Starting phenix.real_space_refine on Sat Sep 12 05:21:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bl8_16103/09_2026/8bl8_16103.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bl8_16103/09_2026/8bl8_16103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bl8_16103/09_2026/8bl8_16103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bl8_16103/09_2026/8bl8_16103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bl8_16103/09_2026/8bl8_16103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bl8_16103/09_2026/8bl8_16103.map" } resolution = 3.21 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= 0.000 sd= 0.043 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 50 5.16 5 C 9279 2.51 5 N 2181 2.21 5 O 2509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s 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: 14019 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2768 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2761 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 18, 'TRANS': 315} Chain breaks: 1 Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2697 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2756 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 18, 'TRANS': 315} Chain breaks: 1 Chain: "E" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2687 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain breaks: 1 Chain: "F" 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: "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: 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: "N" 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: "O" 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: "A" 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: "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: "C" 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: "D" 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: 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 Time building chain proxies: 2.83, per 1000 atoms: 0.20 Number of scatterers: 14019 At special positions: 0 Unit cell: (96.18, 96.18, 121.37, 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 50 16.00 O 2509 8.00 N 2181 7.00 C 9279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG 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 N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 104 " " NAG B 501 " - " ASN B 104 " " NAG C 501 " - " ASN C 104 " " NAG D 501 " - " ASN D 104 " " NAG E 501 " - " ASN E 104 " " NAG F 1 " - " ASN A 186 " " NAG G 1 " - " ASN A 170 " " NAG H 1 " - " ASN B 186 " " NAG I 1 " - " ASN B 170 " " NAG J 1 " - " ASN C 186 " " NAG K 1 " - " ASN C 170 " " NAG L 1 " - " ASN D 186 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 186 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 508.3 milliseconds 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 42.1% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 98 through 103 removed outlier: 4.190A pdb=" N ASP A 103 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 242 through 264 removed outlier: 4.407A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 3.516A pdb=" N PHE A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 292 Processing helix chain 'A' and resid 303 through 330 Processing helix chain 'A' and resid 444 through 477 removed outlier: 3.649A pdb=" N TYR A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 45 removed outlier: 4.342A pdb=" N ASN B 44 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 4.221A pdb=" N ASP B 103 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 163 through 166 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 270 through 295 Processing helix chain 'B' and resid 303 through 329 removed outlier: 3.504A pdb=" N ILE B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 477 removed outlier: 3.725A pdb=" N TYR B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.240A pdb=" N ASP C 103 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 163 through 166 Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 249 through 264 removed outlier: 3.736A pdb=" N PHE C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 removed outlier: 3.850A pdb=" N VAL C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 327 Processing helix chain 'C' and resid 447 through 476 removed outlier: 4.329A pdb=" N LYS C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 removed outlier: 4.210A pdb=" N ASN D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.245A pdb=" N ASP D 103 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 163 through 166 Processing helix chain 'D' and resid 192 through 199 Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 249 through 262 removed outlier: 3.601A pdb=" N ILE D 261 " --> pdb=" O MET D 257 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 270 through 295 removed outlier: 3.547A pdb=" N ILE D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 330 Processing helix chain 'D' and resid 444 through 476 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 98 through 103 removed outlier: 4.190A pdb=" N ASP E 103 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 192 through 199 Processing helix chain 'E' and resid 242 through 249 Processing helix chain 'E' and resid 249 through 263 Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 270 through 293 removed outlier: 3.606A pdb=" N VAL E 274 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE E 289 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 316 removed outlier: 3.566A pdb=" N VAL