Starting phenix.real_space_refine on Fri Jul 3 16:22:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgb_50391/07_2026/9fgb_50391.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgb_50391/07_2026/9fgb_50391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fgb_50391/07_2026/9fgb_50391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgb_50391/07_2026/9fgb_50391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fgb_50391/07_2026/9fgb_50391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgb_50391/07_2026/9fgb_50391.map" } resolution = 3.8 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= 0.019 sd= 0.089 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 82 5.16 5 C 9695 2.51 5 N 2430 2.21 5 O 2767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14977 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2793 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 330} Chain breaks: 1 Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2716 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 315} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2720 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2672 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "E" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2701 Classifications: {'peptide': 329} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Chain: "a" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "b" 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 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 Time building chain proxies: 2.61, per 1000 atoms: 0.17 Number of scatterers: 14977 At special positions: 0 Unit cell: (99.6389, 111.361, 137.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 3 15.00 O 2767 8.00 N 2430 7.00 C 9695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS F 429 " - pdb=" SG CYS F 502 " 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 ALPHA1-2 " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " ALPHA1-3 " BMA G 3 " - " MAN G 6 " " MAN G 4 " - " MAN G 5 " " BMA H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 5 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 10 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 8 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG C 501 " - " ASN C 208 " " NAG G 1 " - " ASN B 149 " " NAG H 1 " - " ASN E 149 " " NAG a 1 " - " ASN A 111 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 111 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 469.2 milliseconds 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 38.8% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.548A pdb=" N THR A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.438A pdb=" N ASP A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.709A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 251 through 276 Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.771A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 416 removed outlier: 3.870A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 11 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.528A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 237 removed outlier: 3.616A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.650A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 308 removed outlier: 3.542A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 446 removed outlier: 3.929A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.590A pdb=" N MET C 102 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 240 through 252 Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 261 through 282 removed outlier: 3.537A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 322 removed outlier: 3.537A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 435 removed outlier: 3.793A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 14 through 23 removed outlier: 4.400A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.628A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.427A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.718A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.540A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 removed outlier: 3.520A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 417 removed outlier: 3.940A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.722A pdb=" N ASN D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.597A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 272 Processing helix chain 'E' and resid 279 through 308 Processing helix chain 'E' and resid 421 through 447 removed outlier: 3.697A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'F' and resid 468 through 471 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 513 through 517 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86 removed outlier: 4.476A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP A 63 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE A 50 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N PHE A 65 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR A 48 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ARG A 67 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE A 46 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER A 69 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASP A 44 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N LYS A 71 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N LYS A 42 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 7.075A pdb=" N ASP A 63 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE A 50 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N PHE A 65 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR A 48 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ARG A 67 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE A 46 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER A 69 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASP A 44 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N