Starting phenix.real_space_refine on Thu Jun 12 08:36:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9boy_44754/06_2025/9boy_44754.cif Found real_map, /net/cci-nas-00/data/ceres_data/9boy_44754/06_2025/9boy_44754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9boy_44754/06_2025/9boy_44754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9boy_44754/06_2025/9boy_44754.map" model { file = "/net/cci-nas-00/data/ceres_data/9boy_44754/06_2025/9boy_44754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9boy_44754/06_2025/9boy_44754.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 9017 2.51 5 N 2216 2.21 5 O 2491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13819 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2814 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 349, 2805 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 349, 2805 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 2867 Chain: "B" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2735 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2735 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2776 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2664 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU A 192 " occ=0.77 ... (16 atoms not shown) pdb=" OE2BGLU A 192 " occ=0.23 Time building chain proxies: 9.52, per 1000 atoms: 0.69 Number of scatterers: 13819 At special positions: 0 Unit cell: (93.79, 93.79, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 2491 8.00 N 2216 7.00 C 9017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " 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 NAG-ASN " NAG A 501 " - " ASN A 38 " " NAG B 502 " - " ASN B 38 " " NAG C 502 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.9 seconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 20 sheets defined 38.6% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.775A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 240 removed outlier: 3.838A pdb=" N ILE A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.542A pdb=" N VAL A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 248 through 272 removed outlier: 3.662A pdb=" N THR A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 Processing helix chain 'A' and resid 387 through 418 removed outlier: 3.976A pdb=" N ARG A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 71 through 74 removed outlier: 4.026A pdb=" N ALA B 74 " --> pdb=" O PRO B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 86 through 93 removed outlier: 4.330A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 239 removed outlier: 3.701A pdb=" N SER B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.579A pdb=" N TRP B 243 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 272 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.864A pdb=" N ILE B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 422 removed outlier: 4.122A pdb=" N ARG B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Proline residue: B 404 - end of helix removed outlier: 3.619A pdb=" N TYR B 418 " --> pdb=" O TYR B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.548A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.822A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 removed outlier: 3.755A pdb=" N ILE C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.767A pdb=" N VAL C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 273 removed outlier: 4.336A pdb=" N ARG C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET C 263 " --> pdb=" O THR C 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 309 Processing helix chain 'C' and resid 387 through 418 removed outlier: 3.984A pdb=" N ARG C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Proline residue: C 404 - end of helix removed outlier: 3.801A pdb=" N VAL C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 418 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 18 Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.942A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 227 removed outlier: 3.885A pdb=" N ILE D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.682A pdb=" N SER D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 244 Processing helix chain 'D' and resid 248 through 271 removed outlier: 3.910A pdb=" N VAL D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.694A pdb=" N PHE D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 420 Proline residue: D 404 - end of helix removed outlier: 3.805A pdb=" N ILE D 412 " --> pdb=" O LEU D 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 109 through 115 removed outlier: 3.864A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.553A pdb=" N THR E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 276 through 298 removed outlier: 3.686A pdb=" N GLY E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 333 removed outlier: 3.688A pdb=" N ASN E 333 " --> pdb=" O GLN E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 474 Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.253A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 129 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 44 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 167 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 5.586A pdb=" N GLU A 103 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N SER A 137 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 105 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 107 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 