E 307 " --> pdb=" O PRO E 303 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR E 308 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE E 309 " --> pdb=" O ILE E 305 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 310 " --> pdb=" O GLY E 306 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 316 " --> pdb=" O CYS E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 477 removed outlier: 4.002A pdb=" N VAL E 448 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.013A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A 154 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.013A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR A 83 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE A 70 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TRP A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR A 68 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ARG A 87 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE A 66 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR A 89 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP A 64 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR A 91 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N SER A 62 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 4.118A pdb=" N SER A 177 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 213 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG A 239 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU A 211 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.945A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL B 154 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.945A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 83 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE B 70 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TRP B 85 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR B 68 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ARG B 87 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 66 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR B 89 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP B 64 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 91 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N SER B 62 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.931A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.931A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 213 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG B 239 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU B 211 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.028A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL C 154 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.028A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL C 79 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL C 73 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 81 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TRP C 85 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL C 67 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG C 87 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL C 65 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR C 89 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE C 63 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR C 91 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL C 61 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.843A pdb=" N SER C 177 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASN C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N MET C 223 " --> pdb=" O ASN C 227 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 213 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG C 239 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU C 211 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.905A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL D 154 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.905A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 79 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL D 73 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR D 81 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TRP D 85 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL D 67 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ARG D 87 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL D 65 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR D 89 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE D 63 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR D 91 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL D 61 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 120 through 122 removed outlier: 4.004A pdb=" N SER D 177 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY D 213 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG D 239 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU D 211 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.036A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL E 154 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.036A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL E 79 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL E 73 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR E 81 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TRP E 85 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL E 67 " --> pdb=" O TRP E 85 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ARG E 87 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL E 65 