 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU B 215 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 227 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG B 213 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN B 229 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 211 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR B 231 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 209 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR B 233 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 130 removed outlier: 5.745A pdb=" N ASN E 157 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU E 176 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN E 102 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE E 89 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N TRP E 104 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR E 87 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE E 106 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N SER E 85 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LYS E 108 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER E 83 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG E 110 " --> pdb=" O HIS E 81 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N HIS E 81 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 82 " --> pdb=" O TYR E 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 139 through 141 removed outlier: 5.120A pdb=" N SER E 205 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL E 254 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL E 261 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 139 through 141 removed outlier: 5.120A pdb=" N SER E 205 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL E 254 " --> pdb=" O SER E 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 103 removed outlier: 5.375A pdb=" N ASN C 130 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU C 147 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR C 71 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU C 65 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 73 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP C 77 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU C 59 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE C 79 " --> pdb=" O MET C 57 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N MET C 57 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ARG C 81 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE C 55 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N PHE C 83 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL C 53 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 5.043A pdb=" N SER C 176 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR C 226 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR C 225 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 215 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 227 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG C 213 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN C 229 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C 211 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR C 231 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR C 209 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR C 233 " --> pdb=" O LEU C 207 " (cutoff:3.500A) 851 hydrogen bonds defined for protein. 2478 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: 2.79 Time building geometry restraints manager: 1.76 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: 3719 1.46 - 1.58: 7790 1.58 - 1.69: 1 1.69 - 1.81: 132 Bond restraints: 16492 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" CB PRO E 50 " pdb=" CG PRO E 50 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.02e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.357 0.049 2.00e-02 2.50e+03 5.92e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" CG PRO E 228 " pdb=" CD PRO E 228 " ideal model delta sigma weight residual 1.503 1.437 0.066 3.40e-02 8.65e+02 3.81e+00 ... (remaining 16487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 22285 2.83 - 5.67: 140 5.67 - 8.50: 24 8.50 - 11.34: 8 11.34 - 14.17: 2 Bond angle restraints: 22459 Sorted by residual: angle pdb=" CA PRO E 50 " pdb=" N PRO E 50 " pdb=" CD PRO E 50 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PRO E 228 " pdb=" CD PRO E 228 " pdb=" CG PRO E 228 " ideal model delta sigma weight residual 103.20 93.45 9.75 1.50e+00 4.44e-01 4.23e+01 angle pdb=" CA PRO E 228 " pdb=" N PRO E 228 " pdb=" CD PRO E 228 " ideal model delta sigma weight residual 112.00 103.30 8.70 1.40e+00 5.10e-01 3.87e+01 angle pdb=" CB PRO E 228 " pdb=" CG PRO E 228 " pdb=" CD PRO E 228 " ideal model delta