44 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.564A pdb=" N GLU A 217 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.581A pdb=" N GLU A 211 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.502A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 44 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.502A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 44 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 177 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 52 removed outlier: 4.747A pdb=" N ILE B 51 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASP B 57 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY B 105 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N SER B 137 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU B 103 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 100 removed outlier: 4.371A pdb=" N HIS B 215 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU B 192 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N GLU B 217 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LYS B 190 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.569A pdb=" N LEU C 85 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 44 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 106 removed outlier: 5.710A pdb=" N GLU C 103 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N SER C 137 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY C 105 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 44 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 177 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.504A pdb=" N CYS C 152 " --> pdb=" O PHE C 214 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N HIS C 215 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU C 192 " --> pdb=" O HIS C 215 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLU C 217 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LYS C 190 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.689A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE D 44 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.689A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE D 44 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.524A pdb=" N GLU D 217 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB7, first strand: chain 'D' and resid 103 through 107 removed outlier: 3.896A pdb=" N GLY D 105 " --> pdb=" O THR D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 107 through 108 removed outlier: 3.528A pdb=" N VAL E 108 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU E 141 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE E 157 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP E 78 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER E 71 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE E 65 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 126 through 130 removed outlier: 6.928A pdb=" N THR E 158 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA E 129 " --> pdb=" O SER E 156 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER E 156 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE E 157 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP E 78 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER E 71 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE E 65 " --> pdb=" O PHE E 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.502A pdb=" N PHE E 122 " --> pdb=" O GLU E 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 224 through 225 724 hydrogen bonds defined for protein. 2046 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: 3.99 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4257 1.34 - 1.46: 3128 1.46 - 1.58: 6631 1.58 - 1.70: 0 1.70 - 1.82: 154 Bond restraints: 14170 Sorted by residual: bond pdb=" C LEU A 255 " pdb=" N GLY A 256 " ideal model delta sigma weight residual 1.331 1.280 0.051 1.46e-02 4.69e+03 1.20e+01 bond pdb=" N LEU E 140 " pdb=" CA LEU E 140 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.37e+00 bond pdb=" N ILE E 139 " pdb=" CA ILE E 139 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.32e+00 bond pdb=" N MET B 246 " pdb=" CA MET B 246 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.30e-02 5.92e+03 5.86e+00 bond pdb=" N ASN A 245 " pdb=" CA ASN A 245 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.25e-02 6.40e+03 5.53e+00 ... (remaining 14165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 18853 1.81 - 3.63: 327 3.63 - 5.44: 70 5.44 - 7.25: 12 7.25 - 9.07: 5 Bond angle restraints: 19267 Sorted by residual: angle pdb=" O LEU A 255 " pdb=" C LEU A 255 " pdb=" N GLY A 256 " ideal model delta sigma weight residual 122.22 117.42 4.80 1.17e+00 7.31e-01 1.69e+01 angle pdb=" CA GLN A 310 " pdb=" CB GLN A 310 " pdb=" CG GLN A 310 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CA LEU A 255 " pdb=" C LEU A 255 " pdb=" N GLY A 256 " ideal model delta sigma weight residual 117.63 122.20 -4.57 1.25e+00 6.40e-01 1.34e+01 angle pdb=" CA ALA B 248 " pdb=" C ALA B 248 " pdb=" O ALA B 248 " ideal model delta sigma weight residual 122.36 118.05 4.31 1.21e+00 6.83e-01 1.27e+01 angle pdb=" C ARG B 252 " pdb=" N VAL B 253 " pdb=" CA VAL B 253 " ideal model delta sigma weight residual 120.46 115.75 4.71 1.37e+00 5.33e-01 1.18e+01 ... (remaining 19262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 7632 17.07 - 34.14: 669 34.14 - 51.21: 165 51.21 - 68.27: 15 68.27 - 85.34: 8 Dihedral angle restraints: 8489 sinusoidal: 