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR E 89 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE E 63 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR E 91 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL E 61 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 120 through 122 removed outlier: 4.058A pdb=" N SER E 177 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN E 227 " --> pdb=" O MET E 223 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET E 223 " --> pdb=" O ASN E 227 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 213 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG E 239 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU E 211 " --> pdb=" O ARG E 239 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2208 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: 2.28 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4169 1.35 - 1.48: 4046 1.48 - 1.61: 6105 1.61 - 1.74: 1 1.74 - 1.87: 85 Bond restraints: 14406 Sorted by residual: bond pdb=" CB PRO E 268 " pdb=" CG PRO E 268 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" CB CYS A 171 " pdb=" SG CYS A 171 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.10e+00 bond pdb=" N ARG E 31 " pdb=" CA ARG E 31 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N ARG A 31 " pdb=" CA ARG A 31 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N ARG B 31 " pdb=" CA ARG B 31 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 14401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 19160 1.67 - 3.34: 443 3.34 - 5.01: 84 5.01 - 6.68: 6 6.68 - 8.35: 1 Bond angle restraints: 19694 Sorted by residual: angle pdb=" CA PRO E 268 " pdb=" N PRO E 268 " pdb=" CD PRO E 268 " ideal model delta sigma weight residual 112.00 103.65 8.35 1.40e+00 5.10e-01 3.56e+01 angle pdb=" N VAL B 126 " pdb=" CA VAL B 126 " pdb=" C VAL B 126 " ideal model delta sigma weight residual 113.42 108.16 5.26 1.17e+00 7.31e-01 2.02e+01 angle pdb=" N PRO E 268 " pdb=" CD PRO E 268 " pdb=" CG PRO E 268 " ideal model delta sigma weight residual 103.20 97.70 5.50 1.50e+00 4.44e-01 1.34e+01 angle pdb=" N PRO E 268 " pdb=" CA PRO E 268 " pdb=" CB PRO E 268 " ideal model delta sigma weight residual 103.51 100.94 2.57 9.60e-01 1.09e+00 7.14e+00 angle pdb=" N GLY D 263 " pdb=" CA GLY D 263 " pdb=" C GLY D 263 " ideal model delta sigma weight residual 114.67 111.76 2.91 1.10e+00 8.26e-01 6.99e+00 ... (remaining 19689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7989 17.96 - 35.93: 637 35.93 - 53.89: 123 53.89 - 71.85: 19 71.85 - 89.81: 12 Dihedral angle restraints: 8780 sinusoidal: 3829 harmonic: 4951 Sorted by residual: dihedral pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual 93.00 163.24 -70.24 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CA ASN D 163 " pdb=" C ASN D 163 " pdb=" N PHE D 164 " pdb=" CA PHE D 164 " ideal model delta harmonic sigma weight residual 180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ASN C 163 " pdb=" C ASN C 163 " pdb=" N PHE C 164 " pdb=" CA PHE C 164 " ideal model delta harmonic sigma weight residual -180.00 -153.94 -26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 8777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2050 0.071 - 0.142: 297 0.142 - 0.213: 2 0.213 - 0.284: 4 0.284 - 0.355: 2 Chirality restraints: 2355 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 170 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ILE B 254 " pdb=" N ILE B 254 " pdb=" C ILE B 254 " pdb=" CB ILE B 254 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA ILE E 254 " pdb=" N ILE E 254 " pdb=" C ILE E 254 " pdb=" CB ILE E 254 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2352 not shown) Planarity restraints: 2383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 267 " 0.069 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO E 268 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO E 268 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 268 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 267 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 268 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 200 " -0.143 9.50e-02 1.11e+02 6.45e-02 3.35e+00 pdb=" NE ARG C 200 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 200 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 200 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 200 " 0.000 2.00e-02 2.50e+03 ... (remaining 2380 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2554 2.77 - 3.30: 13850 3.30 - 3.84: 23296 3.84 - 4.37: 27058 4.37 - 4.90: 47787 Nonbonded interactions: 114545 Sorted by model distance: nonbonded pdb=" OD2 ASP A 167 " pdb=" NE2 GLN A 169 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG A 273 " pdb=" OD1 ASP A 450 " model vdw 2.246 3.120 nonbonded pdb=" OD1 ASP D 64 " pdb=" N VAL D 65 " model vdw 2.307 3.120 nonbonded pdb=" O ASP B 160 " pdb=" OD1 ASP B 160 " model vdw 2.313 3.040 nonbonded pdb=" OD2 ASP C 260 " pdb=" OH TYR C 457 " model vdw 2.316 3.040 ... (remaining 114540 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 31 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 129 or (resid 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 320 or resid 44 \ 6 through 476 or resid 501)) selection = (chain 'B' and (resid 31 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 129 or (resid 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 320 or resid 44 \ 6 through 476 or resid 501)) selection = (chain 'C' and (resid 31 through 320 or resid 446 through 501)) selection = (chain 'D' and (resid 31 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 129 or (resid 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 320 or resid 44 \ 6 through 501)) selection = (chain 'E' and (resid 31 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 129 or (resid 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 320 or resid 44 \ 6 through 476 or resid 501)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.660 Find NCS groups from input model: 0.420 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 0.163 14436 Z= 0.179 Angle : 0.635 8.350 19779 Z= 0.331 Chirality : 0.046 0.355 2355 Planarity : 0.005 0.100 2368 Dihedral : 13.409 89.814 5563 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.06 % Allowed : 11.55 % Favored : 88.