LYS A 71 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N LYS A 42 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.347A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.348A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 7.000A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.231A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 95 through 98 removed outlier: 3.625A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 118 " --> pdb=" O ASP C 148 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU C 150 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER C 116 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 98 removed outlier: 3.625A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU C 71 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS C 184 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET C 57 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N SER C 186 " --> pdb=" O MET C 57 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N VAL C 59 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N VAL C 188 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 12.178A pdb=" N SER C 61 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N VAL C 190 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 13.771A pdb=" N GLY C 63 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.687A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.687A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.590A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP D 63 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE D 50 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N PHE D 65 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR D 48 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG D 67 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE D 46 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER D 69 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP D 44 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LYS D 71 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LYS D 42 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.949A pdb=" N ASP D 63 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE D 50 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N PHE D 65 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR D 48 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG D 67 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE D 46 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER D 69 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP D 44 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LYS D 71 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LYS D 42 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.228A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.437A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.942A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.171A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.171A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR E 205 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN E 197 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG E 207 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER E 195 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER E 209 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU E 193 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER E 211 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS E 191 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG E 213 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.773A pdb=" N MET F 441 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA F 457 " --> pdb=" O MET F 441 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP F 443 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 13 819 hydrogen bonds defined for protein. 2301 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: 2.57 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2425 1.32 - 1.45: 4464 1.45 - 1.57: 8320 1.57 - 1.69: 4 1.69 - 1.81: 141 Bond restraints: 15354 Sorted by residual: bond pdb=" O4 PIO A 501 " pdb=" P4 PIO A 501 " ideal model delta sigma weight residual 1.710 1.625 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" O5 PIO A 501 " pdb=" P5 PIO A 501 " ideal model delta sigma weight residual 1.699 1.627 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C5 PIO A 501 " pdb=" O5 PIO A 501 " ideal model delta sigma weight residual 1.388 1.443 -0.055 2.00e-02 2.50e+03 7.61e+00 bond pdb=" O13 PIO A 501 " pdb=" P1 PIO A 501 " ideal model delta sigma weight residual 1.651 1.597 0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" C4 PIO A 501 " pdb=" O4 PIO A 501 " ideal model delta sigma weight residual 1.389 1.441 -0.052 2.00e-02 2.50e+03 6.89e+00 ... (remaining 15349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 19701 1.19 - 2.38: 895 2.38 - 3.58: 236 3.58 - 4.77: 24 4.77 - 5.96: 15 Bond angle restraints: 20871 Sorted by residual: angle pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 113.00 109.54 3.46 1.30e+00 5.92e-01 7.08e+00 angle pdb=" CA TYR B 299 " pdb=" CB TYR B 299 " pdb=" CG TYR B 299 " ideal model delta sigma weight residual 113.90 109.31 4.59 1.80e+00 3.09e-01 6.50e+00 angle pdb=" C VAL F 427 " pdb=" N SER F 428 " pdb=" CA SER F 428 " ideal model delta sigma weight residual 123.05 118.59 4.46 1.79e+00 3.12e-01 6.22e+00 angle pdb=" N ASP B 282 " pdb=" CA ASP B 282 " pdb=" C ASP B 282 " ideal model delta sigma weight residual 111.69 108.71 2.98 1.23e+00 6.61e-01 5.87e+00 angle pdb=" C LEU B 210 " pdb=" N SER B 211 " pdb=" CA SER B 211 " ideal model delta sigma weight residual 122.73 119.05 3.68 1.62e+00 3.81e-01 5.15e+00 ... (remaining 20866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 9122 21.11 - 42.21: 208 42.21 - 63.32: 18 63.32 - 84.43: 29 84.43 - 105.53: 17 Dihedral angle restraints: 9394 sinusoidal: 4134 harmonic: 5260 Sorted by residual: dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.82 