3406 harmonic: 5083 Sorted by residual: dihedral pdb=" CB CYS E 221 " pdb=" SG CYS E 221 " pdb=" SG CYS E 233 " pdb=" CB CYS E 233 " ideal model delta sinusoidal sigma weight residual -86.00 -171.34 85.34 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 46.70 46.30 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual 93.00 48.61 44.39 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 8486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1619 0.043 - 0.087: 405 0.087 - 0.130: 155 0.130 - 0.173: 12 0.173 - 0.217: 4 Chirality restraints: 2195 Sorted by residual: chirality pdb=" CA ILE E 139 " pdb=" N ILE E 139 " pdb=" C ILE E 139 " pdb=" CB ILE E 139 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA MET A 246 " pdb=" N MET A 246 " pdb=" C MET A 246 " pdb=" CB MET A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 2192 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 239 " 0.029 2.00e-02 2.50e+03 2.32e-02 1.34e+01 pdb=" CG TRP A 239 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 239 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 239 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 239 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 239 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 239 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 255 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" C LEU A 255 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU A 255 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 256 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 245 " -0.013 2.00e-02 2.50e+03 2.64e-02 7.00e+00 pdb=" C ASN B 245 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN B 245 " -0.017 2.00e-02 2.50e+03 pdb=" N MET B 246 " -0.015 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 199 2.64 - 3.21: 13040 3.21 - 3.77: 21089 3.77 - 4.34: 28020 4.34 - 4.90: 46371 Nonbonded interactions: 108719 Sorted by model distance: nonbonded pdb=" OG1 THR C 55 " pdb=" OD1 ASP C 57 " model vdw 2.079 3.040 nonbonded pdb=" OE1 GLU C 169 " pdb=" OH TYR C 197 " model vdw 2.124 3.040 nonbonded pdb=" OD2 ASP D 148 " pdb=" NE2 GLN D 150 " model vdw 2.162 3.120 nonbonded pdb=" OD2 ASP E 171 " pdb=" NH1 ARG E 242 " model vdw 2.222 3.120 nonbonded pdb=" O LEU D 98 " pdb=" OG1 THR E 135 " model vdw 2.224 3.040 ... (remaining 108714 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 9 through 191 or resid 193 through 310 or resid 386 throug \ h 395 or (resid 396 through 401 and (name N or name CA or name C or name O or na \ me CB )) or resid 402 through 421 or (resid 422 and (name N or name CA or name C \ or name O or name CB )) or resid 501)) selection = (chain 'B' and (resid 9 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 191 or resid 193 through 310 or res \ id 386 through 387 or (resid 388 and (name N or name CA or name C or name O or n \ ame CB )) or resid 389 through 392 or (resid 393 and (name N or name CA or name \ C or name O or name CB )) or resid 394 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )) or resid 502)) selection = (chain 'C' and (resid 9 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 191 or resid 193 through 387 or (re \ sid 388 and (name N or name CA or name C or name O or name CB )) or resid 389 th \ rough 392 or (resid 393 and (name N or name CA or name C or name O or name CB )) \ or resid 394 through 396 or (resid 397 through 401 and (name N or name CA or na \ me C or name O or name CB )) or resid 402 through 422 or resid 502)) selection = (chain 'D' and (resid 9 through 191 or resid 193 through 310 or resid 386 throug \ h 387 or (resid 388 and (name N or name CA or name C or name O or name CB )) or \ resid 389 through 392 or (resid 393 and (name N or name CA or name C or name O o \ r name CB )) or resid 394 through 396 or (resid 397 through 401 and (name N or n \ ame CA or name C or name O or name CB )) or resid 402 through 421 or (resid 422 \ and (name N or name CA or name C or name O or name CB )) or resid 501)) } 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=0.23 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.770 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 0.051 14185 Z= 0.183 Angle : 0.631 9.067 19302 Z= 0.336 Chirality : 0.044 0.217 2195 Planarity : 0.004 0.035 2411 Dihedral : 13.391 83.214 5155 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 1.73 % Allowed : 15.33 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1695 helix: 1.79 (0.23), residues: 547 sheet: -1.23 (0.28), residues: 360 loop : -0.86 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 239 HIS 0.002 0.001 HIS C 215 PHE 0.019 0.001 PHE C 306 TYR 0.020 0.001 TYR B 301 ARG 0.007 0.000 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00906 ( 5) link_NAG-ASN : angle 2.57657 ( 15) hydrogen bonds : bond 0.17909 ( 638) hydrogen bonds : angle 8.00558 ( 2046) SS BOND : bond 0.00285 ( 10) SS BOND : angle 1.70022 ( 20) covalent geometry : bond 0.00382 (14170) covalent geometry : angle 0.62467 (19267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8376 (tm-30) REVERT: A 287 MET cc_start: 0.8243 (tpp) cc_final: 0.7669 (mmm) REVERT: B 56 MET cc_start: 0.8120 (tpp) cc_final: 0.7882 (mtp) REVERT: B 188 LEU cc_start: 0.9009 (tp) cc_final: 0.8582 (pp) REVERT: B 292 LEU cc_start: 0.9058 (tp) cc_final: 0.8362 (tt) REVERT: B 391 ARG cc_start: 0.6831 (mpp80) cc_final: 0.6320 (mmm160) REVERT: C 225 ILE cc_start: 0.9182 (tp) cc_final: 0.8878 (tp) REVERT: C 287 MET cc_start: 0.8046 (mmm) cc_final: 0.7588 (mmm) REVERT: D 102 ASN cc_start: 0.8544 (p0) cc_final: 0.7538 (p0) REVERT: E 133 ASP cc_start: 0.8075 (p0) cc_final: 0.7512 (p0) REVERT: E 324 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 26 outliers final: 20 residues processed: 223 average time/residue: 0.2236 time to fit residues: 76.4341 Evaluate side-chains 221 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.5980 chunk 128 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN E 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099578 restraints weight = 36929.