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.21), residues: 1636 helix: 1.91 (0.21), residues: 593 sheet: -0.87 (0.23), residues: 451 loop : -0.87 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 200 TYR 0.012 0.001 TYR E 138 PHE 0.014 0.001 PHE D 264 TRP 0.016 0.001 TRP C 475 HIS 0.002 0.001 HIS D 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (14406) covalent geometry : angle 0.62274 / 0.33 (19694) SS BOND : bond 0.00223 / 0.13 ( 5) SS BOND : angle 1.72062 / 1.06 ( 10) hydrogen bonds : bond 0.14012 / 9.49 ( 707) hydrogen bonds : angle 6.89431 / 4.92 ( 2208) link_BETA1-4 : bond 0.00309 / 0.20 ( 10) link_BETA1-4 : angle 1.91616 / 1.43 ( 30) link_NAG-ASN : bond 0.00345 / 0.25 ( 15) link_NAG-ASN : angle 2.05614 / 1.31 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.9110 (tptt) cc_final: 0.8606 (mmmm) REVERT: A 457 TYR cc_start: 0.8464 (t80) cc_final: 0.8249 (t80) REVERT: B 77 ASN cc_start: 0.8935 (m-40) cc_final: 0.8473 (m110) REVERT: B 78 GLN cc_start: 0.9060 (mm110) cc_final: 0.8857 (mm-40) REVERT: B 89 TYR cc_start: 0.7667 (p90) cc_final: 0.7137 (p90) REVERT: D 152 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8355 (tm-30) REVERT: E 184 ASP cc_start: 0.8367 (m-30) cc_final: 0.8123 (m-30) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.0970 time to fit residues: 34.3142 Evaluate side-chains 196 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 154 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 GLN B 152 GLN C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109736 restraints weight = 18291.475| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.80 r_work: 0.3139 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14436 Z= 0.124 Angle : 0.610 6.507 19779 Z= 0.314 Chirality : 0.045 0.217 2355 Planarity : 0.004 0.048 2368 Dihedral : 6.035 57.341 2357 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.87 % Allowed : 12.06 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.45 (0.21), residues: 1636 helix: 2.22 (0.20), residues: 596 sheet: -0.88 (0.23), residues: 438 loop : -0.66 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 87 TYR 0.019 0.001 TYR E 89 PHE 0.028 0.001 PHE B 264 TRP 0.013 0.001 TRP E 190 HIS 0.002 0.000 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14406) covalent geometry : angle 0.60158 / 0.31 (19694) SS BOND : bond 0.00193 / 0.12 ( 5) SS BOND : angle 1.49671 / 0.91 ( 10) hydrogen bonds : bond 0.04105 / 2.70 ( 707) hydrogen bonds : angle 5.05063 / 3.58 ( 2208) link_BETA1-4 : bond 0.00364 / 0.22 ( 10) link_BETA1-4 : angle 1.16414 / 0.90 ( 30) link_NAG-ASN : bond 0.00430 / 0.32 ( 15) link_NAG-ASN : angle 1.87844 / 1.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.9078 (tptt) cc_final: 0.8609 (mmmm) REVERT: A 284 TYR cc_start: 0.7650 (m-80) cc_final: 0.7440 (m-10) REVERT: B 78 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8888 (mm-40) REVERT: B 80 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7888 (pt) REVERT: B 89 TYR cc_start: 0.7492 (p90) cc_final: 0.6954 (p90) REVERT: B 158 SER cc_start: 0.8776 (p) cc_final: 0.8522 (t) REVERT: C 204 MET cc_start: 0.8232 (ttp) cc_final: 0.7718 (ttm) REVERT: D 80 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8159 (pt) REVERT: D 152 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 169 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8309 (mm110) REVERT: D 444 ARG cc_start: 0.4162 (mpp-170) cc_final: 0.3800 (mpt180) REVERT: E 89 TYR cc_start: 0.7788 (p90) cc_final: 0.7444 (p90) REVERT: E 124 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: E 272 GLU cc_start: 0.7927 (mp0) cc_final: 0.7554 (mt-10) outliers start: 29 outliers final: 14 residues processed: 246 average time/residue: 0.0965 time to fit residues: 36.9726 Evaluate side-chains 222 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 124 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 114 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN B 152 GLN C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106619 restraints weight = 18678.189| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.88 r_work: 0.3077 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14436 Z= 0.160 Angle : 0.586 6.809 19779 Z= 0.300 Chirality : 0.044 0.164 2355 Planarity : 0.004 0.052 2368 Dihedral : 5.960 58.311 2357 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.32 % Allowed : 13.74 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.21), residues: 1636 helix: 2.29 (0.20), residues: 596 sheet: -0.97 (0.23), residues: 442 loop : -0.65 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 87 TYR 0.015 0.001 TYR E 89 PHE 0.016 0.001 PHE B 264 TRP 0.011 0.001 TRP B 475 HIS 0.001 0.000 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (14406) covalent geometry : angle 0.57851 / 0.30 (19694) SS BOND : bond 0.00440 / 