105.53 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.44 105.15 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.25 104.96 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 9391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.930: 2448 0.930 - 1.860: 0 1.860 - 2.789: 0 2.789 - 3.719: 0 3.719 - 4.649: 2 Chirality restraints: 2450 Sorted by residual: chirality pdb=" C1 MAN a 6 " pdb=" O2 MAN a 5 " pdb=" C2 MAN a 6 " pdb=" O5 MAN a 6 " both_signs ideal model delta sigma weight residual False 2.40 -2.25 4.65 2.00e-02 2.50e+03 5.40e+04 chirality pdb=" C1 MAN a 5 " pdb=" O2 MAN a 4 " pdb=" C2 MAN a 5 " pdb=" O5 MAN a 5 " both_signs ideal model delta sigma weight residual False 2.40 -2.25 4.65 2.00e-02 2.50e+03 5.40e+04 chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN D 111 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2447 not shown) Planarity restraints: 2539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 205 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C SER A 205 " 0.055 2.00e-02 2.50e+03 pdb=" O SER A 205 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 206 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 396 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C SER D 396 " 0.052 2.00e-02 2.50e+03 pdb=" O SER D 396 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG D 397 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 300 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C ALA A 300 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 300 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 301 " 0.017 2.00e-02 2.50e+03 ... (remaining 2536 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1872 2.75 - 3.29: 13800 3.29 - 3.83: 24855 3.83 - 4.36: 29756 4.36 - 4.90: 51397 Nonbonded interactions: 121680 Sorted by model distance: nonbonded pdb=" NH2 ARG D 274 " pdb=" OD2 ASP D 287 " model vdw 2.214 3.120 nonbonded pdb=" O3 MAN a 5 " pdb=" O2 MAN a 6 " model vdw 2.220 3.040 nonbonded pdb=" O PHE E 221 " pdb=" OG1 THR E 225 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR A 122 " pdb=" OD1 ASP A 124 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 267 " pdb=" OH TYR A 294 " model vdw 2.237 3.040 ... (remaining 121675 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 13 through 312 or resid 389 through 418)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 10 through 308 or resid 420 through 447)) selection = (chain 'E' and resid 10 through 447) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'b' selection = chain 'e' } 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 group one per residue 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: 0.330 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: 12.370 Find NCS groups from input model: 0.260 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 0.085 15392 Z= 0.213 Angle : 0.624 5.959 20979 Z= 0.326 Chirality : 0.140 4.649 2450 Planarity : 0.005 0.032 2532 Dihedral : 11.346 105.532 5992 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.56 % Allowed : 2.57 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % 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: 0.89 (0.21), residues: 1761 helix: 0.87 (0.21), residues: 580 sheet: 0.73 (0.25), residues: 422 loop : 0.47 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 250 TYR 0.025 0.001 TYR B 299 PHE 0.015 0.001 PHE C 255 TRP 0.026 0.002 TRP B 67 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (15354) covalent geometry : angle 0.61745 / 0.33 (20871) SS BOND : bond 0.00208 / 0.11 ( 6) SS BOND : angle 0.88852 / 0.55 ( 12) hydrogen bonds : bond 0.12419 / 8.12 ( 728) hydrogen bonds : angle 5.95582 / 4.11 ( 2301) link_ALPHA1-2 : bond 0.00203 / 0.10 ( 3) link_ALPHA1-2 : angle 1.25627 / 0.75 ( 9) link_ALPHA1-3 : bond 0.00393 / 0.17 ( 7) link_ALPHA1-3 : angle 1.29787 / 0.79 ( 21) link_ALPHA1-6 : bond 0.00238 / 0.13 ( 5) link_ALPHA1-6 : angle 1.18494 / 0.63 ( 15) link_BETA1-4 : bond 0.00472 / 0.25 ( 10) link_BETA1-4 : angle 1.38808 / 0.85 ( 30) link_NAG-ASN : bond 0.00239 / 0.16 ( 7) link_NAG-ASN : angle 1.73145 / 1.13 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 237 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8533 (t) REVERT: B 115 MET cc_start: 0.8155 (ptm) cc_final: 0.7782 (ptt) REVERT: B 153 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 282 ASP cc_start: 0.8534 (m-30) cc_final: 0.8321 (m-30) REVERT: C 252 TRP cc_start: 0.8758 (m-10) cc_final: 0.8421 (m-10) REVERT: D 266 MET cc_start: 0.9151 (mmm) cc_final: 0.8830 (mmt) REVERT: D 286 MET cc_start: 0.8300 (ttp) cc_final: 0.8071 (ttm) REVERT: D 288 TRP cc_start: 0.7115 (m100) cc_final: 0.6722 (m-10) outliers start: 9 outliers final: 2 residues processed: 245 average time/residue: 0.1158 time to fit residues: 41.4431 Evaluate side-chains 131 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain D residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS B 41 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS C 80 GLN C 122 HIS C 128 ASN C 163 HIS F 6 GLN F 460 GLN ** F 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055099 restraints weight = 62394.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056696 restraints weight = 34073.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.057793 restraints weight = 23526.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.058437 restraints weight = 18582.