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103197 restraints weight = 19422.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103151 restraints weight = 15380.905| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14185 Z= 0.142 Angle : 0.609 7.821 19302 Z= 0.311 Chirality : 0.045 0.284 2195 Planarity : 0.004 0.032 2411 Dihedral : 6.335 58.653 2001 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.96 % Favored : 95.92 % Rotamer: Outliers : 2.13 % Allowed : 14.60 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1695 helix: 1.82 (0.22), residues: 549 sheet: -1.00 (0.29), residues: 347 loop : -0.86 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 239 HIS 0.003 0.001 HIS A 109 PHE 0.017 0.001 PHE B 48 TYR 0.021 0.001 TYR B 301 ARG 0.006 0.000 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 5) link_NAG-ASN : angle 2.66679 ( 15) hydrogen bonds : bond 0.04355 ( 638) hydrogen bonds : angle 5.51030 ( 2046) SS BOND : bond 0.00435 ( 10) SS BOND : angle 1.49365 ( 20) covalent geometry : bond 0.00314 (14170) covalent geometry : angle 0.60312 (19267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8327 (p0) cc_final: 0.7895 (p0) REVERT: A 266 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: A 287 MET cc_start: 0.8144 (tpp) cc_final: 0.7630 (mmm) REVERT: B 56 MET cc_start: 0.8114 (tpp) cc_final: 0.7912 (mtp) REVERT: B 103 GLU cc_start: 0.8588 (tt0) cc_final: 0.8309 (tt0) REVERT: B 188 LEU cc_start: 0.8982 (tp) cc_final: 0.8565 (pp) REVERT: B 391 ARG cc_start: 0.6857 (mpp80) cc_final: 0.6221 (mmm160) REVERT: C 225 ILE cc_start: 0.9197 (tp) cc_final: 0.8946 (tp) REVERT: D 102 ASN cc_start: 0.8545 (p0) cc_final: 0.7795 (p0) REVERT: D 147 MET cc_start: 0.8180 (mpp) cc_final: 0.7752 (mtp) REVERT: D 226 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8121 (tm-30) REVERT: D 292 LEU cc_start: 0.8962 (mm) cc_final: 0.8547 (tp) REVERT: E 125 ASN cc_start: 0.8658 (t0) cc_final: 0.8107 (t0) REVERT: E 133 ASP cc_start: 0.7733 (p0) cc_final: 0.7449 (p0) REVERT: E 324 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7798 (tm-30) outliers start: 32 outliers final: 25 residues processed: 236 average time/residue: 0.2116 time to fit residues: 77.5427 Evaluate side-chains 223 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 239 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 8 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 = 0.3648 r_free = 0.3648 target = 0.130742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100429 restraints weight = 47831.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102336 restraints weight = 24942.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102621 restraints weight = 22051.774| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14185 Z= 0.150 Angle : 0.594 9.218 19302 Z= 0.302 Chirality : 0.044 0.198 2195 Planarity : 0.004 0.032 2411 Dihedral : 5.649 56.181 1976 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.78 % Favored : 96.10 % Rotamer: Outliers : 2.93 % Allowed : 15.73 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1695 helix: 1.83 (0.22), residues: 548 sheet: -1.03 (0.28), residues: 361 loop : -0.79 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 239 HIS 0.002 0.001 HIS A 109 PHE 0.016 0.001 PHE B 410 TYR 0.015 0.001 TYR D 301 ARG 0.005 0.000 ARG B 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 5) link_NAG-ASN : angle 2.61367 ( 15) hydrogen bonds : bond 0.04039 ( 638) hydrogen bonds : angle 5.15425 ( 2046) SS BOND : bond 0.00370 ( 10) SS BOND : angle 1.79119 ( 20) covalent geometry : bond 0.00343 (14170) covalent geometry : angle 0.58725 (19267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8340 (p0) cc_final: 0.7914 (p0) REVERT: A 226 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 261 LEU cc_start: 0.8922 (tp) cc_final: 0.8526 (pp) REVERT: A 266 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: A 287 MET cc_start: 0.8140 (tpp) cc_final: 0.7559 (mmm) REVERT: B 103 GLU cc_start: 0.8565 (tt0) cc_final: 0.8324 (tt0) REVERT: B 188 LEU cc_start: 0.8989 (tp) cc_final: 0.8571 (pp) REVERT: B 292 LEU cc_start: 0.9076 (tp) cc_final: 0.8418 (tt) REVERT: B 391 ARG cc_start: 0.7043 (mpp80) cc_final: 0.6347 (mmm160) REVERT: C 225 ILE cc_start: 0.9192 (tp) cc_final: 0.8891 (tp) REVERT: C 287 MET cc_start: 0.7917 (mmm) cc_final: 0.7504 (mmm) REVERT: D 102 ASN cc_start: 0.8547 (p0) cc_final: 0.7807 (p0) REVERT: D 147 MET cc_start: 0.7909 (mpp) cc_final: 0.7355 (mtp) REVERT: D 226 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8184 (tm-30) REVERT: D 227 MET cc_start: 0.7835 (mtt) cc_final: 0.7580 (mtt) REVERT: D 292 LEU cc_start: 0.8982 (mm) cc_final: 0.8518 (tp) REVERT: E 125 ASN cc_start: 0.8661 (t0) cc_final: 0.8096 (t0) REVERT: E 126 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8811 (tm-30) REVERT: E 133 ASP cc_start: 0.7797 (p0) cc_final: 0.7517 (p0) REVERT: E 243 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6968 (mt0) outliers start: 44 outliers final: 26 residues processed: 233 average time/residue: 0.2199 time to fit residues: 79.0967 Evaluate side-chains 224 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 239 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 155 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 = 0.3625 r_free = 0.3625 target = 0.129067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096999 restraints weight = 54588.