sigma weight residual 106.10 92.32 13.78 3.20e+00 9.77e-02 1.85e+01 angle pdb=" CA PRO E 228 " pdb=" CB PRO E 228 " pdb=" CG PRO E 228 " ideal model delta sigma weight residual 104.50 96.53 7.97 1.90e+00 2.77e-01 1.76e+01 ... (remaining 22454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.96: 9185 22.96 - 45.93: 717 45.93 - 68.89: 131 68.89 - 91.86: 23 91.86 - 114.82: 11 Dihedral angle restraints: 10067 sinusoidal: 4338 harmonic: 5729 Sorted by residual: 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 28.36 64.64 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CA GLN E 197 " pdb=" C GLN E 197 " pdb=" N ASN E 198 " pdb=" CA ASN E 198 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA MET E 223 " pdb=" C MET E 223 " pdb=" N GLN E 224 " pdb=" CA GLN E 224 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 10064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 2645 0.237 - 0.475: 6 0.475 - 0.712: 0 0.712 - 0.949: 1 0.949 - 1.186: 1 Chirality restraints: 2653 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN E 198 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.52e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 125 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CG LEU D 273 " pdb=" CB LEU D 273 " pdb=" CD1 LEU D 273 " pdb=" CD2 LEU D 273 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 2650 not shown) Planarity restraints: 2731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 49 " 0.087 5.00e-02 4.00e+02 1.21e-01 2.36e+01 pdb=" N PRO E 50 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO E 50 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO E 50 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 198 " -0.034 2.00e-02 2.50e+03 3.10e-02 1.20e+01 pdb=" CG ASN E 198 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN E 198 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN E 198 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 247 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO C 248 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 248 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 248 " -0.039 5.00e-02 4.00e+02 ... (remaining 2728 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 334 2.69 - 3.24: 15276 3.24 - 3.80: 26650 3.80 - 4.35: 35870 4.35 - 4.90: 58631 Nonbonded interactions: 136761 Sorted by model distance: nonbonded pdb=" OG1 THR E 277 " pdb=" OH TYR E 337 " model vdw 2.141 3.040 nonbonded pdb=" ND2 ASN C 66 " pdb=" O PRO C 68 " model vdw 2.163 3.120 nonbonded pdb=" O PHE D 349 " pdb=" OG SER D 352 " model vdw 2.194 3.040 nonbonded pdb=" OE2 GLU B 80 " pdb=" OH TYR B 148 " model vdw 2.205 3.040 nonbonded pdb=" O ARG D 63 " pdb=" NE ARG D 63 " model vdw 2.205 3.120 ... (remaining 136756 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 548) selection = (chain 'B' and resid 23 through 548) selection = (chain 'C' and resid 23 through 548) } ncs_group { reference = chain 'D' 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.150 Find NCS groups from input model: 0.410 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 16523 Z= 0.169 Angle : 0.706 14.291 22538 Z= 0.337 Chirality : 0.053 1.186 2653 Planarity : 0.005 0.121 2718 Dihedral : 16.562 114.821 6334 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.36 % Allowed : 22.35 % Favored : 76.29 % 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: 0.92 (0.19), residues: 1904 helix: 2.33 (0.19), residues: 737 sheet: 0.15 (0.26), residues: 412 loop : -0.86 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 514 TYR 0.021 0.002 TYR D 337 PHE 0.029 0.002 PHE E 237 TRP 0.021 0.001 TRP C 539 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (16492) covalent geometry : angle 0.66186 / 0.33 (22459) SS BOND : bond 0.00088 / 0.04 ( 5) SS BOND : angle 1.19460 / 0.52 ( 10) hydrogen bonds : bond 0.14580 / 9.57 ( 841) hydrogen bonds : angle 6.42303 / 4.40 ( 2478) Misc. bond : bond 0.00111 / 0.04 ( 3) link_BETA1-4 : bond 0.00777 / 0.46 ( 10) link_BETA1-4 : angle 2.60915 / 1.74 ( 30) link_NAG-ASN : bond 0.00719 / 0.46 ( 13) link_NAG-ASN : angle 5.48024 / 3.95 ( 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 262 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8218 (pt0) cc_final: 0.7850 (pt0) REVERT: E 50 PRO cc_start: 0.8106 (Cg_exo) cc_final: 0.7857 (Cg_exo) REVERT: C 269 MET cc_start: 0.3641 (ptt) cc_final: 0.3051 (ptm) outliers start: 24 outliers final: 19 residues processed: 257 average time/residue: 0.5853 time to fit residues: 166.9870 Evaluate side-chains 245 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 526 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS E 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.159203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120260 