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058951 restraints weight = 16130.915| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15392 Z= 0.149 Angle : 0.591 7.935 20979 Z= 0.300 Chirality : 0.043 0.231 2450 Planarity : 0.004 0.049 2532 Dihedral : 10.741 114.081 2650 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.13 % Allowed : 7.34 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1761 helix: 1.96 (0.21), residues: 576 sheet: 0.73 (0.25), residues: 428 loop : 0.55 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 445 TYR 0.023 0.001 TYR B 299 PHE 0.027 0.001 PHE A 298 TRP 0.011 0.001 TRP B 67 HIS 0.016 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (15354) covalent geometry : angle 0.57892 / 0.30 (20871) SS BOND : bond 0.00191 / 0.12 ( 6) SS BOND : angle 0.70106 / 0.43 ( 12) hydrogen bonds : bond 0.04117 / 2.72 ( 728) hydrogen bonds : angle 4.67494 / 3.25 ( 2301) link_ALPHA1-2 : bond 0.00702 / 0.35 ( 3) link_ALPHA1-2 : angle 2.82380 / 1.43 ( 9) link_ALPHA1-3 : bond 0.00771 / 0.43 ( 7) link_ALPHA1-3 : angle 1.84435 / 1.12 ( 21) link_ALPHA1-6 : bond 0.00539 / 0.31 ( 5) link_ALPHA1-6 : angle 1.64801 / 0.94 ( 15) link_BETA1-4 : bond 0.00342 / 0.19 ( 10) link_BETA1-4 : angle 1.81659 / 1.20 ( 30) link_NAG-ASN : bond 0.00166 / 0.10 ( 7) link_NAG-ASN : angle 1.32213 / 0.82 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9095 (mmm) cc_final: 0.8770 (tpp) REVERT: B 55 MET cc_start: 0.9244 (mmm) cc_final: 0.8528 (mmm) REVERT: B 229 SER cc_start: 0.9660 (m) cc_final: 0.9396 (p) REVERT: B 282 ASP cc_start: 0.8596 (m-30) cc_final: 0.8385 (m-30) REVERT: B 283 MET cc_start: 0.9153 (mmt) cc_final: 0.8941 (tpp) REVERT: C 70 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8523 (mmm) REVERT: C 168 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: C 223 MET cc_start: 0.8745 (mmm) cc_final: 0.8260 (mmt) REVERT: C 252 TRP cc_start: 0.8789 (m-10) cc_final: 0.8451 (m-10) REVERT: D 90 MET cc_start: 0.8469 (mmt) cc_final: 0.8198 (mmm) REVERT: D 213 MET cc_start: 0.8901 (mmm) cc_final: 0.8600 (mmm) REVERT: D 266 MET cc_start: 0.9248 (mmm) cc_final: 0.8859 (mmt) REVERT: D 288 TRP cc_start: 0.7230 (m100) cc_final: 0.6866 (m-10) REVERT: F 441 MET cc_start: 0.6616 (mtp) cc_final: 0.6230 (mtp) REVERT: F 446 GLN cc_start: 0.8996 (tp40) cc_final: 0.8554 (tp40) REVERT: F 500 TYR cc_start: 0.8611 (m-80) cc_final: 0.7443 (m-80) outliers start: 18 outliers final: 9 residues processed: 145 average time/residue: 0.0942 time to fit residues: 21.2952 Evaluate side-chains 138 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 486 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 59 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 0.0060 chunk 175 optimal weight: 50.0000 chunk 159 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 5.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 110 HIS E 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.067384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052219 restraints weight = 64857.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053662 restraints weight = 36650.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054656 restraints weight = 25921.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055291 restraints weight = 20847.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055660 restraints weight = 18154.261| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15392 Z= 0.270 Angle : 0.661 7.934 20979 Z= 0.331 Chirality : 0.044 0.193 2450 Planarity : 0.004 0.053 2532 Dihedral : 9.839 109.342 2647 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.44 % Allowed : 7.78 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1761 helix: 2.20 (0.21), residues: 574 sheet: 0.59 (0.24), residues: 430 loop : 0.53 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 29 TYR 0.027 0.002 TYR B 299 PHE 0.029 0.002 PHE A 298 TRP 0.012 0.001 TRP B 67 HIS 0.006 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.27 (15354) covalent geometry : angle 0.65059 / 0.33 (20871) SS BOND : bond 0.00190 / 0.10 ( 6) SS BOND : angle 0.62236 / 0.39 ( 12) hydrogen bonds : bond 0.04237 / 2.78 ( 728) hydrogen bonds : angle 4.56482 / 3.18 ( 2301) link_ALPHA1-2 : bond 0.00593 / 0.29 ( 3) link_ALPHA1-2 : angle 2.51514 / 1.35 ( 9) link_ALPHA1-3 : bond 0.00570 / 0.35 ( 7) link_ALPHA1-3 : angle 2.01397 / 1.24 ( 21) link_ALPHA1-6 : bond 0.00505 / 0.31 ( 5) link_ALPHA1-6 : angle 1.86385 / 1.03 ( 15) link_BETA1-4 : bond 0.00438 / 0.26 ( 10) link_BETA1-4 : angle 1.68465 / 1.14 ( 30) link_NAG-ASN : bond 0.00336 / 0.16 ( 7) link_NAG-ASN : angle 1.71383 / 1.07 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.8925 (mmm) cc_final: 0.8357 (mmm) REVERT: B 55 MET cc_start: 0.9211 (mmm) cc_final: 0.8697 (mmm) REVERT: B 61 MET cc_start: 0.9205 (ptp) cc_final: 0.8957 (ptp) REVERT: B 286 MET cc_start: 0.8347 (tpp) cc_final: 0.8134 (tmm) REVERT: C 70 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8473 (mmm) REVERT: C 247 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9271 (tt) REVERT: C 252 TRP cc_start: 0.8913 (m-10) cc_final: 0.8610 (m-10) REVERT: C 313 GLU cc_start: 0.8216 (tp30) cc_final: 0.7989 (tp30) REVERT: D 266 MET cc_start: 0.9234 (mmm) cc_final: 0.8870 (mmt) REVERT: D 288 TRP cc_start: 0.7215 (m100) cc_final: 0.7000 (m-10) REVERT: E 227 MET cc_start: 0.8585 (tmm) cc_final: 0.8304 (tmm) REVERT: E 272 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8883 (pp) REVERT: E 443 TRP cc_start: 0.7043 (m100) cc_final: 0.6722 (t60) REVERT: F 441 MET cc_start: 0.6853 (mtp) cc_final: 0.6502 (mtp) REVERT: F 500 TYR cc_start: 0.8593 (m-80) cc_final: 0.7515 (m-80) outliers start: 23 outliers final: 13 residues processed: 134 average time/residue: 0.0997 time to fit residues: 20.5792 Evaluate side-chains 129 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 486 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052813 restraints weight = 63826.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054335 restraints weight = 35125.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055380 restraints weight = 24446.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.055996 restraints weight = 19460.