0.21 ( 5) SS BOND : angle 1.39224 / 0.87 ( 10) hydrogen bonds : bond 0.03960 / 2.64 ( 707) hydrogen bonds : angle 4.79219 / 3.39 ( 2208) link_BETA1-4 : bond 0.00231 / 0.14 ( 10) link_BETA1-4 : angle 1.36165 / 1.07 ( 30) link_NAG-ASN : bond 0.00284 / 0.20 ( 15) link_NAG-ASN : angle 1.64327 / 1.08 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.8073 (p90) cc_final: 0.7856 (p90) REVERT: A 195 LYS cc_start: 0.9113 (tptt) cc_final: 0.8625 (mmmm) REVERT: A 284 TYR cc_start: 0.7752 (m-80) cc_final: 0.7472 (m-10) REVERT: B 77 ASN cc_start: 0.9018 (m-40) cc_final: 0.8670 (m110) REVERT: B 78 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8880 (mm-40) REVERT: B 80 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7836 (pt) REVERT: B 158 SER cc_start: 0.8726 (p) cc_final: 0.8436 (t) REVERT: C 204 MET cc_start: 0.8216 (ttp) cc_final: 0.7789 (ttm) REVERT: D 80 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8195 (pt) REVERT: D 152 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8525 (tm-30) REVERT: D 444 ARG cc_start: 0.4318 (mpp-170) cc_final: 0.4013 (mpt180) REVERT: E 35 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8515 (tt) REVERT: E 75 GLU cc_start: 0.7937 (mp0) cc_final: 0.7632 (mp0) REVERT: E 80 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8582 (tp) REVERT: E 89 TYR cc_start: 0.7989 (p90) cc_final: 0.7632 (p90) REVERT: E 124 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: E 221 PHE cc_start: 0.8341 (t80) cc_final: 0.8099 (t80) outliers start: 36 outliers final: 18 residues processed: 249 average time/residue: 0.0981 time to fit residues: 37.8795 Evaluate side-chains 226 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 135 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 GLN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108938 restraints weight = 18534.852| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.82 r_work: 0.3113 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14436 Z= 0.115 Angle : 0.544 6.817 19779 Z= 0.277 Chirality : 0.043 0.173 2355 Planarity : 0.004 0.051 2368 Dihedral : 5.714 57.507 2357 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.84 % Allowed : 14.65 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.21), residues: 1636 helix: 2.43 (0.20), residues: 597 sheet: -0.98 (0.23), residues: 446 loop : -0.52 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.012 0.001 TYR E 89 PHE 0.026 0.001 PHE B 264 TRP 0.010 0.001 TRP D 475 HIS 0.002 0.000 HIS B 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (14406) covalent geometry : angle 0.53918 / 0.28 (19694) SS BOND : bond 0.00155 / 0.09 ( 5) SS BOND : angle 1.16179 / 0.71 ( 10) hydrogen bonds : bond 0.03445 / 2.26 ( 707) hydrogen bonds : angle 4.57124 / 3.24 ( 2208) link_BETA1-4 : bond 0.00328 / 0.19 ( 10) link_BETA1-4 : angle 1.12049 / 0.87 ( 30) link_NAG-ASN : bond 0.00303 / 0.22 ( 15) link_NAG-ASN : angle 1.34999 / 0.91 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.9065 (tptt) cc_final: 0.8579 (mmmm) REVERT: A 284 TYR cc_start: 0.7766 (m-80) cc_final: 0.7528 (m-10) REVERT: A 468 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8357 (mt) REVERT: B 77 ASN cc_start: 0.9025 (m-40) cc_final: 0.8591 (m110) REVERT: B 78 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8866 (mm-40) REVERT: B 80 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7799 (pt) REVERT: B 158 SER cc_start: 0.8699 (p) cc_final: 0.8412 (t) REVERT: C 204 MET cc_start: 0.8119 (ttp) cc_final: 0.7656 (ttm) REVERT: D 80 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8152 (pt) REVERT: D 152 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8549 (tm-30) REVERT: D 444 ARG cc_start: 0.4599 (mpp-170) cc_final: 0.4325 (mpt180) REVERT: E 75 GLU cc_start: 0.7924 (mp0) cc_final: 0.7685 (mp0) REVERT: E 80 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8544 (tp) REVERT: E 124 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: E 221 PHE cc_start: 0.8285 (t80) cc_final: 0.8064 (t80) outliers start: 44 outliers final: 25 residues processed: 254 average time/residue: 0.0959 time to fit residues: 38.1145 Evaluate side-chains 234 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 86 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 111 optimal weight: 0.0570 chunk 146 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 109 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.6574 > 50:) chunk 115 optimal weight: 0.0050 chunk 24 optimal weight: 10.0000 overall best weight: 1.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107917 restraints weight = 18527.083| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.85 r_work: 0.3097 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14436 Z= 0.135 Angle : 0.557 7.125 19779 Z= 0.282 Chirality : 0.044 0.269 2355 Planarity : 0.004 0.052 2368 Dihedral : 5.663 57.186 2357 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.16 % Allowed : 15.23 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.21), residues: 1636 helix: 2.50 (0.20), residues: 596 sheet: -1.00 (0.23), residues: 454 loop : -0.53 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.013 0.001 TYR E 89 PHE 0.015 0.001 PHE B 264 TRP 0.010 0.001 TRP D 475 HIS 0.002 0.000 HIS B 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (14406) covalent geometry : angle 0.55143 / 0.28 (19694) SS BOND : bond 0.00148 / 0.08 ( 5) SS BOND : angle 1.23094 / 0.79 ( 10) hydrogen bonds : bond 0.03451 / 2.28 ( 707) hydrogen bonds : angle 4.51885 / 3.20 ( 2208) link_BETA1-4 : bond 0.00272 / 0.15 ( 10) link_BETA1-4 : angle 1.19980 / 0.95 ( 30) link_NAG-ASN : bond 0.00167 / 0.11 ( 15) link_NAG-ASN : angle 1.37518 / 0.93 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 0.502 Fit side-chains REVERT: A 124 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: A 284 TYR cc_start: 0.7814 (m-80) cc_final: 0.7508 (m-10) REVERT: B 77 ASN cc_start: 0.9001 (m-40) cc_final: 0.8591 (m110) REVERT: B 78 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8870 (mm-40) REVERT: B 80 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7865 (pt) REVERT: B 152 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8189 (mp-120) REVERT: B 158 SER cc_start: 0.8719 (p) cc_final: 0.8444 (t) REVERT: B 257 MET cc_start: 0.8039 (mtp) cc_final: 0.7767 (mtp) REVERT: C 64 ASP cc_start: 0.8480 (t0) cc_final: 0.8240 (t0) REVERT: C 103 ASP cc_start: 0.8421 (t0) cc_final: 0.7742 (t0) REVERT: C 204 MET cc_start: 0.8174 (ttp) cc_final: 0.7724 (ttm) REVERT: D 152 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8551 (tm-30) REVERT: D 444 ARG cc_start: 0.4794 (mpp-170) cc_final: 0.4517 (mpt180) REVERT: E 89 TYR cc_start: 0.8111 (p90) cc_final: 0.7675 (p90) REVERT: E 124 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: E 152 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8491 (tm-30) REVERT: E 221 PHE cc_start: 0.8279 (t80) cc_final: 0.8065 (t80) outliers start: 49 outliers final: 29 residues processed: 255 average time/residue: 0.0919 time to fit residues: 36.8835 Evaluate side-chains 228 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 129 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 chunk 111 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN C 78 GLN E 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109429 restraints weight = 18455.756| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.79 r_work: 0.3120 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14436 Z= 0.112 Angle : 0.534 6.768 19779 Z= 0.270 Chirality : 0.043 0.173 2355 Planarity : 0.004 0.052 2368 Dihedral : 5.509 57.310 2357 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.03 % Allowed : 15.94 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.21), residues: 1636 helix: 2.61 (0.20), residues: 596 sheet: -0.97 (0.23), residues: 443 loop : -0.43 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 200 TYR 0.010 0.001 TYR E 89 PHE 0.019 0.001 PHE C 221 TRP 0.009 0.001 TRP C 475 HIS 0.001 0.000 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (14406) covalent geometry : angle 0.52934 / 0.27 (19694) SS BOND : bond 0.00134 / 0.07 ( 5) SS BOND : angle 1.16537 / 0.79 ( 10) hydrogen bonds : bond 0.03246 / 2.13 ( 707) hydrogen bonds : angle 4.42216 / 3.13 ( 2208) link_BETA1-4 : bond 0.00333 / 0.20 ( 10) link_BETA1-4 : angle 1.10087 / 0.87 ( 30) link_NAG-ASN : bond 0.00147 / 0.10 ( 15) link_NAG-ASN : angle 1.27773 / 0.87 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.473 Fit side-chains REVERT: A 124 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: A 208 GLU cc_start: 0.7817 (tt0) cc_final: 0.7004 (tp30) REVERT: A 284 TYR cc_start: 0.7694 (m-80) cc_final: 0.7413 (m-10) REVERT: B 77 ASN cc_start: 0.8981 (m-40) cc_final: 0.8565 (m110) REVERT: B 78 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8863 (mm-40) REVERT: B 80 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7793 (pt) REVERT: B 152 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8199 (mp-120) REVERT: B 158 SER cc_start: 0.8693 (p) cc_final: 0.8416 (t) REVERT: B 257 MET cc_start: 0.8056 (mtp) cc_final: 0.7667 (mtp) REVERT: C 204 MET cc_start: 0.8032 (ttp) cc_final: 0.7586 (ttm) REVERT: D 76 LYS cc_start: 0.8929 (tptm) cc_final: 0.8712 (tptm) REVERT: D 80 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8109 (pt) REVERT: D 152 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8519 (tm-30) REVERT: D 444 ARG cc_start: 0.4535 (mpp-170) cc_final: 0.4325 (mpt180) REVERT: E 89 TYR cc_start: 0.8177 (p90) cc_final: 0.7652 (p90) REVERT: E 124 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: E 152 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8479 (tm-30) REVERT: E 221 PHE cc_start: 0.8241 (t80) cc_final: 0.8029 (t80) outliers start: 47 outliers final: 31 residues processed: 251 average time/residue: 0.0952 time to fit residues: 36.9728 Evaluate side-chains 238 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 88 optimal weight: 0.1980 chunk 132 optimal weight: 0.0670 chunk 104 optimal weight: 3.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110268 restraints weight = 18354.017| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.79 r_work: 0.3155 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14436 Z= 0.107 Angle : 0.531 7.271 19779 Z= 0.268 Chirality : 0.043 0.221 2355 Planarity : 0.004 0.054 2368 Dihedral : 5.390 56.544 2357 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.65 % Allowed : 16.58 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.22), residues: 1636 helix: 2.71 (0.20), residues: 595 sheet: -0.96 (0.23), residues: 454 loop : -0.40 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 200 TYR 0.010 0.001 TYR E 89 PHE 0.020 0.001 PHE C 221 TRP 0.009 0.001 TRP C 475 HIS 0.002 0.000 HIS C 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14406) covalent geometry : angle 0.52617 / 0.27 (19694) SS BOND : bond 0.00142 / 0.07 ( 5) SS BOND : angle 1.03160 / 0.69 ( 10) hydrogen bonds : bond 0.03163 / 2.07 ( 707) hydrogen bonds : angle 4.34648 / 3.09 ( 2208) link_BETA1-4 : bond 0.00309 / 0.18 ( 10) link_BETA1-4 : angle 1.10589 / 0.87 ( 30) link_NAG-ASN : bond 0.00152 / 0.11 ( 