restraints weight = 16732.963| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.92 r_work: 0.3220 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16523 Z= 0.167 Angle : 0.686 14.396 22538 Z= 0.329 Chirality : 0.047 0.613 2653 Planarity : 0.004 0.054 2718 Dihedral : 10.123 110.424 2630 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.97 % Allowed : 18.60 % 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: 0.95 (0.19), residues: 1904 helix: 2.32 (0.19), residues: 755 sheet: 0.09 (0.25), residues: 420 loop : -0.85 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 514 TYR 0.020 0.002 TYR D 337 PHE 0.028 0.002 PHE E 237 TRP 0.020 0.001 TRP B 539 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (16492) covalent geometry : angle 0.64625 / 0.32 (22459) SS BOND : bond 0.00196 / 0.13 ( 5) SS BOND : angle 0.60641 / 0.27 ( 10) hydrogen bonds : bond 0.04620 / 2.92 ( 841) hydrogen bonds : angle 4.96673 / 3.40 ( 2478) Misc. bond : bond 0.00035 / 0.02 ( 3) link_BETA1-4 : bond 0.00624 / 0.35 ( 10) link_BETA1-4 : angle 2.06533 / 1.37 ( 30) link_NAG-ASN : bond 0.00583 / 0.32 ( 13) link_NAG-ASN : angle 5.29540 / 3.66 ( 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 316 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 246 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8375 (pt0) cc_final: 0.8014 (pt0) REVERT: A 294 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7621 (mm-40) REVERT: D 123 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7542 (mmm) REVERT: D 218 ASP cc_start: 0.7727 (m-30) cc_final: 0.7477 (m-30) REVERT: D 257 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8042 (mm-40) REVERT: D 301 LYS cc_start: 0.6902 (mmtm) cc_final: 0.6690 (mmtt) REVERT: B 147 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7815 (tp) REVERT: B 192 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8678 (ptpt) REVERT: E 51 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6617 (pp) REVERT: E 150 ASP cc_start: 0.8397 (m-30) cc_final: 0.8026 (m-30) REVERT: E 172 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: E 312 MET cc_start: 0.7451 (tpp) cc_final: 0.7158 (mtp) REVERT: E 549 MET cc_start: 0.7683 (ttp) cc_final: 0.7453 (tpp) REVERT: C 269 MET cc_start: 0.3664 (ptt) cc_final: 0.3334 (mmm) REVERT: C 339 MET cc_start: 0.3956 (OUTLIER) cc_final: 0.2986 (pp-130) outliers start: 70 outliers final: 29 residues processed: 285 average time/residue: 0.5681 time to fit residues: 181.3644 Evaluate side-chains 263 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 526 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 75 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 132 HIS D 229 ASN B 36 ASN E 119 ASN E 163 ASN C 36 ASN C 66 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.158589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119655 restraints weight = 16923.621| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.92 r_work: 0.3216 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16523 Z= 0.151 Angle : 0.647 13.418 22538 Z= 0.308 Chirality : 0.046 0.495 2653 Planarity : 0.004 0.048 2718 Dihedral : 9.048 112.939 2615 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.37 % Allowed : 18.55 % Favored : 77.08 % 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: 1.08 (0.19), residues: 1904 helix: 2.58 (0.19), residues: 737 sheet: 0.07 (0.25), residues: 420 loop : -0.81 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 514 TYR 0.018 0.002 TYR E 337 PHE 0.018 0.002 PHE E 237 TRP 0.019 0.001 TRP B 539 HIS 0.003 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (16492) covalent geometry : angle 0.60865 / 0.30 (22459) SS BOND : bond 0.00232 / 0.16 ( 5) SS BOND : angle 0.31372 / 0.18 ( 10) hydrogen bonds : bond 0.04370 / 2.77 ( 841) hydrogen bonds : angle 4.72564 / 3.25 ( 2478) Misc. bond : bond 0.00016 / 0.01 ( 3) link_BETA1-4 : bond 0.00588 / 0.34 ( 10) link_BETA1-4 : angle 2.16416 / 1.44 ( 30) link_NAG-ASN : bond 0.00617 / 0.35 ( 13) link_NAG-ASN : angle 5.00327 / 3.43 ( 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 316 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 239 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 THR cc_start: 0.8823 (m) cc_final: 0.8564 (p) REVERT: A 294 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7586 (mm-40) REVERT: D 123 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7690 (mmm) REVERT: D 156 MET cc_start: 0.6958 (mpt) cc_final: 0.6476 (mpt) REVERT: D 172 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8412 (tm-30) REVERT: D 237 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6125 (p90) REVERT: D 257 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8090 (mm-40) REVERT: D 300 GLU cc_start: 0.6409 (pp20) cc_final: 