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056445 restraints weight = 16946.748| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15392 Z= 0.157 Angle : 0.561 8.130 20979 Z= 0.281 Chirality : 0.042 0.208 2450 Planarity : 0.004 0.070 2532 Dihedral : 9.312 108.540 2647 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.51 % Allowed : 9.16 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.20), residues: 1761 helix: 2.32 (0.21), residues: 574 sheet: 0.60 (0.25), residues: 422 loop : 0.50 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 445 TYR 0.024 0.001 TYR B 299 PHE 0.023 0.001 PHE A 298 TRP 0.007 0.001 TRP D 70 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (15354) covalent geometry : angle 0.54876 / 0.28 (20871) SS BOND : bond 0.00156 / 0.08 ( 6) SS BOND : angle 0.52650 / 0.31 ( 12) hydrogen bonds : bond 0.03795 / 2.51 ( 728) hydrogen bonds : angle 4.28972 / 3.00 ( 2301) link_ALPHA1-2 : bond 0.01020 / 0.49 ( 3) link_ALPHA1-2 : angle 2.57687 / 1.36 ( 9) link_ALPHA1-3 : bond 0.00779 / 0.45 ( 7) link_ALPHA1-3 : angle 1.95732 / 1.19 ( 21) link_ALPHA1-6 : bond 0.00615 / 0.36 ( 5) link_ALPHA1-6 : angle 1.78403 / 1.00 ( 15) link_BETA1-4 : bond 0.00307 / 0.17 ( 10) link_BETA1-4 : angle 1.58518 / 1.05 ( 30) link_NAG-ASN : bond 0.00131 / 0.07 ( 7) link_NAG-ASN : angle 1.45288 / 0.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8860 (tpp) cc_final: 0.8541 (mmm) REVERT: B 55 MET cc_start: 0.9243 (mmm) cc_final: 0.8783 (mmm) REVERT: B 61 MET cc_start: 0.9264 (ptp) cc_final: 0.8945 (ptp) REVERT: C 70 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8343 (mmm) REVERT: C 223 MET cc_start: 0.8689 (mmm) cc_final: 0.8329 (mmt) REVERT: C 247 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9275 (tt) REVERT: C 252 TRP cc_start: 0.8831 (m-10) cc_final: 0.8426 (m-10) REVERT: C 313 GLU cc_start: 0.8254 (tp30) cc_final: 0.7934 (tp30) REVERT: D 213 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8839 (mmm) REVERT: D 229 GLN cc_start: 0.8634 (tp40) cc_final: 0.8429 (tp40) REVERT: D 266 MET cc_start: 0.9183 (mmm) cc_final: 0.8845 (mmt) REVERT: D 286 MET cc_start: 0.8294 (tpp) cc_final: 0.8089 (tpp) REVERT: D 288 TRP cc_start: 0.7325 (m100) cc_final: 0.6816 (m-10) REVERT: E 227 MET cc_start: 0.8633 (tmm) cc_final: 0.8321 (tmm) REVERT: E 272 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8946 (pp) REVERT: E 443 TRP cc_start: 0.6934 (m100) cc_final: 0.6577 (t60) REVERT: F 441 MET cc_start: 0.6946 (mtp) cc_final: 0.6607 (mtp) outliers start: 24 outliers final: 13 residues processed: 137 average time/residue: 0.0889 time to fit residues: 19.0801 Evaluate side-chains 131 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 486 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 160 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 175 optimal weight: 40.0000 chunk 134 optimal weight: 9.9990 chunk 90 optimal weight: 0.0050 chunk 12 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052670 restraints weight = 64463.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054127 restraints weight = 36337.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055114 restraints weight = 25679.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055692 restraints weight = 20662.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056125 restraints weight = 18138.227| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15392 Z= 0.168 Angle : 0.568 8.449 20979 Z= 0.281 Chirality : 0.042 0.222 2450 Planarity : 0.004 0.053 2532 Dihedral : 8.748 106.314 2647 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.69 % Allowed : 9.54 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.20), residues: 1761 helix: 2.42 (0.21), residues: 572 sheet: 0.54 (0.25), residues: 420 loop : 0.45 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 445 TYR 0.023 0.001 TYR B 299 PHE 0.026 0.001 PHE A 298 TRP 0.007 0.001 TRP A 70 HIS 0.003 0.001 HIS E 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (15354) covalent geometry : angle 0.55670 / 0.28 (20871) SS BOND : bond 0.00185 / 0.10 ( 6) SS BOND : angle 0.42733 / 0.24 ( 12) hydrogen bonds : bond 0.03704 / 2.45 ( 728) hydrogen bonds : angle 4.18494 / 2.92 ( 2301) link_ALPHA1-2 : bond 0.00906 / 0.44 ( 3) link_ALPHA1-2 : angle 2.51141 / 1.33 ( 9) link_ALPHA1-3 : bond 0.00803 / 0.46 ( 7) link_ALPHA1-3 : angle 2.01613 / 1.22 ( 21) link_ALPHA1-6 : bond 0.00670 / 0.39 ( 5) link_ALPHA1-6 : angle 1.77944 / 0.99 ( 15) link_BETA1-4 : bond 0.00326 / 0.18 ( 10) link_BETA1-4 : angle 1.54061 / 1.00 ( 30) link_NAG-ASN : bond 0.00147 / 0.07 ( 7) link_NAG-ASN : angle 1.51242 / 0.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8887 (tpp) cc_final: 0.8517 (mmm) REVERT: A 266 MET cc_start: 0.8904 (mmm) cc_final: 0.8378 (mmm) REVERT: A 406 ILE cc_start: 0.9491 (tp) cc_final: 0.9289 (tt) REVERT: B 61 MET cc_start: 0.9222 (ptp) cc_final: 0.9019 (ptp) REVERT: C 70 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8081 (mmm) REVERT: C 102 MET cc_start: 0.8937 (mmm) cc_final: 0.8421 (mmm) REVERT: C 223 MET cc_start: 0.8746 (mmm) cc_final: 0.8524 (mmt) REVERT: C 247 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9276 (tt) REVERT: C 252 TRP cc_start: 0.8797 (m-10) cc_final: 0.8432 (m-10) REVERT: C 313 GLU cc_start: 0.8219 (tp30) cc_final: 0.7944 (tp30) REVERT: D 213 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8811 (mmm) REVERT: D 229 GLN cc_start: 0.8727 (tp40) cc_final: 0.8523 (tp40) REVERT: D 236 MET cc_start: 0.9191 (mtm) cc_final: 0.8981 (mtm) REVERT: D 266 MET cc_start: 0.9191 (mmm) cc_final: 0.8873 (mmt) REVERT: D 286 MET cc_start: 0.8335 (tpp) cc_final: 0.8086 (tpp) REVERT: D 288 TRP cc_start: 0.7286 (m100) cc_final: 0.6800 (m-10) REVERT: E 55 MET cc_start: 0.8338 (mmm) cc_final: 0.8120 (tpt) REVERT: E 137 MET cc_start: 0.8149 (mmm) cc_final: 0.7881 (mmm) REVERT: E 227 MET cc_start: 0.8559 (tmm) cc_final: 0.8249 (tmm) REVERT: E 272 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8977 (pp) REVERT: E 443 TRP cc_start: 0.7031 (m100) cc_final: 0.6751 (t60) REVERT: F 441 MET cc_start: 0.6882 (mtp) cc_final: 0.6532 (mtp) REVERT: F 446 GLN cc_start: 0.8869 (tp40) cc_final: 0.8132 (mp10) REVERT: F 500 TYR cc_start: 0.8786 (m-80) cc_final: 0.7982 (m-80) REVERT: F 501 TYR cc_start: 0.9102 (m-10) cc_final: 0.8866 (m-10) outliers start: 27 outliers final: 15 residues processed: 135 average time/residue: 0.0968 time to fit residues: 20.5543 Evaluate side-chains 137 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 486 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 112 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN F 488 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050865 restraints weight = 64936.