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098636 restraints weight = 21823.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099271 restraints weight = 17866.644| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14185 Z= 0.191 Angle : 0.615 9.788 19302 Z= 0.314 Chirality : 0.045 0.197 2195 Planarity : 0.004 0.033 2411 Dihedral : 5.550 58.070 1970 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.96 % Favored : 95.92 % Rotamer: Outliers : 3.60 % Allowed : 16.40 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1695 helix: 1.83 (0.22), residues: 549 sheet: -1.05 (0.29), residues: 345 loop : -0.87 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 239 HIS 0.002 0.001 HIS C 109 PHE 0.034 0.001 PHE A 407 TYR 0.019 0.001 TYR C 223 ARG 0.005 0.000 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 5) link_NAG-ASN : angle 2.62970 ( 15) hydrogen bonds : bond 0.03954 ( 638) hydrogen bonds : angle 4.95390 ( 2046) SS BOND : bond 0.00341 ( 10) SS BOND : angle 2.00490 ( 20) covalent geometry : bond 0.00439 (14170) covalent geometry : angle 0.60741 (19267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8376 (p0) cc_final: 0.8106 (p0) REVERT: A 261 LEU cc_start: 0.8953 (tp) cc_final: 0.8541 (pp) REVERT: A 287 MET cc_start: 0.8399 (tpp) cc_final: 0.7774 (mmm) REVERT: B 188 LEU cc_start: 0.8999 (tp) cc_final: 0.8582 (pp) REVERT: B 195 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8644 (mt) REVERT: B 292 LEU cc_start: 0.9115 (tp) cc_final: 0.8429 (tt) REVERT: B 391 ARG cc_start: 0.7058 (mpp80) cc_final: 0.6389 (mmm160) REVERT: C 225 ILE cc_start: 0.9227 (tp) cc_final: 0.8911 (tp) REVERT: C 287 MET cc_start: 0.8152 (mmm) cc_final: 0.7740 (mmm) REVERT: D 102 ASN cc_start: 0.8564 (p0) cc_final: 0.7809 (p0) REVERT: D 147 MET cc_start: 0.8239 (mpp) cc_final: 0.7403 (mtp) REVERT: D 226 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8101 (tm-30) REVERT: D 227 MET cc_start: 0.7930 (mtt) cc_final: 0.7694 (mtt) REVERT: D 292 LEU cc_start: 0.8988 (mm) cc_final: 0.8500 (tp) REVERT: D 412 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7331 (mp) REVERT: E 125 ASN cc_start: 0.8640 (t0) cc_final: 0.8047 (t0) REVERT: E 133 ASP cc_start: 0.7801 (p0) cc_final: 0.7573 (p0) REVERT: E 243 GLN cc_start: 0.7323 (pt0) cc_final: 0.7003 (mt0) REVERT: E 322 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7203 (mm) REVERT: E 324 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7798 (tm-30) outliers start: 54 outliers final: 38 residues processed: 242 average time/residue: 0.2192 time to fit residues: 82.5312 Evaluate side-chains 236 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 239 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 129 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 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 = 0.3648 r_free = 0.3648 target = 0.130913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100560 restraints weight = 44218.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102253 restraints weight = 23384.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.102798 restraints weight = 19833.282| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14185 Z= 0.138 Angle : 0.590 9.919 19302 Z= 0.298 Chirality : 0.044 0.195 2195 Planarity : 0.003 0.034 2411 Dihedral : 5.490 59.442 1970 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.49 % Favored : 96.39 % Rotamer: Outliers : 3.27 % Allowed : 17.80 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1695 helix: 1.73 (0.22), residues: 560 sheet: -0.98 (0.29), residues: 345 loop : -0.87 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 239 HIS 0.001 0.000 HIS A 201 PHE 0.014 0.001 PHE B 410 TYR 0.015 0.001 TYR D 301 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 5) link_NAG-ASN : angle 2.63593 ( 15) hydrogen bonds : bond 0.03664 ( 638) hydrogen bonds : angle 4.73926 ( 2046) SS BOND : bond 0.00358 ( 10) SS BOND : angle 1.66748 ( 20) covalent geometry : bond 0.00313 (14170) covalent geometry : angle 0.58308 (19267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8462 (ppp) cc_final: 0.7995 (ppp) REVERT: A 102 ASN cc_start: 0.8401 (p0) cc_final: 0.8106 (p0) REVERT: A 261 LEU cc_start: 0.8942 (tp) cc_final: 0.8516 (pp) REVERT: A 287 MET cc_start: 0.8254 (tpp) cc_final: 0.7659 (mmm) REVERT: B 188 LEU cc_start: 0.8990 (tp) cc_final: 0.8583 (pp) REVERT: B 195 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8604 (mt) REVERT: B 211 GLU cc_start: 0.7521 (tp30) cc_final: 0.7247 (tp30) REVERT: B 292 LEU cc_start: 0.9102 (tp) cc_final: 0.8465 (tt) REVERT: B 391 ARG cc_start: 0.7087 (mpp80) cc_final: 0.6419 (mmm160) REVERT: C 225 ILE cc_start: 0.9198 (tp) cc_final: 0.8881 (tp) REVERT: D 102 ASN cc_start: 0.8555 (p0) cc_final: 0.7796 (p0) REVERT: D 147 MET cc_start: 0.8210 (mpp) cc_final: 0.7870 (mtp) REVERT: D 226 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8157 (tm-30) REVERT: D 292 LEU cc_start: 0.8967 (mm) cc_final: 0.8445 (tp) REVERT: D 409 ILE cc_start: 0.8911 (tp) cc_final: 0.8522 (tp) REVERT: D 412 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7365 (mp) REVERT: E 125 ASN cc_start: 0.8637 (t0) cc_final: 0.8118 (t0) REVERT: E 133 ASP cc_start: 0.7857 (p0) cc_final: 0.7585 (p0) REVERT: E 243 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: E 322 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7195 (mm) outliers start: 49 outliers final: 34 residues processed: 237 average time/residue: 0.2107 time to fit residues: 78.4264 Evaluate side-chains 233 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 239 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 49 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 118 optimal weight: 0.4980 chunk 69 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 = 0.3658 r_free = 0.3658 target = 0.131773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101037 restraints weight = 42780.