15) link_NAG-ASN : angle 1.26270 / 0.86 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8648 (t0) cc_final: 0.8170 (t0) REVERT: A 124 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: A 208 GLU cc_start: 0.7769 (tt0) cc_final: 0.7223 (tp30) REVERT: A 284 TYR cc_start: 0.7674 (m-80) cc_final: 0.7400 (m-10) REVERT: B 77 ASN cc_start: 0.9014 (m-40) cc_final: 0.8604 (m110) REVERT: B 78 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8879 (mm-40) REVERT: B 80 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7723 (pt) REVERT: B 152 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8185 (mp-120) REVERT: B 158 SER cc_start: 0.8683 (p) cc_final: 0.8436 (t) REVERT: B 257 MET cc_start: 0.8025 (mtp) cc_final: 0.7568 (mtp) REVERT: D 76 LYS cc_start: 0.8898 (tptm) cc_final: 0.8686 (tptm) REVERT: D 80 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8076 (pt) REVERT: D 152 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D 313 MET cc_start: 0.8246 (tpp) cc_final: 0.7852 (tpp) REVERT: D 451 LYS cc_start: 0.8209 (mmtp) cc_final: 0.7323 (tttm) REVERT: E 89 TYR cc_start: 0.8187 (p90) cc_final: 0.7636 (p90) REVERT: E 152 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8235 (tm-30) REVERT: E 221 PHE cc_start: 0.8138 (t80) cc_final: 0.7923 (t80) outliers start: 41 outliers final: 32 residues processed: 234 average time/residue: 0.0941 time to fit residues: 34.4893 Evaluate side-chains 245 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106637 restraints weight = 18636.715| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.81 r_work: 0.3087 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14436 Z= 0.155 Angle : 0.556 6.389 19779 Z= 0.281 Chirality : 0.044 0.213 2355 Planarity : 0.004 0.051 2368 Dihedral : 5.537 57.097 2357 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.77 % Allowed : 16.58 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.22), residues: 1636 helix: 2.70 (0.20), residues: 596 sheet: -0.97 (0.23), residues: 454 loop : -0.43 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.014 0.001 TYR E 89 PHE 0.021 0.001 PHE C 221 TRP 0.021 0.001 TRP E 472 HIS 0.001 0.000 HIS C 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (14406) covalent geometry : angle 0.55056 / 0.28 (19694) SS BOND : bond 0.00183 / 0.09 ( 5) SS BOND : angle 1.36997 / 0.92 ( 10) hydrogen bonds : bond 0.03370 / 2.23 ( 707) hydrogen bonds : angle 4.39377 / 3.12 ( 2208) link_BETA1-4 : bond 0.00204 / 0.13 ( 10) link_BETA1-4 : angle 1.20359 / 0.96 ( 30) link_NAG-ASN : bond 0.00256 / 0.18 ( 15) link_NAG-ASN : angle 1.32818 / 0.88 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.509 Fit side-chains REVERT: A 74 ASP cc_start: 0.8705 (t0) cc_final: 0.8188 (t0) REVERT: A 76 LYS cc_start: 0.8815 (tptp) cc_final: 0.8600 (tptp) REVERT: A 124 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: A 208 GLU cc_start: 0.7708 (tt0) cc_final: 0.7184 (tp30) REVERT: A 259 MET cc_start: 0.8332 (tpp) cc_final: 0.8093 (tpp) REVERT: A 280 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 284 TYR cc_start: 0.7638 (m-80) cc_final: 0.7315 (m-10) REVERT: B 77 ASN cc_start: 0.9036 (m-40) cc_final: 0.8700 (m110) REVERT: B 78 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8858 (mm-40) REVERT: B 80 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7786 (pt) REVERT: B 152 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8214 (mp-120) REVERT: B 158 SER cc_start: 0.8724 (p) cc_final: 0.8518 (t) REVERT: B 257 MET cc_start: 0.8047 (mtp) cc_final: 0.7549 (mtp) REVERT: C 204 MET cc_start: 0.8170 (ttp) cc_final: 0.7747 (ttm) REVERT: D 80 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8171 (pt) REVERT: D 152 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8479 (tm-30) REVERT: D 313 MET cc_start: 0.8343 (tpp) cc_final: 0.7951 (tpp) REVERT: D 451 LYS cc_start: 0.8179 (mmtp) cc_final: 0.7384 (tttm) REVERT: E 89 TYR cc_start: 0.8218 (p90) cc_final: 0.7665 (p90) REVERT: E 152 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8561 (tm-30) REVERT: E 221 PHE cc_start: 0.8162 (t80) cc_final: 0.7936 (t80) outliers start: 43 outliers final: 34 residues processed: 234 average time/residue: 0.0945 time to fit residues: 34.7690 Evaluate side-chains 235 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 72 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 GLN C 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108329 restraints weight = 18581.223| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.80 r_work: 0.3112 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14436 Z= 0.115 Angle : 0.539 6.534 19779 Z= 0.273 Chirality : 0.044 0.210 2355 Planarity : 0.004 0.050 2368 Dihedral : 5.417 56.530 2357 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.97 % Allowed : 16.52 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.22), residues: 1636 helix: 2.76 (0.20), residues: 596 sheet: -0.96 (0.24), residues: 441 loop : -0.39 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 200 TYR 0.011 0.001 TYR E 89 PHE 0.021 0.001 PHE C 221 TRP 0.016 0.001 TRP E 472 HIS 0.001 0.000 HIS C 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14406) covalent geometry : angle 0.53480 / 0.27 (19694) SS BOND : bond 0.00129 / 0.07 ( 5) SS BOND : angle 1.00586 / 0.70 ( 10) hydrogen bonds : bond 0.03170 / 2.08 ( 707) hydrogen bonds : angle 4.32807 / 3.08 ( 2208) link_BETA1-4 : bond 0.00295 / 0.17 ( 10) link_BETA1-4 : angle 1.08943 / 0.86 ( 30) link_NAG-ASN : bond 0.00200 / 0.15 ( 15) link_NAG-ASN : angle 1.30105 / 0.89 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8686 (t0) cc_final: 0.8162 (t0) REVERT: A 124 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: A 208 GLU cc_start: 0.7743 (tt0) cc_final: 0.7221 (tp30) REVERT: A 259 MET cc_start: 0.8302 (tpp) cc_final: 0.8070 (tpp) REVERT: A 280 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8105 (tt) REVERT: A 284 TYR cc_start: 0.7628 (m-80) cc_final: 0.7307 (m-10) REVERT: B 77 ASN cc_start: 0.9041 (m-40) cc_final: 0.8617 (m110) REVERT: B 78 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8870 (mm-40) REVERT: B 80 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7715 (pt) REVERT: B 152 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8192 (mp-120) REVERT: B 257 MET cc_start: 0.7981 (mtp) cc_final: 0.7487 (mtp) REVERT: B 288 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7234 (mp) REVERT: B 449 LEU cc_start: 0.7568 (mp) cc_final: 0.7365 (mp) REVERT: D 80 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8099 (pt) REVERT: D 152 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8479 (tm-30) REVERT: D 451 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7360 (tttm) REVERT: E 89 TYR cc_start: 0.8197 (p90) cc_final: 0.7685 (p90) REVERT: E 152 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8342 (tm-30) REVERT: E 221 PHE cc_start: 0.8104 (t80) cc_final: 0.7881 (t80) outliers start: 46 outliers final: 32 residues processed: 241 average time/residue: 0.0921 time to fit residues: 35.2125 Evaluate side-chains 236 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 5 optimal weight: 3.9990 chunk 146 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104271 restraints weight = 18650.155| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.19 r_work: 0.3064 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14436 Z= 0.120 Angle : 0.541 6.540 19779 Z= 0.273 Chirality : 0.044 0.197 2355 Planarity : 0.004 0.050 2368 Dihedral : 5.378 56.532 2357 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.52 % Allowed : 17.16 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.22), residues: 1636 helix: 2.77 (0.20), residues: 596 sheet: -0.95 (0.24), residues: 441 loop : -0.37 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 200 TYR 0.012 0.001 TYR E 89 PHE 0.022 0.001 PHE C 221 TRP 0.015 0.001 TRP E 472 HIS 0.001 0.000 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (14406) covalent geometry : angle 0.53619 / 0.27 (19694) SS BOND : bond 0.00138 / 0.07 ( 5) SS BOND : angle 1.10155 / 0.74 ( 10) hydrogen bonds : bond 0.03180 / 2.08 ( 707) hydrogen bonds : angle 4.31176 / 3.06 ( 2208) link_BETA1-4 : bond 0.00262 / 0.16 ( 10) link_BETA1-4 : angle 1.14290 / 0.91 ( 30) link_NAG-ASN : bond 0.00222 / 0.16 ( 15) link_NAG-ASN : angle 1.26370 / 0.85 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8712 (t0) cc_final: 0.8178 (t0) REVERT: A 124 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: A 208 GLU cc_start: 0.7873 (tt0) cc_final: 0.7291 (tp30) REVERT: A 259 MET cc_start: 0.8242 (tpp) cc_final: 0.8009 (tpp) REVERT: A 280 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8064 (tt) REVERT: A 284 TYR cc_start: 0.7626 (m-80) cc_final: 0.7307 (m-10) REVERT: B 152 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8230 (mp-120) REVERT: B 257 MET cc_start: 0.8047 (mtp) cc_final: 0.7554 (mtp) REVERT: B 288 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7150 (mp) REVERT: C 204 MET cc_start: 0.8123 (ttp) cc_final: 0.7689 (mtp) REVERT: D 72 ASN cc_start: 0.8478 (t0) cc_final: 0.8169 (t0) REVERT: D 80 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8102 (pt) REVERT: D 152 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8537 (tm-30) REVERT: D 451 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7336 (tttm) REVERT: E 89 TYR cc_start: 0.8300 (p90) cc_final: 0.7751 (p90) REVERT: E 138 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: E 152 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8403 (tm-30) REVERT: E 221 PHE cc_start: 0.8112 (t80) cc_final: 0.7880 (t80) outliers start: 39 outliers final: 33 residues processed: 232 average time/residue: 0.0989 time to fit residues: 35.6886 Evaluate side-chains 238 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 160 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN C 78 GLN C 476 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105580 restraints weight = 18651.802| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.85 r_work: 0.3072 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14436 Z= 0.179 Angle : 0.584 6.482 19779 Z= 0.296 Chirality : 0.045 0.212 2355 Planarity : 0.004 0.052 2368 Dihedral : 5.579 57.282 2357 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.77 % Allowed : 17.10 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.22), residues: 1636 helix: 2.74 (0.20), residues: 596 sheet: -0.99 (0.23), residues: 454 loop : -0.43 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 200 TYR 0.015 0.001 TYR E 89 PHE 0.023 0.001 PHE C 221 TRP 0.019 0.001 TRP C 472 HIS 0.002 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (14406) covalent geometry : angle 0.57917 / 0.30 (19694) SS BOND : bond 0.00179 / 0.10 ( 5) SS BOND : angle 1.39860 / 0.96 ( 10) hydrogen bonds : bond 0.03437 / 2.27 ( 707) hydrogen bonds : angle 4.39299 / 3.12 ( 2208) link_BETA1-4 : bond 0.00194 / 0.13 ( 10) link_BETA1-4 : angle 1.22897 / 0.98 ( 30) link_NAG-ASN : bond 0.00303 / 0.22 ( 15) link_NAG-ASN : angle 1.35437 / 0.89 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3097.71 seconds wall clock time: 53 minutes 55.44 seconds (3235.44 seconds total)