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052201 restraints weight = 37406.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053095 restraints weight = 26772.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053622 restraints weight = 21810.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054068 restraints weight = 19284.506| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 15392 Z= 0.343 Angle : 0.722 8.302 20979 Z= 0.359 Chirality : 0.045 0.231 2450 Planarity : 0.004 0.050 2532 Dihedral : 8.511 106.898 2647 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.76 % Allowed : 10.29 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1761 helix: 2.05 (0.21), residues: 574 sheet: 0.23 (0.25), residues: 430 loop : 0.29 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 221 TYR 0.027 0.002 TYR B 299 PHE 0.028 0.002 PHE A 298 TRP 0.009 0.001 TRP B 67 HIS 0.012 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.34 (15354) covalent geometry : angle 0.70999 / 0.36 (20871) SS BOND : bond 0.00322 / 0.16 ( 6) SS BOND : angle 0.71079 / 0.42 ( 12) hydrogen bonds : bond 0.04345 / 2.85 ( 728) hydrogen bonds : angle 4.62257 / 3.22 ( 2301) link_ALPHA1-2 : bond 0.00773 / 0.38 ( 3) link_ALPHA1-2 : angle 2.58073 / 1.36 ( 9) link_ALPHA1-3 : bond 0.00670 / 0.40 ( 7) link_ALPHA1-3 : angle 2.38908 / 1.44 ( 21) link_ALPHA1-6 : bond 0.00651 / 0.38 ( 5) link_ALPHA1-6 : angle 1.96078 / 1.07 ( 15) link_BETA1-4 : bond 0.00353 / 0.18 ( 10) link_BETA1-4 : angle 1.70267 / 1.07 ( 30) link_NAG-ASN : bond 0.00425 / 0.21 ( 7) link_NAG-ASN : angle 1.98608 / 1.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8767 (tpp) cc_final: 0.8471 (mmm) REVERT: A 266 MET cc_start: 0.9051 (mmm) cc_final: 0.8576 (mmm) REVERT: B 55 MET cc_start: 0.9027 (mmm) cc_final: 0.8667 (mmm) REVERT: C 70 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8041 (mmm) REVERT: C 102 MET cc_start: 0.8933 (mmm) cc_final: 0.8301 (mmm) REVERT: C 130 MET cc_start: 0.8030 (tmm) cc_final: 0.7654 (tmm) REVERT: C 247 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9225 (tt) REVERT: C 307 VAL cc_start: 0.9648 (m) cc_final: 0.9385 (p) REVERT: D 266 MET cc_start: 0.9263 (mmm) cc_final: 0.8949 (mmt) REVERT: D 286 MET cc_start: 0.8486 (tpp) cc_final: 0.8259 (tpp) REVERT: D 288 TRP cc_start: 0.7288 (m100) cc_final: 0.6847 (m-10) REVERT: D 393 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7083 (t70) REVERT: E 55 MET cc_start: 0.8484 (mmm) cc_final: 0.8087 (mmm) REVERT: E 272 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8866 (pp) REVERT: E 282 ASP cc_start: 0.8972 (m-30) cc_final: 0.8649 (t0) REVERT: E 443 TRP cc_start: 0.7068 (m100) cc_final: 0.6693 (t60) REVERT: F 441 MET cc_start: 0.6740 (mtp) cc_final: 0.6407 (mtp) outliers start: 28 outliers final: 18 residues processed: 132 average time/residue: 0.1023 time to fit residues: 21.0942 Evaluate side-chains 136 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 486 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.052687 restraints weight = 63010.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054087 restraints weight = 35908.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.055040 restraints weight = 25552.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055597 restraints weight = 20610.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.056055 restraints weight = 18124.731| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15392 Z= 0.145 Angle : 0.579 10.817 20979 Z= 0.286 Chirality : 0.043 0.233 2450 Planarity : 0.003 0.042 2532 Dihedral : 8.015 102.644 2647 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.76 % Allowed : 10.41 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1761 helix: 2.25 (0.21), residues: 573 sheet: 0.33 (0.25), residues: 428 loop : 0.43 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 445 TYR 0.023 0.001 TYR B 299 PHE 0.024 0.001 PHE A 298 TRP 0.007 0.001 TRP D 70 HIS 0.002 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15354) covalent geometry : angle 0.56749 / 0.28 (20871) SS BOND : bond 0.00133 / 0.07 ( 6) SS BOND : angle 0.43496 / 0.25 ( 12) hydrogen bonds : bond 0.03813 / 2.55 ( 728) hydrogen bonds : angle 4.21757 / 2.94 ( 2301) link_ALPHA1-2 : bond 0.00978 / 0.47 ( 3) link_ALPHA1-2 : angle 2.59402 / 1.38 ( 9) link_ALPHA1-3 : bond 0.00854 / 0.49 ( 7) link_ALPHA1-3 : angle 2.02549 / 1.23 ( 21) link_ALPHA1-6 : bond 0.00773 / 0.43 ( 5) link_ALPHA1-6 : angle 1.68509 / 0.92 ( 15) link_BETA1-4 : bond 0.00329 / 0.19 ( 10) link_BETA1-4 : angle 1.54303 / 1.00 ( 30) link_NAG-ASN : bond 0.00113 / 0.06 ( 7) link_NAG-ASN : angle 1.55055 / 0.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.9139 (mmm) cc_final: 0.8879 (mmm) REVERT: C 70 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8041 (mmm) REVERT: C 102 MET cc_start: 0.8844 (mmm) cc_final: 0.8229 (mmm) REVERT: C 130 MET cc_start: 0.7915 (tmm) cc_final: 0.7517 (tmm) REVERT: C 247 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9210 (tt) REVERT: C 252 TRP cc_start: 0.8773 (m-10) cc_final: 0.8414 (m-10) REVERT: C 307 VAL cc_start: 0.9599 (m) cc_final: 0.9389 (p) REVERT: D 90 MET cc_start: 0.8431 (mmt) cc_final: 0.8219 (mmm) REVERT: D 266 MET cc_start: 0.9184 (mmm) cc_final: 0.8875 (mmt) REVERT: D 286 MET cc_start: 0.8305 (tpp) cc_final: 0.7945 (tpp) REVERT: D 288 TRP cc_start: 0.7153 (m100) cc_final: 0.6734 (m-10) REVERT: E 55 MET cc_start: 0.8503 (mmm) cc_final: 0.8192 (tpt) REVERT: E 268 LEU cc_start: 0.9289 (mm) cc_final: 0.9083 (mp) REVERT: E 443 TRP cc_start: 0.6963 (m100) cc_final: 0.6695 (t60) REVERT: F 441 MET cc_start: 0.7012 (mtp) cc_final: 0.6696 (mtp) REVERT: F 474 PHE cc_start: 0.8685 (m-80) cc_final: 0.8419 (m-10) outliers start: 28 outliers final: 15 residues processed: 139 average time/residue: 0.0979 time to fit residues: 21.0858 Evaluate side-chains 135 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 476 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 161 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.067621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052668 restraints weight = 64264.