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102806 restraints weight = 22796.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103561 restraints weight = 18630.649| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14185 Z= 0.126 Angle : 0.587 10.016 19302 Z= 0.295 Chirality : 0.044 0.195 2195 Planarity : 0.003 0.034 2411 Dihedral : 5.340 59.657 1968 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.72 % Favored : 96.16 % Rotamer: Outliers : 3.93 % Allowed : 17.53 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1695 helix: 1.79 (0.22), residues: 554 sheet: -0.90 (0.29), residues: 345 loop : -0.89 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 239 HIS 0.001 0.000 HIS A 109 PHE 0.015 0.001 PHE C 306 TYR 0.014 0.001 TYR D 301 ARG 0.005 0.000 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 5) link_NAG-ASN : angle 2.62299 ( 15) hydrogen bonds : bond 0.03472 ( 638) hydrogen bonds : angle 4.56711 ( 2046) SS BOND : bond 0.00354 ( 10) SS BOND : angle 1.53406 ( 20) covalent geometry : bond 0.00283 (14170) covalent geometry : angle 0.58131 (19267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8343 (p0) cc_final: 0.8044 (p0) REVERT: A 195 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8076 (mt) REVERT: A 261 LEU cc_start: 0.8926 (tp) cc_final: 0.8492 (pp) REVERT: A 263 MET cc_start: 0.7844 (mmm) cc_final: 0.7522 (ttm) REVERT: A 287 MET cc_start: 0.8151 (tpp) cc_final: 0.7576 (mmm) REVERT: B 103 GLU cc_start: 0.8545 (tt0) cc_final: 0.8249 (tt0) REVERT: B 188 LEU cc_start: 0.8973 (tp) cc_final: 0.8606 (pp) REVERT: B 195 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 211 GLU cc_start: 0.7481 (tp30) cc_final: 0.7245 (tp30) REVERT: B 292 LEU cc_start: 0.9095 (tp) cc_final: 0.8464 (tt) REVERT: B 391 ARG cc_start: 0.7068 (mpp80) cc_final: 0.6406 (mmm160) REVERT: C 225 ILE cc_start: 0.9166 (tp) cc_final: 0.8834 (tp) REVERT: C 287 MET cc_start: 0.7681 (mmm) cc_final: 0.7352 (mmm) REVERT: D 102 ASN cc_start: 0.8501 (p0) cc_final: 0.7754 (p0) REVERT: D 147 MET cc_start: 0.7267 (mpp) cc_final: 0.6905 (mtp) REVERT: D 226 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8161 (tm-30) REVERT: D 227 MET cc_start: 0.7943 (mtt) cc_final: 0.7656 (mtt) REVERT: D 292 LEU cc_start: 0.8964 (mm) cc_final: 0.8452 (tp) REVERT: D 409 ILE cc_start: 0.8866 (tp) cc_final: 0.8478 (tp) REVERT: D 412 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7495 (mp) REVERT: E 125 ASN cc_start: 0.8585 (t0) cc_final: 0.8024 (t0) REVERT: E 126 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8730 (tm-30) REVERT: E 133 ASP cc_start: 0.7791 (p0) cc_final: 0.7517 (p0) REVERT: E 243 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6948 (mt0) REVERT: E 322 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7203 (mm) outliers start: 59 outliers final: 43 residues processed: 244 average time/residue: 0.2050 time to fit residues: 78.7756 Evaluate side-chains 247 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 239 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 418 TYR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 90 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 = 0.3593 r_free = 0.3593 target = 0.126932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099575 restraints weight = 64240.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103038 restraints weight = 61621.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106065 restraints weight = 18472.656| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14185 Z= 0.268 Angle : 0.671 10.052 19302 Z= 0.342 Chirality : 0.046 0.200 2195 Planarity : 0.004 0.037 2411 Dihedral : 5.637 57.337 1968 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 4.47 % Allowed : 17.33 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1695 helix: 1.85 (0.23), residues: 553 sheet: -1.11 (0.29), residues: 346 loop : -0.94 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 239 HIS 0.003 0.001 HIS C 109 PHE 0.020 0.002 PHE A 44 TYR 0.024 0.002 TYR C 223 ARG 0.004 0.000 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 5) link_NAG-ASN : angle 2.56251 ( 15) hydrogen bonds : bond 0.03871 ( 638) hydrogen bonds : angle 4.82089 ( 2046) SS BOND : bond 0.00348 ( 10) SS BOND : angle 1.72874 ( 20) covalent geometry : bond 0.00624 (14170) covalent geometry : angle 0.66497 (19267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 204 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8531 (ppp) cc_final: 0.8148 (ppp) REVERT: A 102 ASN cc_start: 0.8534 (p0) cc_final: 0.8065 (p0) REVERT: A 195 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 261 LEU cc_start: 0.8906 (tp) cc_final: 0.8496 (pp) REVERT: A 287 MET cc_start: 0.8467 (tpp) cc_final: 0.7905 (mmm) REVERT: B 188 LEU cc_start: 0.8956 (tp) cc_final: 0.8609 (pp) REVERT: B 195 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 211 GLU cc_start: 0.7428 (tt0) cc_final: 0.7182 (tp30) REVERT: B 292 LEU cc_start: 0.9228 (tp) cc_final: 0.8516 (tt) REVERT: B 391 ARG cc_start: 0.6923 (mpp80) cc_final: 0.6400 (mmm160) REVERT: C 213 ARG cc_start: 0.8175 (mmt90) cc_final: 0.7925 (mtt180) REVERT: C 225 ILE cc_start: 0.9258 (tp) cc_final: 0.8940 (tp) REVERT: D 102 ASN cc_start: 0.8580 (p0) cc_final: 0.7806 (p0) REVERT: D 147 MET cc_start: 0.7700 (mpp) cc_final: 0.7065 (mtp) REVERT: D 292 LEU cc_start: 0.8947 (mm) cc_final: 0.8467 (tp) REVERT: D 409 ILE cc_start: 0.8869 (tp) cc_final: 0.8505 (tp) REVERT: E 125 ASN cc_start: 0.8664 (t0) cc_final: 0.8103 (t0) REVERT: E 243 GLN cc_start: 0.7358 (pt0) cc_final: 0.7077 (mt0) REVERT: E 322 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7349 (mm) REVERT: E 324 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7828 (tm-30) outliers start: 67 outliers final: 52 residues processed: 245 average time/residue: 0.2263 time to fit residues: 86.0075 Evaluate side-chains 252 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 239 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 418 TYR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 121 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 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 = 0.3638 r_free = 0.3638 target = 0.130799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102650 restraints weight = 48630.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103909 restraints weight = 38427.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105020 restraints weight = 26570.924| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14185 Z= 0.132 Angle : 0.609 10.223 19302 Z= 0.307 Chirality : 0.044 0.189 2195 Planarity : 0.004 0.039 2411 Dihedral : 5.424 56.038 1968 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 3.33 % Allowed : 18.60 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1695 helix: 1.90 (0.23), residues: 548 sheet: -0.96 (0.29), residues: 344 loop : -0.88 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 239 HIS 0.001 0.001 HIS A 201 PHE 0.016 0.001 PHE C 306 TYR 0.022 0.001 TYR D 301 ARG 0.003 0.000 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 2.62465 ( 15) hydrogen bonds : bond 0.03486 ( 638) hydrogen bonds : angle 4.60194 ( 2046) SS BOND : bond 0.00398 ( 10) SS BOND : angle 1.95405 ( 20) covalent geometry : bond 0.00297 (14170) covalent geometry : angle 0.60203 (19267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8240 (p0) cc_final: 0.7961 (p0) REVERT: A 195 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8015 (mt) REVERT: A 261 LEU cc_start: 0.8846 (tp) cc_final: 0.8422 (pp) REVERT: A 287 MET cc_start: 0.8111 (tpp) cc_final: 0.7686 (mmm) REVERT: B 188 LEU cc_start: 0.8835 (tp) cc_final: 0.8600 (pp) REVERT: B 211 GLU cc_start: 0.7279 (tt0) cc_final: 0.7073 (tp30) REVERT: B 292 LEU cc_start: 0.9147 (tp) cc_final: 0.8500 (tt) REVERT: B 391 ARG cc_start: 0.6749 (mpp80) cc_final: 0.6258 (mmm160) REVERT: C 213 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7810 (mtt180) REVERT: C 225 ILE cc_start: 0.9182 (tp) cc_final: 0.8848 (tp) REVERT: C 296 SER cc_start: 0.8864 (p) cc_final: 0.8532 (t) REVERT: D 292 LEU cc_start: 0.8871 (mm) cc_final: 0.8478 (tp) REVERT: D 409 ILE cc_start: 0.8769 (tp) cc_final: 0.8390 (tp) REVERT: E 125 ASN cc_start: 0.8416 (t0) cc_final: 0.7931 (t0) REVERT: E 243 GLN cc_start: 0.7333 (pt0) cc_final: 0.7021 (mt0) REVERT: E 322 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7270 (mm) outliers start: 50 outliers final: 39 residues processed: 236 average time/residue: 0.2072 time to fit residues: 76.2178 Evaluate side-chains 236 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 239 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 113 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 = 0.3619 r_free = 0.3619 target = 0.129513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101084 restraints weight = 50504.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103439 restraints weight = 41787.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104423 restraints weight = 24610.614| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14185 Z= 0.170 Angle : 0.621 10.257 19302 Z= 0.315 Chirality : 0.044 0.194 2195 Planarity : 0.004 0.045 2411 Dihedral : 5.329 55.657 1966 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 3.33 % Allowed : 18.20 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1695 helix: 1.93 (0.22), residues: 548 sheet: -0.95 (0.29), residues: 348 loop : -0.88 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 239 HIS 0.002 0.000 HIS A 201 PHE 0.036 0.001 PHE B 145 TYR 0.022 0.001 TYR B 222 ARG 0.002 0.000 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 5) link_NAG-ASN : angle 2.54440 ( 15) hydrogen bonds : bond 0.03513 ( 638) hydrogen bonds : angle 4.60583 ( 2046) SS BOND : bond 0.00379 ( 10) SS BOND : angle 1.93125 ( 20) covalent geometry : bond 0.00395 (14170) covalent geometry : angle 0.61393 (19267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8495 (ppp) cc_final: 0.8292 (ppp) REVERT: A 47 SER cc_start: 0.8507 (p) cc_final: 0.8257 (p) REVERT: A 102 ASN cc_start: 0.8391 (p0) cc_final: 0.8100 (p0) REVERT: A 195 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8055 (mt) REVERT: A 261 LEU cc_start: 0.8899 (tp) cc_final: 0.8465 (pp) REVERT: A 263 MET cc_start: 0.8003 (ttm) cc_final: 