0.5115 (tt0) REVERT: D 301 LYS cc_start: 0.7006 (mmtm) cc_final: 0.6760 (mmtt) REVERT: D 349 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.5728 (p90) REVERT: D 549 MET cc_start: 0.6639 (tpp) cc_final: 0.6111 (mpp) REVERT: E 51 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6527 (pp) REVERT: E 75 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7518 (ptpt) REVERT: E 149 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6766 (ttp-110) REVERT: E 150 ASP cc_start: 0.8461 (m-30) cc_final: 0.8129 (m-30) REVERT: E 172 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: E 235 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7860 (mtmp) REVERT: E 537 VAL cc_start: 0.7058 (t) cc_final: 0.6764 (t) REVERT: E 548 ARG cc_start: 0.7857 (tpt170) cc_final: 0.7449 (tpt90) REVERT: C 269 MET cc_start: 0.3793 (ptt) cc_final: 0.3427 (mmm) REVERT: C 339 MET cc_start: 0.3974 (OUTLIER) cc_final: 0.3011 (pp-130) outliers start: 77 outliers final: 35 residues processed: 288 average time/residue: 0.5424 time to fit residues: 175.6394 Evaluate side-chains 280 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 526 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 146 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN D 132 HIS B 36 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123380 restraints weight = 17647.634| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.95 r_work: 0.3307 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 16523 Z= 0.274 Angle : 0.781 17.211 22538 Z= 0.372 Chirality : 0.052 0.540 2653 Planarity : 0.005 0.049 2718 Dihedral : 8.700 112.713 2608 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.05 % Allowed : 17.87 % Favored : 77.08 % 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: 0.67 (0.19), residues: 1904 helix: 2.06 (0.18), residues: 750 sheet: 0.01 (0.25), residues: 424 loop : -1.00 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 514 TYR 0.025 0.002 TYR E 337 PHE 0.024 0.002 PHE E 237 TRP 0.019 0.002 TRP A 539 HIS 0.007 0.001 HIS C 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.27 (16492) covalent geometry : angle 0.74433 / 0.36 (22459) SS BOND : bond 0.00280 / 0.15 ( 5) SS BOND : angle 0.85998 / 0.40 ( 10) hydrogen bonds : bond 0.04974 / 3.13 ( 841) hydrogen bonds : angle 4.84064 / 3.32 ( 2478) Misc. bond : bond 0.00041 / 0.02 ( 3) link_BETA1-4 : bond 0.00543 / 0.32 ( 10) link_BETA1-4 : angle 2.22145 / 1.52 ( 30) link_NAG-ASN : bond 0.00529 / 0.31 ( 13) link_NAG-ASN : angle 5.44678 / 3.75 ( 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 335 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 246 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7652 (mm-40) REVERT: D 172 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: D 205 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8757 (p) REVERT: D 237 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.6351 (p90) REVERT: D 257 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8040 (mm-40) REVERT: D 300 GLU cc_start: 0.6612 (pp20) cc_final: 0.5251 (tt0) REVERT: D 301 LYS cc_start: 0.7192 (mmtm) cc_final: 0.6946 (mmtt) REVERT: D 332 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8322 (tt) REVERT: D 337 TYR cc_start: 0.7376 (m-80) cc_final: 0.7093 (m-10) REVERT: D 349 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6169 (p90) REVERT: E 51 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6708 (pp) REVERT: E 75 LYS cc_start: 0.7852 (mmtp) cc_final: 0.7344 (ptpt) REVERT: E 150 ASP cc_start: 0.8558 (m-30) cc_final: 0.8297 (m-30) REVERT: E 166 LYS cc_start: 0.5770 (OUTLIER) cc_final: 0.5512 (mtpt) REVERT: E 537 VAL cc_start: 0.7277 (t) cc_final: 0.6983 (t) REVERT: E 548 ARG cc_start: 0.7940 (tpt170) cc_final: 0.7501 (tpt90) REVERT: C 269 MET cc_start: 0.3989 (ptt) cc_final: 0.3588 (mmm) REVERT: C 275 SER cc_start: 0.8069 (p) cc_final: 0.7829 (m) REVERT: C 339 MET cc_start: 0.4285 (OUTLIER) cc_final: 0.3227 (pp-130) outliers start: 89 outliers final: 42 residues processed: 305 average time/residue: 0.5438 time to fit residues: 186.5356 Evaluate side-chains 281 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 511 VAL 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: 0.4980 chunk 23 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS B 36 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.164049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128406 restraints weight = 17688.100| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.87 r_work: 0.3386 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16523 Z= 0.128 Angle : 0.644 14.209 22538 Z= 0.303 Chirality : 0.046 0.608 2653 Planarity : 0.004 0.043 2718 Dihedral : 8.282 116.976 2600 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.86 % Allowed : 19.46 % Favored : 76.69 % 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: 1.05 (0.19), residues: 1904 helix: 2.57 (0.19), residues: 734 sheet: 0.10 (0.24), residues: 452 loop : -0.91 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 514 TYR 0.019 0.001 TYR E 337 PHE 0.016 0.001 PHE E 175 TRP 0.021 0.001 TRP A 539 HIS 0.002 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16492) covalent geometry : angle 0.60153 / 0.29 (22459) SS BOND : bond 0.00168 / 0.09 ( 5) SS BOND : angle 0.27308 / 0.13 ( 10) hydrogen bonds : bond 0.04092 / 2.59 ( 841) hydrogen bonds : angle 4.63640 / 3.19 ( 2478) Misc. bond : bond 0.00013 / 0.01 ( 3) link_BETA1-4 : bond 0.00648 / 0.36 ( 10) link_BETA1-4 : angle 2.03444 / 1.38 ( 30) link_NAG-ASN : bond 0.00707 / 0.37 ( 13) link_NAG-ASN : angle 5.30519 / 3.82 ( 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 318 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 250 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ARG cc_start: 0.7223 (mpt90) cc_final: 0.6938 (mpt90) REVERT: A 293 ASP cc_start: 0.7994 (m-30) cc_final: 0.7707 (m-30) REVERT: A 294 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7615 (mm-40) REVERT: D 172 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: D 218 ASP cc_start: 0.7771 (m-30) cc_final: 0.7478 (m-30) REVERT: D 237 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6384 (p90) REVERT: D 257 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8107 (mm-40) REVERT: D 300 GLU cc_start: 0.6600 (pp20) cc_final: 0.5266 (tt0) REVERT: D 301 LYS cc_start: 0.7207 (mmtm) cc_final: 0.6984 (mmtt) REVERT: D 337 TYR cc_start: 0.7273 (m-80) cc_final: 0.6992 (m-80) REVERT: D 349 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6155 (p90) REVERT: D 552 TYR cc_start: 0.7133 (t80) cc_final: 0.6835 (t80) REVERT: E 75 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7531 (ptpt) REVERT: E 146 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7660 (mptp) REVERT: E 150 ASP cc_start: 0.8458 (m-30) cc_final: 0.8077 (m-30) REVERT: E 172 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: E 175 PHE cc_start: 0.8725 (t80) cc_final: 0.8056 (t80) REVERT: E 537 VAL cc_start: 0.7247 (t) cc_final: 0.6902 (t) REVERT: C 269 MET cc_start: 0.3960 (ptt) cc_final: 0.3618 (mmm) REVERT: C 275 SER cc_start: 0.8188 (p) cc_final: 0.7883 (m) REVERT: C 339 MET cc_start: 0.3957 (OUTLIER) cc_final: 0.2833 (pp-130) outliers start: 68 outliers final: 30 residues processed: 293 average time/residue: 0.5294 time to fit residues: 174.7201 Evaluate side-chains 278 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 526 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 122 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 chunk 67 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS D 159 GLN E 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.164548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128737 restraints weight = 17589.389| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.88 r_work: 0.3387 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16523 Z= 0.126 Angle : 0.622 15.935 22538 Z= 0.293 Chirality : 0.046 0.521 2653 Planarity : 0.004 0.041 2718 Dihedral : 8.070 116.468 2596 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.80 % Allowed : 20.08 % Favored : 76.12 % 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: 1.13 (0.19), residues: 1904 helix: 2.70 (0.19), residues: 734 sheet: 0.11 (0.24), residues: 452 loop : -0.91 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 514 TYR 0.019 0.001 TYR E 337 PHE 0.013 0.001 PHE E 175 TRP 0.018 0.001 TRP A 507 HIS 0.002 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (16492) covalent geometry : angle 0.58056 / 0.28 (22459) SS BOND : bond 0.00156 / 0.10 ( 5) SS BOND : angle 0.32851 / 0.14 ( 10) hydrogen bonds : bond 0.03956 / 2.51 ( 841) hydrogen bonds : angle 4.52199 / 3.11 ( 2478) Misc. bond : bond 0.00020 / 0.01 ( 3) link_BETA1-4 : bond 0.00608 / 0.35 ( 10) link_BETA1-4 : angle 1.94041 / 1.33 ( 30) link_NAG-ASN : bond 0.00761 / 0.38 ( 13) link_NAG-ASN : angle 5.13632 / 3.63 ( 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 315 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.7993 (m-30) cc_final: 0.7705 (m-30) REVERT: A 294 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7583 (mm-40) REVERT: D 172 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8315 (tm-30) REVERT: D 218 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: D 237 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.6081 (p90) REVERT: D 257 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8093 (mm-40) REVERT: D 300 GLU cc_start: 0.6618 (pp20) cc_final: 0.5256 (tt0) REVERT: D 301 LYS cc_start: 0.7179 (mmtm) cc_final: 0.6912 (mmtt) REVERT: D 337 TYR cc_start: 0.7242 (m-80) cc_final: 0.6951 (m-80) REVERT: D 349 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.5877 (p90) REVERT: D 552 TYR cc_start: 0.7100 (t80) cc_final: 0.6773 (t80) REVERT: E 46 MET cc_start: 0.3243 (OUTLIER) cc_final: 0.2611 (tmm) REVERT: E 75 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7516 (ptpt) REVERT: E 150 ASP cc_start: 0.8425 (m-30) cc_final: 0.8021 (m-30) REVERT: E 163 ASN cc_start: 0.8138 (t0) cc_final: 0.7886 (t0) REVERT: E 175 PHE cc_start: 0.8721 (t80) cc_final: 0.8082 (t80) REVERT: E 537 VAL cc_start: 0.7187 (t) cc_final: 0.6854 (t) REVERT: E 548 ARG cc_start: 0.7964 (tmt-80) cc_final: 0.7660 (tpt90) REVERT: E 551 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.6882 (tp40) REVERT: C 269 MET cc_start: 0.3888 (ptt) cc_final: 0.3580 (mmm) REVERT: C 339 MET cc_start: 0.3761 (OUTLIER) cc_final: 0.2718 (pp-130) outliers start: 67 outliers final: 40 residues processed: 291 average time/residue: 0.5451 time to fit residues: 178.6254 Evaluate side-chains 287 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 526 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 66 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126021 restraints weight = 17718.824| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.86 r_work: 0.3348 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16523 Z= 0.187 Angle : 0.678 14.960 22538 Z= 0.322 Chirality : 0.048 0.460 2653 Planarity : 0.004 0.040 2718 Dihedral : 8.107 117.319 2596 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.31 % Allowed : 19.80 % Favored : 75.89 % 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: 0.98 (0.19), residues: 1904 helix: 2.55 (0.19), residues: 732 sheet: 0.03 (0.24), residues: 424 loop : -0.92 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 514 TYR 0.021 0.002 TYR D 337 PHE 0.014 0.002 PHE A 55 TRP 0.016 0.001 TRP B 539 HIS 0.004 0.001 HIS C 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (16492) covalent geometry : angle 0.64131 / 0.31 (22459) SS BOND : bond 0.00277 / 0.19 ( 5) SS BOND : angle 0.64432 / 0.29 ( 10) hydrogen bonds : bond 0.04309 / 2.72 ( 841) hydrogen bonds : angle 4.57456 / 3.14 ( 2478) Misc. bond : bond 0.00040 / 0.02 ( 3) link_BETA1-4 : bond 0.00631 / 0.36 ( 10) link_BETA1-4 : angle 2.07093 / 1.41 ( 30) link_NAG-ASN : bond 0.00735 / 0.36 ( 13) link_NAG-ASN : angle 5.07674 / 3.54 ( 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 317 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 241 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.8050 (m-30) cc_final: 0.7769 (m-30) REVERT: A 294 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7656 (mm-40) REVERT: D 46 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5201 (ttp) REVERT: D 172 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8370 (tm-30) REVERT: D 237 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.6375 (p90) REVERT: D 257 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8054 (mm-40) REVERT: D 300 GLU cc_start: 0.6654 (pp20) cc_final: 0.5290 (tt0) REVERT: D 301 LYS cc_start: 0.7228 (mmtm) cc_final: 0.6956 (mmtt) REVERT: D 337 TYR cc_start: 0.7333 (m-80) cc_final: 0.7098 (m-80) REVERT: D 349 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.5846 (p90) REVERT: D 552 TYR cc_start: 0.7101 (t80) cc_final: 0.6848 (t80) REVERT: E 75 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7526 (ptpt) REVERT: E 150 ASP cc_start: 0.8383 (m-30) cc_final: 0.8027 (m-30) REVERT: E 163 ASN cc_start: 0.8091 (t0) cc_final: 0.7765 (t0) REVERT: E 166 LYS cc_start: 0.5438 (OUTLIER) cc_final: 0.5217 (mtpm) REVERT: E 172 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: E 175 PHE cc_start: 0.8723 (t80) cc_final: 0.8067 (t80) REVERT: E 551 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.6600 (tp40) REVERT: C 339 MET cc_start: 0.3907 (OUTLIER) cc_final: 0.2918 (pp-130) outliers start: 76 outliers final: 50 residues processed: 292 average time/residue: 0.5462 time to fit residues: 179.5307 Evaluate side-chains 298 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 541 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 132 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127556 restraints weight = 17767.062| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.87 r_work: 0.3368 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16523 Z= 0.141 Angle : 0.629 13.930 22538 Z= 0.300 Chirality : 0.045 0.443 2653 Planarity : 0.004 0.039 2718 Dihedral : 8.063 120.012 2596 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.86 % Allowed : 20.25 % Favored : 75.89 % 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: 1.10 (0.19), residues: 1904 helix: 2.70 (0.19), residues: 734 