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054083 restraints weight = 36591.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.055044 restraints weight = 25932.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055612 restraints weight = 20960.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.056083 restraints weight = 18409.722| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15392 Z= 0.128 Angle : 0.584 9.422 20979 Z= 0.282 Chirality : 0.042 0.232 2450 Planarity : 0.003 0.044 2532 Dihedral : 7.478 97.738 2647 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.44 % Allowed : 10.92 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.20), residues: 1761 helix: 2.41 (0.21), residues: 568 sheet: 0.44 (0.25), residues: 428 loop : 0.44 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 269 TYR 0.021 0.001 TYR B 299 PHE 0.026 0.001 PHE A 298 TRP 0.008 0.001 TRP D 70 HIS 0.002 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (15354) covalent geometry : angle 0.57343 / 0.28 (20871) SS BOND : bond 0.00121 / 0.07 ( 6) SS BOND : angle 0.39931 / 0.22 ( 12) hydrogen bonds : bond 0.03604 / 2.41 ( 728) hydrogen bonds : angle 4.06308 / 2.83 ( 2301) link_ALPHA1-2 : bond 0.01113 / 0.54 ( 3) link_ALPHA1-2 : angle 2.65500 / 1.42 ( 9) link_ALPHA1-3 : bond 0.00861 / 0.49 ( 7) link_ALPHA1-3 : angle 1.96868 / 1.19 ( 21) link_ALPHA1-6 : bond 0.00810 / 0.45 ( 5) link_ALPHA1-6 : angle 1.58271 / 0.87 ( 15) link_BETA1-4 : bond 0.00363 / 0.21 ( 10) link_BETA1-4 : angle 1.51273 / 0.96 ( 30) link_NAG-ASN : bond 0.00080 / 0.04 ( 7) link_NAG-ASN : angle 1.49342 / 0.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8813 (tpp) cc_final: 0.8435 (tpp) REVERT: A 112 MET cc_start: 0.7407 (ttm) cc_final: 0.6734 (mtt) REVERT: A 213 MET cc_start: 0.9141 (mmm) cc_final: 0.8916 (mmm) REVERT: A 266 MET cc_start: 0.8697 (mmm) cc_final: 0.8308 (mmm) REVERT: C 70 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7997 (mmm) REVERT: C 130 MET cc_start: 0.7886 (tmm) cc_final: 0.7450 (tmm) REVERT: C 247 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9228 (tt) REVERT: C 252 TRP cc_start: 0.8735 (m-10) cc_final: 0.8412 (m-10) REVERT: C 307 VAL cc_start: 0.9613 (m) cc_final: 0.9412 (p) REVERT: D 286 MET cc_start: 0.8378 (tpp) cc_final: 0.8128 (tpp) REVERT: D 288 TRP cc_start: 0.7196 (m100) cc_final: 0.6743 (m-10) REVERT: E 55 MET cc_start: 0.8463 (mmm) cc_final: 0.8084 (tpt) REVERT: E 443 TRP cc_start: 0.6949 (m100) cc_final: 0.6681 (t60) REVERT: F 441 MET cc_start: 0.6909 (mtp) cc_final: 0.6665 (mtp) REVERT: F 446 GLN cc_start: 0.8966 (tp40) cc_final: 0.8195 (mp10) REVERT: F 468 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8673 (p0) REVERT: F 474 PHE cc_start: 0.8627 (m-80) cc_final: 0.8194 (m-80) outliers start: 23 outliers final: 15 residues processed: 135 average time/residue: 0.0918 time to fit residues: 19.4266 Evaluate side-chains 137 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 468 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 84 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.065873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.050889 restraints weight = 65478.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.052252 restraints weight = 37542.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.053183 restraints weight = 26874.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053713 restraints weight = 21815.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.054150 restraints weight = 19266.279| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15392 Z= 0.291 Angle : 0.703 9.367 20979 Z= 0.345 Chirality : 0.045 0.226 2450 Planarity : 0.004 0.042 2532 Dihedral : 7.267 96.290 2647 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.44 % Allowed : 11.36 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1761 helix: 2.18 (0.21), residues: 570 sheet: 0.14 (0.25), residues: 439 loop : 0.43 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 213 TYR 0.025 0.002 TYR B 299 PHE 0.028 0.002 PHE A 298 TRP 0.010 0.001 TRP E 67 HIS 0.006 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.29 (15354) covalent geometry : angle 0.69153 / 0.34 (20871) SS BOND : bond 0.00251 / 0.13 ( 6) SS BOND : angle 0.63200 / 0.37 ( 12) hydrogen bonds : bond 0.04099 / 2.70 ( 728) hydrogen bonds : angle 4.45553 / 3.09 ( 2301) link_ALPHA1-2 : bond 0.01068 / 0.52 ( 3) link_ALPHA1-2 : angle 2.72757 / 1.46 ( 9) link_ALPHA1-3 : bond 0.00721 / 0.42 ( 7) link_ALPHA1-3 : angle 2.28400 / 1.37 ( 21) link_ALPHA1-6 : bond 0.00752 / 0.42 ( 5) link_ALPHA1-6 : angle 1.70262 / 0.94 ( 15) link_BETA1-4 : bond 0.00360 / 0.19 ( 10) link_BETA1-4 : angle 1.62832 / 1.01 ( 30) link_NAG-ASN : bond 0.00311 / 0.16 ( 7) link_NAG-ASN : angle 1.86835 / 1.