0.7712 (mmm) REVERT: A 287 MET cc_start: 0.8166 (tpp) cc_final: 0.7747 (mmm) REVERT: B 188 LEU cc_start: 0.8841 (tp) cc_final: 0.8610 (pp) REVERT: B 211 GLU cc_start: 0.7348 (tt0) cc_final: 0.7136 (tp30) REVERT: B 292 LEU cc_start: 0.9157 (tp) cc_final: 0.8499 (tt) REVERT: B 391 ARG cc_start: 0.7016 (mpp80) cc_final: 0.6456 (mmm160) REVERT: C 213 ARG cc_start: 0.8099 (mmt90) cc_final: 0.7840 (mtt180) REVERT: C 225 ILE cc_start: 0.9181 (tp) cc_final: 0.8864 (tp) REVERT: C 296 SER cc_start: 0.8903 (p) cc_final: 0.8575 (t) REVERT: D 292 LEU cc_start: 0.8900 (mm) cc_final: 0.8477 (tp) REVERT: D 409 ILE cc_start: 0.8843 (tp) cc_final: 0.8463 (tp) REVERT: E 125 ASN cc_start: 0.8498 (t0) cc_final: 0.7982 (t0) REVERT: E 197 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: E 243 GLN cc_start: 0.7386 (pt0) cc_final: 0.7074 (mt0) REVERT: E 322 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7210 (mm) outliers start: 50 outliers final: 42 residues processed: 233 average time/residue: 0.2094 time to fit residues: 76.4434 Evaluate side-chains 242 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 239 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 118 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN E 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102286 restraints weight = 47234.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105713 restraints weight = 28707.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105501 restraints weight = 20848.445| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14185 Z= 0.115 Angle : 0.603 10.478 19302 Z= 0.302 Chirality : 0.043 0.192 2195 Planarity : 0.004 0.046 2411 Dihedral : 5.178 55.471 1966 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.25 % Favored : 96.63 % Rotamer: Outliers : 2.33 % Allowed : 19.40 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1695 helix: 1.85 (0.22), residues: 555 sheet: -0.75 (0.30), residues: 347 loop : -0.89 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 239 HIS 0.001 0.001 HIS D 215 PHE 0.033 0.001 PHE B 145 TYR 0.021 0.001 TYR D 301 ARG 0.002 0.000 ARG D 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 5) link_NAG-ASN : angle 2.64522 ( 15) hydrogen bonds : bond 0.03300 ( 638) hydrogen bonds : angle 4.46511 ( 2046) SS BOND : bond 0.00367 ( 10) SS BOND : angle 1.73475 ( 20) covalent geometry : bond 0.00255 (14170) covalent geometry : angle 0.59667 (19267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.8491 (p) cc_final: 0.8245 (p) REVERT: A 102 ASN cc_start: 0.8299 (p0) cc_final: 0.8009 (p0) REVERT: A 195 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8025 (mt) REVERT: A 261 LEU cc_start: 0.8947 (tp) cc_final: 0.8483 (pp) REVERT: A 263 MET cc_start: 0.7814 (ttm) cc_final: 0.7577 (mmm) REVERT: A 287 MET cc_start: 0.8080 (tpp) cc_final: 0.7613 (mmm) REVERT: B 188 LEU cc_start: 0.8887 (tp) cc_final: 0.8671 (pp) REVERT: B 211 GLU cc_start: 0.7353 (tt0) cc_final: 0.7110 (tp30) REVERT: B 292 LEU cc_start: 0.9056 (tp) cc_final: 0.8480 (tt) REVERT: C 213 ARG cc_start: 0.8066 (mmt90) cc_final: 0.7830 (mtt180) REVERT: C 225 ILE cc_start: 0.9142 (tp) cc_final: 0.8821 (tp) REVERT: C 296 SER cc_start: 0.8916 (p) cc_final: 0.8644 (t) REVERT: D 102 ASN cc_start: 0.8144 (p0) cc_final: 0.7177 (p0) REVERT: D 292 LEU cc_start: 0.8892 (mm) cc_final: 0.8415 (tp) REVERT: D 409 ILE cc_start: 0.8859 (tp) cc_final: 0.8501 (tp) REVERT: E 125 ASN cc_start: 0.8517 (t0) cc_final: 0.7968 (t0) REVERT: E 133 ASP cc_start: 0.7512 (p0) cc_final: 0.7237 (p0) REVERT: E 243 GLN cc_start: 0.7369 (pt0) cc_final: 0.7088 (mt0) REVERT: E 303 TYR cc_start: 0.8826 (p90) cc_final: 0.8571 (p90) REVERT: E 322 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7218 (mm) outliers start: 35 outliers final: 28 residues processed: 245 average time/residue: 0.2267 time to fit residues: 87.8625 Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 239 TRP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 410 PHE Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 465 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 159 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.0040 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 = 0.3660 r_free = 0.3660 target = 0.132399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103661 restraints weight = 50661.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106443 restraints weight = 43589.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108511 restraints weight = 21278.104| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14185 Z= 0.120 Angle : 0.611 10.374 19302 Z= 0.306 Chirality : 0.044 0.241 2195 Planarity : 0.003 0.047 2411 Dihedral : 5.148 55.498 1966 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 2.27 % Allowed : 19.93 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1695 helix: 1.79 (0.22), residues: 561 sheet: -0.65 (0.30), residues: 346 loop : -0.84 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 239 HIS 0.001 0.000 HIS A 109 PHE 0.012 0.001 PHE B 410 TYR 0.034 0.001 TYR C 301 ARG 0.005 0.000 ARG B 391 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 5) link_NAG-ASN : angle 2.59660 ( 15) hydrogen bonds : bond 0.03265 ( 638) hydrogen bonds : angle 4.40263 ( 2046) SS BOND : bond 0.00370 ( 10) SS BOND : angle 1.70251 ( 20) covalent geometry : bond 0.00267 (14170) covalent geometry : angle 0.60508 (19267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4400.29 seconds wall clock time: 77 minutes 3.22 seconds (4623.22 seconds total)