sheet: 0.09 (0.24), residues: 448 loop : -0.96 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 514 TYR 0.025 0.001 TYR E 337 PHE 0.023 0.001 PHE B 346 TRP 0.019 0.001 TRP A 539 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (16492) covalent geometry : angle 0.59570 / 0.29 (22459) SS BOND : bond 0.00169 / 0.11 ( 5) SS BOND : angle 0.40833 / 0.19 ( 10) hydrogen bonds : bond 0.04006 / 2.54 ( 841) hydrogen bonds : angle 4.51697 / 3.10 ( 2478) Misc. bond : bond 0.00023 / 0.01 ( 3) link_BETA1-4 : bond 0.00634 / 0.36 ( 10) link_BETA1-4 : angle 1.98454 / 1.34 ( 30) link_NAG-ASN : bond 0.00598 / 0.35 ( 13) link_NAG-ASN : angle 4.58081 / 3.27 ( 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 310 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 242 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.8032 (m-30) cc_final: 0.7744 (m-30) REVERT: A 294 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: D 172 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: D 237 PHE cc_start: 0.6880 (OUTLIER) cc_final: 0.6230 (p90) REVERT: D 257 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8075 (mm-40) REVERT: D 300 GLU cc_start: 0.6728 (pp20) cc_final: 0.5328 (tt0) REVERT: D 301 LYS cc_start: 0.7230 (mmtm) cc_final: 0.6982 (mmtt) REVERT: D 349 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.5799 (p90) REVERT: D 552 TYR cc_start: 0.7216 (t80) cc_final: 0.6948 (t80) REVERT: E 51 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6661 (pp) REVERT: E 75 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7508 (ptpt) REVERT: E 150 ASP cc_start: 0.8390 (m-30) cc_final: 0.8023 (m-30) REVERT: E 163 ASN cc_start: 0.8099 (t0) cc_final: 0.7761 (t0) REVERT: E 172 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: E 548 ARG cc_start: 0.8006 (tmt-80) cc_final: 0.7416 (tpt90) REVERT: E 551 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6620 (tp40) REVERT: C 339 MET cc_start: 0.3801 (OUTLIER) cc_final: 0.2739 (pp-130) outliers start: 68 outliers final: 48 residues processed: 289 average time/residue: 0.5364 time to fit residues: 174.3508 Evaluate side-chains 297 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 240 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 541 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 186 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127637 restraints weight = 17703.228| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.99 r_work: 0.3364 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16523 Z= 0.126 Angle : 0.625 15.042 22538 Z= 0.295 Chirality : 0.046 0.609 2653 Planarity : 0.003 0.039 2718 Dihedral : 7.811 112.500 2596 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.35 % Allowed : 20.93 % Favored : 75.72 % 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: 1.16 (0.19), residues: 1904 helix: 2.78 (0.19), residues: 734 sheet: 0.10 (0.24), residues: 448 loop : -0.94 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 514 TYR 0.034 0.001 TYR E 155 PHE 0.035 0.001 PHE E 175 TRP 0.018 0.001 TRP A 539 HIS 0.002 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16492) covalent geometry : angle 0.58831 / 0.29 (22459) SS BOND : bond 0.00146 / 0.10 ( 5) SS BOND : angle 0.34678 / 0.15 ( 10) hydrogen bonds : bond 0.03850 / 2.44 ( 841) hydrogen bonds : angle 4.49864 / 3.08 ( 2478) Misc. bond : bond 0.00024 / 0.01 ( 3) link_BETA1-4 : bond 0.00630 / 0.36 ( 10) link_BETA1-4 : angle 1.93074 / 1.31 ( 30) link_NAG-ASN : bond 0.00714 / 0.35 ( 13) link_NAG-ASN : angle 4.88178 / 3.36 ( 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 309 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 250 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7991 (tt0) REVERT: A 293 ASP cc_start: 0.7977 (m-30) cc_final: 0.7690 (m-30) REVERT: A 294 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7593 (mm-40) REVERT: D 172 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: D 237 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6260 (p90) REVERT: D 257 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8081 (mm-40) REVERT: D 300 GLU cc_start: 0.6747 (pp20) cc_final: 0.5338 (tt0) REVERT: D 301 LYS cc_start: 0.7245 (mmtm) cc_final: 0.6989 (mmtt) REVERT: D 349 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.5788 (p90) REVERT: D 552 TYR cc_start: 0.7218 (t80) cc_final: 0.6901 (t80) REVERT: E 51 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6637 (pp) REVERT: E 75 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7497 (ptpt) REVERT: E 150 ASP cc_start: 0.8380 (m-30) cc_final: 0.7991 (m-30) REVERT: E 163 ASN cc_start: 0.8245 (t0) cc_final: 0.7778 (t0) REVERT: E 175 PHE cc_start: 0.8574 (t80) cc_final: 0.8273 (t80) REVERT: E 548 ARG cc_start: 0.8056 (tmt-80) cc_final: 0.7768 (tpt90) REVERT: E 551 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6675 (tp40) REVERT: C 339 MET cc_start: 0.3926 (OUTLIER) cc_final: 0.2830 (pp-130) outliers start: 59 outliers final: 42 residues processed: 288 average time/residue: 0.5259 time to fit residues: 170.5334 Evaluate side-chains 293 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 541 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 8 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127877 restraints weight = 17566.047| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.85 r_work: 0.3371 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16523 Z= 0.147 Angle : 0.652 14.775 22538 Z= 0.306 Chirality : 0.047 0.555 2653 Planarity : 0.004 0.039 2718 Dihedral : 7.907 116.154 2596 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.18 % Allowed : 21.21 % Favored : 75.61 % 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: 1.14 (0.19), residues: 1904 helix: 2.71 (0.19), residues: 736 sheet: 0.12 (0.24), residues: 448 loop : -0.92 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 514 TYR 0.040 0.002 TYR D 337 PHE 0.026 0.001 PHE E 175 TRP 0.017 0.001 TRP A 539 HIS 0.003 0.001 HIS C 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (16492) covalent geometry : angle 0.61302 / 0.30 (22459) SS BOND : bond 0.00193 / 0.13 ( 5) SS BOND : angle 0.45681 / 0.21 ( 10) hydrogen bonds : bond 0.03957 / 2.50 ( 841) hydrogen bonds : angle 4.50775 / 3.09 ( 2478) Misc. bond : bond 0.00022 / 0.01 ( 3) link_BETA1-4 : bond 0.00617 / 0.36 ( 10) link_BETA1-4 : angle 1.95731 / 1.32 ( 30) link_NAG-ASN : bond 0.00694 / 0.35 ( 13) link_NAG-ASN : angle 5.08837 / 3.55 ( 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 303 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.7945 (m-30) cc_final: 0.7667 (m-30) REVERT: A 294 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7619 (mm-40) REVERT: D 172 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8339 (tm-30) REVERT: D 218 ASP cc_start: 0.7674 (m-30) cc_final: 0.7319 (m-30) REVERT: D 237 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6258 (p90) REVERT: D 257 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8079 (mm-40) REVERT: D 300 GLU cc_start: 0.6760 (pp20) cc_final: 0.5368 (tt0) REVERT: D 301 LYS cc_start: 0.7287 (mmtm) cc_final: 0.7033 (mmtt) REVERT: D 349 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.5917 (p90) REVERT: D 552 TYR cc_start: 0.7173 (t80) cc_final: 0.6930 (t80) REVERT: E 51 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6697 (pp) REVERT: E 75 LYS cc_start: 0.8000 (mmtp) cc_final: 0.7532 (ptpt) REVERT: E 150 ASP cc_start: 0.8363 (m-30) cc_final: 0.7997 (m-30) REVERT: E 163 ASN cc_start: 0.8169 (t0) cc_final: 0.7759 (t0) REVERT: E 175 PHE cc_start: 0.8601 (t80) cc_final: 0.8232 (t80) REVERT: E 548 ARG cc_start: 0.8022 (tmt-80) cc_final: 0.7448 (tpt90) REVERT: E 551 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6645 (tp40) REVERT: C 339 MET cc_start: 0.3962 (OUTLIER) cc_final: 0.2838 (pp-130) outliers start: 56 outliers final: 44 residues processed: 284 average time/residue: 0.5013 time to fit residues: 160.5744 Evaluate side-chains 292 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 349 PHE Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 541 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 102 optimal weight: 0.0570 chunk 185 optimal weight: 0.0010 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130291 restraints weight = 17641.068| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.86 r_work: 0.3412 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16523 Z= 0.115 Angle : 0.625 13.912 22538 Z= 0.292 Chirality : 0.045 0.511 2653 Planarity : 0.003 0.038 2718 Dihedral : 7.794 116.943 2596 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.78 % Allowed : 21.72 % Favored : 75.50 % 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: 1.20 (0.19), residues: 1904 helix: 2.76 (0.19), residues: 746 sheet: 0.13 (0.24), residues: 452 loop : -0.93 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 514 TYR 0.037 0.001 TYR D 337 PHE 0.027 0.001 PHE E 175 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 0.00257 / 0.11 (16492) covalent geometry : angle 0.58908 / 0.28 (22459) SS BOND : bond 0.00109 / 0.07 ( 5) SS BOND : angle 0.25190 / 0.11 ( 10) hydrogen bonds : bond 0.03716 / 2.36 ( 841) hydrogen bonds : angle 4.45521 / 3.06 ( 2478) Misc. bond : bond 0.00010 / 0.00 ( 3) link_BETA1-4 : bond 0.00635 / 0.37 ( 10) link_BETA1-4 : angle 1.91050 / 1.29 ( 30) link_NAG-ASN : bond 0.00798 / 0.39 ( 13) link_NAG-ASN : angle 4.76798 / 3.34 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5664.21 seconds wall clock time: 97 minutes 27.13 seconds (5847.13 seconds total)