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8787 (tpp) cc_final: 0.8468 (mmm) REVERT: A 112 MET cc_start: 0.7527 (ttm) cc_final: 0.6932 (mtt) REVERT: A 148 MET cc_start: 0.8747 (mtm) cc_final: 0.7662 (mpp) REVERT: A 228 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8851 (mm) REVERT: A 266 MET cc_start: 0.8931 (mmm) cc_final: 0.8526 (mmm) REVERT: B 55 MET cc_start: 0.8826 (mmm) cc_final: 0.8556 (mmm) REVERT: C 70 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7839 (mmm) REVERT: C 130 MET cc_start: 0.8024 (tmm) cc_final: 0.7734 (tmm) REVERT: C 247 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9239 (tt) REVERT: C 307 VAL cc_start: 0.9631 (m) cc_final: 0.9365 (p) REVERT: D 213 MET cc_start: 0.8840 (mmm) cc_final: 0.8490 (mtp) REVERT: D 286 MET cc_start: 0.8505 (tpp) cc_final: 0.8177 (tpp) REVERT: D 288 TRP cc_start: 0.7239 (m100) cc_final: 0.6845 (m-10) REVERT: D 393 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7313 (t70) REVERT: E 55 MET cc_start: 0.8494 (mmm) cc_final: 0.8241 (mmm) REVERT: E 443 TRP cc_start: 0.7075 (m100) cc_final: 0.6814 (t60) REVERT: F 446 GLN cc_start: 0.8800 (tp40) cc_final: 0.7838 (mp10) REVERT: F 468 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8682 (p0) REVERT: F 500 TYR cc_start: 0.8674 (m-80) cc_final: 0.7591 (m-80) outliers start: 23 outliers final: 16 residues processed: 128 average time/residue: 0.1034 time to fit residues: 20.6327 Evaluate side-chains 136 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain F residue 476 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 146 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 97 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.051995 restraints weight = 64350.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053362 restraints weight = 36906.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054299 restraints weight = 26337.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.054889 restraints weight = 21357.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055310 restraints weight = 18734.476| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15392 Z= 0.167 Angle : 0.622 10.323 20979 Z= 0.302 Chirality : 0.043 0.225 2450 Planarity : 0.003 0.045 2532 Dihedral : 6.859 91.351 2647 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.44 % Allowed : 11.42 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1761 helix: 2.21 (0.21), residues: 569 sheet: 0.16 (0.25), residues: 433 loop : 0.49 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.026 0.001 TYR F 501 PHE 0.026 0.001 PHE A 298 TRP 0.007 0.001 TRP E 67 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (15354) covalent geometry : angle 0.61133 / 0.30 (20871) SS BOND : bond 0.00139 / 0.08 ( 6) SS BOND : angle 0.49508 / 0.29 ( 12) hydrogen bonds : bond 0.03791 / 2.52 ( 728) hydrogen bonds : angle 4.22052 / 2.93 ( 2301) link_ALPHA1-2 : bond 0.01324 / 0.64 ( 3) link_ALPHA1-2 : angle 2.73640 / 1.55 ( 9) link_ALPHA1-3 : bond 0.00785 / 0.45 ( 7) link_ALPHA1-3 : angle 1.99291 / 1.21 ( 21) link_ALPHA1-6 : bond 0.00849 / 0.46 ( 5) link_ALPHA1-6 : angle 1.50342 / 0.83 ( 15) link_BETA1-4 : bond 0.00354 / 0.21 ( 10) link_BETA1-4 : angle 1.53918 / 0.97 ( 30) link_NAG-ASN : bond 0.00133 / 0.07 ( 7) link_NAG-ASN : angle 1.57264 / 0.98 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8844 (tpp) cc_final: 0.8568 (mmm) REVERT: A 112 MET cc_start: 0.7472 (ttm) cc_final: 0.6870 (mtt) REVERT: A 148 MET cc_start: 0.8558 (mtm) cc_final: 0.7620 (mpp) REVERT: A 213 MET cc_start: 0.9153 (mmm) cc_final: 0.8939 (mmm) REVERT: A 266 MET cc_start: 0.8832 (mmm) cc_final: 0.8349 (mmm) REVERT: B 55 MET cc_start: 0.8837 (mmm) cc_final: 0.8530 (mmm) REVERT: C 70 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8082 (mmm) REVERT: C 102 MET cc_start: 0.8629 (mmp) cc_final: 0.8407 (mmp) REVERT: C 130 MET cc_start: 0.7943 (tmm) cc_final: 0.7656 (tmm) REVERT: C 247 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9256 (tt) REVERT: C 252 TRP cc_start: 0.8803 (m-10) cc_final: 0.8459 (m-10) REVERT: D 213 MET cc_start: 0.8835 (mmm) cc_final: 0.8499 (mtp) REVERT: D 286 MET cc_start: 0.8465 (tpp) cc_final: 0.8214 (tpp) REVERT: D 288 TRP cc_start: 0.7211 (m100) cc_final: 0.6771 (m-10) REVERT: D 393 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7288 (t70) REVERT: E 55 MET cc_start: 0.8703 (mmm) cc_final: 0.8312 (tpt) REVERT: E 443 TRP cc_start: 0.6993 (m100) cc_final: 0.6768 (t60) REVERT: F 446 GLN cc_start: 0.8796 (tp40) cc_final: 0.7860 (mp10) REVERT: F 468 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8618 (p0) REVERT: F 474 PHE cc_start: 0.8735 (m-10) cc_final: 0.8533 (m-10) REVERT: F 500 TYR cc_start: 0.8692 (m-80) cc_final: 0.7562 (m-80) outliers start: 23 outliers final: 15 residues processed: 131 average time/residue: 0.1001 time to fit residues: 20.6736 Evaluate side-chains 137 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain F residue 476 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 167 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.068612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.053738 restraints weight = 63617.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.055163 restraints weight = 36303.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.056151 restraints weight = 25806.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056771 restraints weight = 20807.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.057074 restraints weight = 18190.528| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15392 Z= 0.104 Angle : 0.598 12.030 20979 Z= 0.284 Chirality : 0.042 0.223 2450 Planarity : 0.003 0.052 2532 Dihedral : 6.125 65.915 2647 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.69 % Allowed : 12.30 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1761 helix: 2.38 (0.21), residues: 569 sheet: 0.35 (0.25), residues: 429 loop : 0.56 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 462 TYR 0.021 0.001 TYR C 199 PHE 0.025 0.001 PHE A 298 TRP 0.009 0.001 TRP A 70 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (15354) covalent geometry : angle 0.58942 / 0.28 (20871) SS BOND : bond 0.00141 / 0.08 ( 6) SS BOND : angle 0.39041 / 0.22 ( 12) hydrogen bonds : bond 0.03387 / 2.27 ( 728) hydrogen bonds : angle 3.96186 / 2.76 ( 2301) link_ALPHA1-2 : bond 0.01328 / 0.65 ( 3) link_ALPHA1-2 : angle 2.68628 / 1.57 ( 9) link_ALPHA1-3 : bond 0.00874 / 0.49 ( 7) link_ALPHA1-3 : angle 1.73068 / 1.06 ( 21) link_ALPHA1-6 : bond 0.00922 / 0.51 ( 5) link_ALPHA1-6 : angle 1.38860 / 0.77 ( 15) link_BETA1-4 : bond 0.00450 / 0.28 ( 10) link_BETA1-4 : angle 1.45154 / 0.92 ( 30) link_NAG-ASN : bond 0.00176 / 0.08 ( 7) link_NAG-ASN : angle 1.31586 / 0.83 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.49 seconds wall clock time: 32 minutes 28.47 seconds (1948.47 seconds total)